{ "datasets" : [ {"dataset":"MSV000100197","datasetNum":"100197","title":"Retention_time_matching_HNRC_dataset","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765529047000","created":"Dec. 12, 2025, 12:44 AM","description":"MS\/MS fragmentation data of retention time for HNRC acquired on Q Exactive - with\nchromatographic separation on a Phenomenex polar C18 column","fileCount":"40","fileSizeKB":"2714759","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"retention;time;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"University of California-San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5752476c74d44c74beefa61ff8ba993e","id":"0"}, {"dataset":"MSV000100196","datasetNum":"100196","title":"NAPRT-mediated deamidated NAD biosynthesis enhances tissue resiliency and suppresses tumorigenesis","user":"jasames","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765493208000","created":"Dec. 11, 2025, 2:46 PM","description":"NAD biosynthetic enzymes are widely considered oncogenic due to their frequent overexpression in cancer to support elevated metabolic demand. This dataset is in support of a manuscript where we identify a tumor-suppressive role for the deamidated NAD biosynthesis pathway in both mice and humans. Unlike the ubiquitously expressed amidated salvage enzyme, NAPRT the first enzyme of the deamidated pathway is selectively enriched in gut epithelial cells, where it sustains NAD levels during stress-induced acute depletion. Loss of NAPRT compromises PARP activity and DNA repair, increasing susceptibility to chemically induced colitis, tumorigenesis, and age-associated spontaneous tumors in mice. Consistently, low NAPRT expression correlates with poor prognosis across multiple human cancers. These findings demonstrate that endogenous deamidated NAD biosynthesis suppresses tumorigenesis, and that enhancing this pathway may offer a strategy for tumor prevention.","fileCount":"1102","fileSizeKB":"108798318","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"NAD;relative quantification;HRMS;DatasetType:Other (targeted measure of NAD related analytes)","pi":[{"name":"Xiaoling Li","email":"lix3@niehs.nih.gov","institution":"National Institute of Environmental Health Sciences","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"903b57bb3fae45ccb998a603695c5daa","id":"1"}, {"dataset":"MSV000100194","datasetNum":"100194","title":"GNPS-Incubation of alkylamine substrates with HepG2 liver cells","user":"hgouda","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765481529000","created":"Dec. 11, 2025, 11:32 AM","description":"Incubation of human HepG2 cells with aldehydes and amines for 24 hrs in humidified atmospheric chamber. Samples were extracted using 80:20 (MeOH:H2O) and samples were analyzed using Orbitrap Exploris","fileCount":"111","fileSizeKB":"4377581","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Host metabolism;Biotransformation;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c4113cca9e624dca919219f23cc1b95b","id":"2"}, {"dataset":"MSV000100190","datasetNum":"100190","title":"Cytoplasmic NAD\/H synthesis via NRK1 regulates inflammatory capacity and promotes survival of CD4+ T cells - GCMS Data","user":"bmarzullo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765457560000","created":"Dec. 11, 2025, 4:52 AM","description":"T cell metabolism increases upon activation, underpinning immune effector functions. Nicotinamide adenine dinucleotide (NAD\/H) is an essential redox cofactor for glycolysis and mitochondrial substrate oxidation. Its phosphorylation to NADP\/H regulates reactive oxygen species (ROS) abundance. NAD\/H levels increase upon T cell activation, but synthesis pathways and implications are not fully characterised. Here, we interrogate the role of the NAD\/H-synthesis enzyme nicotinamide riboside kinase 1 (NRK1), the expression of which increases upon stimulation of both human and murine CD4+ T cells. Functionally, NRK1 activity restrains activation and cytokine production of CD4+ T cells while promoting survival. These activities are linked to increased NRK1 expression in the cytoplasm, where it locally raises NAD\/H levels. This supports glycolysis, but more profoundly impacts cytoplasmic NADP\/H generation, thereby controlling ROS abundance and nuclear NFAT-translocation. During fungal and viral infection, T-cell-intrinsic NRK1 maintains effector CD4+ T cell abundance within affected tissues and draining lymph nodes, thus supporting infection control. Taken together, these data confirm that subcellular regulation of immune cell metabolism determines immune responses at the level of organism.","fileCount":"16","fileSizeKB":"241460","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Agilent GCMS 7890B 5977A","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CD4+ T Cells, 13C-Glucose, 13C-Glutamine, NRK1, NAD;DatasetType:Metabolomics","pi":[{"name":"Sarah Dimeloe","email":"s.k.dimeloe@bham.ac.uk","institution":"University of Birmingham ","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"e9f481d0180b4d3d897196cb9f0e0fc9","id":"3"}, {"dataset":"MSV000100189","datasetNum":"100189","title":"Cytoplasmic NAD\/H synthesis via NRK1 regulates inflammatory capacity and promotes survival of CD4+ T cells - LCMS Data","user":"bmarzullo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765457218000","created":"Dec. 11, 2025, 4:46 AM","description":"T cell metabolism increases upon activation, underpinning immune effector functions. Nicotinamide adenine dinucleotide (NAD\/H) is an essential redox cofactor for glycolysis and mitochondrial substrate oxidation. Its phosphorylation to NADP\/H regulates reactive oxygen species (ROS) abundance. NAD\/H levels increase upon T cell activation, but synthesis pathways and implications are not fully characterised. Here, we interrogate the role of the NAD\/H-synthesis enzyme nicotinamide riboside kinase 1 (NRK1), the expression of which increases upon stimulation of both human and murine CD4+ T cells. Functionally, NRK1 activity restrains activation and cytokine production of CD4+ T cells while promoting survival. These activities are linked to increased NRK1 expression in the cytoplasm, where it locally raises NAD\/H levels. This supports glycolysis, but more profoundly impacts cytoplasmic NADP\/H generation, thereby controlling ROS abundance and nuclear NFAT-translocation. During fungal and viral infection, T-cell-intrinsic NRK1 maintains effector CD4+ T cell abundance within affected tissues and draining lymph nodes, thus supporting infection control. Taken together, these data confirm that subcellular regulation of immune cell metabolism determines immune responses at the level of organism.","fileCount":"10","fileSizeKB":"9992126","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Agilent LC-QToF G6546A","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CD4+ T Cells, 1,2-13C-Glucose, NRK1, NAD;DatasetType:Metabolomics","pi":[{"name":"Sarah Dimeloe","email":"s.k.dimeloe@bham.ac.uk","institution":"University of Birmingham ","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b074573fb9244efd9ce63a733827d47c","id":"4"}, {"dataset":"MSV000100182","datasetNum":"100182","title":"Ischemic cardiac organoid proteome map ","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765427959000","created":"Dec. 10, 2025, 8:39 PM","description":"In this study, we demonstrate the use of human cardiac organoids (comprised of cardiomyocyte, fibroblast, and endothelial origin) to model IR injury through a model of hypoxia and reoxygenation and therapeutic nanovesicle remodelling. Engineered nanovesicles (NVs), generated directly from human stem cells (SC), have been shown to influence cardiac tissue repair, and provide a platform for the reproducible, rapid, and scalable cell free-mediated therapy. Functionally, we demonstrate that administration of NVs (from different human induced pluripotent stem cell (iPSC) origin) during reoxygenation significantly increase cardiomyocyte survival and preserve contractility function (contractile duration, relaxation time, relaxation:contraction velocity). A mass-spectrometry-based proteomics approach was applied to decipher protein dynamics and molecular mechanisms of IR injury in human cardiac organoids following NV treatments","fileCount":"43","fileSizeKB":"32482278","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"cardiac;organoids;Ischemic;proteome remodelling;DatasetType:Proteomics","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD071853","task":"c8f6e13af8694e17a37d275d5c12f88c","id":"5"}, {"dataset":"MSV000100179","datasetNum":"100179","title":"GNPS Marine Bacteria SL10 Vibrio furnissii ESI-pos-QTOF","user":"AugustoL","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765403372000","created":"Dec. 10, 2025, 1:49 PM","description":"UPLC-ESI-pos-HRMS\/MS analysis of incubation extracts of Vibrio furnissii. Metabolic analysis for dereplication of secondary microbial metabolites.","fileCount":"8","fileSizeKB":"66167","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vibrio furnissii (NCBITaxon:29494)","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"marine bacteria;Vibrio;DatasetType:Other (metabolic analysis)","pi":[{"name":"Augusto Leonardo dos Santos","email":"augusto.leonardo@unifesp.br","institution":"UNIFESP, Diadema","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"76efab7e3d8f49799de8addf0d945e4f","id":"6"}, {"dataset":"MSV000100178","datasetNum":"100178","title":"GNPS - eDNAID Thrust 3 test samples M03","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765397682000","created":"Dec. 10, 2025, 12:14 PM","description":"Water samples (ocean and river) as tests for eDNAID Thrust study (part of Qiita ID 16188). Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). Method MS1 Res60K DDA Top5","fileCount":"66","fileSizeKB":"5049523","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples - water","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;DOM;DatasetType:Metabolomics","pi":[{"name":"Rob Knight","email":"robknight@ucsd.edu","institution":"UCSD","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3905f9fa99934fb38d11acb5a358f63b","id":"7"}, {"dataset":"MSV000100177","datasetNum":"100177","title":"GNPS - eDNAID Thrust 3 test samples M02","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765397534000","created":"Dec. 10, 2025, 12:12 PM","description":"Water samples (ocean and river) as tests for eDNAID Thrust study (part of Qiita ID 16188). Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). Method MS1 Res120K DDA Top5","fileCount":"66","fileSizeKB":"5171434","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples - water","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;DOM;DatasetType:Metabolomics","pi":[{"name":"Rob Knight","email":"robknight@ucsd.edu","institution":"UCSD","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"43f656cf908e4510802a865e32149afb","id":"8"}, {"dataset":"MSV000100172","datasetNum":"100172","title":"Early root-root interactions weaken foliar defense responses against Septoria tritici blotch in a durum wheat varietal mixture","user":"LauraMathieu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765357770000","created":"Dec. 10, 2025, 1:09 AM","description":"The interactions between co-cultivated plant cultivars are increasingly recognized as influencing their susceptibility to pathogens in mixtures. However, the underlying mechanisms remain largely unexplored. Using a model of durum wheat cultivar mixtures where susceptibility to Septoria foliar disease is increased, we combined aerial and root phenotyping with transcriptional analyses and untargeted metabolomics to elucidate the potential signaling cascade driving this modulation of susceptibility. We observed contrasting root architectures between cultivars in mixture. Molecular analysis showed a delayed induction of defense-related genes and metabolites following pathogen inoculation in plants grown in mixture compared to pure stand. The findings suggest that root architecture potentially triggers a competitive response that could delay the induction of defense responses following pathogen inoculation. Altogether, these results point to a possible interplay between root architecture, resource competition, plant metabolism, and defense modulation in shaping plant-pathogen interactions within varietal mixtures.","fileCount":"379","fileSizeKB":"8358831","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum turgidum subsp. durum (NCBITaxon:4567)","instrument":"Vanquish ultra-high-pressure liquid chromatography (UHPLC);QEX+ mass spectrometer interfaced with an electrospray (ESI) ionisation source (ThermoScientific, Bremen, Germany)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Wheat;Septoria tritici blotch;Varietal mixtures;Plant-plant interactions;Belowground processes;Resource competition;Defense delay;DatasetType:Metabolomics","pi":[{"name":"Louis-Valentin Meteignier","email":"louis-valentin.meteignier@inrae.fr","institution":"INRAE","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"8e994283bd5b4173880f40cf421fe50e","id":"9"}, {"dataset":"MSV000100171","datasetNum":"100171","title":"Root phenolics as potential drivers of preformed defenses and reduced disease susceptibility in a paradigm bread wheat mixture","user":"LauraMathieu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765357113000","created":"Dec. 10, 2025, 12:58 AM","description":"Plant-plant interactions modulate foliar disease susceptibility in intraspecific mixtures. However, the molecular events including signals and responses underlying the reduction in disease susceptibility remain largely unexplored. \nHere, we developed an experimental system that can abolish root-mediated interactions between plants in a model of bread wheat varietal mixture. We then performed transcriptomic and metabolomic analyses to uncover the molecular responses linked to decreased susceptibility to Septoria tritici blotch in plant-plant interactions. \nOur analysis revealed that disrupting root chemical interactions impaired the reduction in susceptibility to Septoria and identified phenolic compounds as potential key mediators. The plant-plant interactions under study triggered significant molecular changes in specialized metabolism, biotic interactions, transporters, and responses to resources. Disrupting root interactions canceled both the macroscopic and molecular responses, thus providing a strong link between them. \nThese insights provide a deeper understanding of the molecular basis of plant-plant interactions and the processes involved in reducing disease susceptibility in intraspecific mixtures.","fileCount":"121","fileSizeKB":"8835141","spectra":"337242","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565)","instrument":"Ultimate 3000 UHPLC system (Thermo Fisher Scientific);QTOF Impact II quadrupole time-of-flight mass spectrometer (Bruker Daltonics, Bremen, Germany)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Multi-omics;Plant-plant interactions;Root exudates;Septoria tritici blotch;Wheat;DatasetType:Metabolomics","pi":[{"name":"Elsa BALLINI","email":"elsa.ballini@supagro.fr","institution":"Institut Agro","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9dd7e1d53b1c4e1fb14d50948ed41380","id":"10"}, {"dataset":"MSV000100170","datasetNum":"100170","title":"Root phenolics as potential drivers of preformed defenses and reduced disease susceptibility in a paradigm bread wheat mixture","user":"LauraMathieu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765356484000","created":"Dec. 10, 2025, 12:48 AM","description":"Plant-plant interactions modulate foliar disease susceptibility in intraspecific mixtures. However, the molecular events including signals and responses underlying the reduction in disease susceptibility remain largely unexplored. \nHere, we developed an experimental system that can abolish root-mediated interactions between plants in a model of bread wheat varietal mixture. We then performed transcriptomic and metabolomic analyses to uncover the molecular responses linked to decreased susceptibility to Septoria tritici blotch in plant-plant interactions. \nOur analysis revealed that disrupting root chemical interactions impaired the reduction in susceptibility to Septoria and identified phenolic compounds as potential key mediators. The plant-plant interactions under study triggered significant molecular changes in specialized metabolism, biotic interactions, transporters, and responses to resources. Disrupting root interactions canceled both the macroscopic and molecular responses, thus providing a strong link between them. \nThese insights provide a deeper understanding of the molecular basis of plant-plant interactions and the processes involved in reducing disease susceptibility in intraspecific mixtures.","fileCount":"379","fileSizeKB":"8358830","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565)","instrument":"Vanquish ultra-high-pressure liquid chromatography (UHPLC);QEX+ mass spectrometer interfaced with an electrospray (ESI) ionisation source (ThermoScientific, Bremen, Germany)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Multi-omics;Plant-plant interactions;Root exudates;Septoria tritici blotch;Wheat;DatasetType:Metabolomics","pi":[{"name":"Elsa BALLINI","email":"elsa.ballini@supagro.fr","institution":"Institut Agro","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4aa1de3bdd3a462cafdaec3ff8e09b57","id":"11"}, {"dataset":"MSV000100169","datasetNum":"100169","title":"Root phenolics as potential drivers of preformed defenses and reduced disease susceptibility in a paradigm bread wheat mixture","user":"LauraMathieu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765356238000","created":"Dec. 10, 2025, 12:43 AM","description":"Plant-plant interactions modulate foliar disease susceptibility in intraspecific mixtures. However, the molecular events including signals and responses underlying the reduction in disease susceptibility remain largely unexplored. \nHere, we developed an experimental system that can abolish root-mediated interactions between plants in a model of bread wheat varietal mixture. We then performed transcriptomic and metabolomic analyses to uncover the molecular responses linked to decreased susceptibility to Septoria tritici blotch in plant-plant interactions. \nOur analysis revealed that disrupting root chemical interactions impaired the reduction in susceptibility to Septoria and identified phenolic compounds as potential key mediators. The plant-plant interactions under study triggered significant molecular changes in specialized metabolism, biotic interactions, transporters, and responses to resources. Disrupting root interactions canceled both the macroscopic and molecular responses, thus providing a strong link between them. \nThese insights provide a deeper understanding of the molecular basis of plant-plant interactions and the processes involved in reducing disease susceptibility in intraspecific mixtures.","fileCount":"81","fileSizeKB":"5499394","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565)","instrument":"Ultimate 3000 UHPLC system (Thermo Fisher Scientific);QTOF Impact II quadrupole time-of-flight mass spectrometer (Bruker Daltonics, Bremen, Germany)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Multi-omics;Plant-plant interactions;Root exudates;Septoria tritici blotch;Wheat;DatasetType:Metabolomics","pi":[{"name":"Elsa BALLINI","email":"elsa.ballini@supagro.fr","institution":"Institut Agro","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b4081f71be0147e0a4616c40059c11be","id":"12"}, {"dataset":"MSV000100168","datasetNum":"100168","title":"Label-free quantification of MCF10A cell culture proteome (DIA) stably expressing BAD3SA in 2D vs 3D","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765320306000","created":"Dec. 9, 2025, 2:45 PM","description":"Global shotgun proteomic analysis using data independent acquisition (DIA) and Spectronaut analysis on the input cell lysates before the enrichment step in proximity labeling experiments, specifically MCF10A cells stably expressing Bcl2-associated agonist of cell death (BAD) with three serine to alanine mutations (S75A, S99A, S118A) fused with miniTurbo (miniTurbo-BAD3SA) in 2D with biotin treatment (n=3) and miniTurbo-BAD3SA in 3D with biotin treatment (n=4). The file \"L20240424-miniTurbo-BAD-WT-vs-3SA-DIA.sne\" contains Spectronaut search result including miniTurbo-BAD WT 2D and 3D shotgun samples found under the identifier MSV000094824 (2D) and MSV000094825 (3D).","fileCount":"9","fileSizeKB":"24103810","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"BAD;miniTurbo;BioID;LFQ;DIA;DatasetType:Proteomics","pi":[{"name":"Ing Swie Goping","email":"igoping@ualberta.ca","institution":"University of Alberta","country":"Canada"},{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD071782","task":"64e5801dd019490cb09578a4c37352c7","id":"13"}, {"dataset":"MSV000100167","datasetNum":"100167","title":"BAD3SA BioID in 2D and 3D MCF10A cell culture","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765319676000","created":"Dec. 9, 2025, 2:34 PM","description":"BioID proximity labeling experiment on bait protein Bcl2-associated agonist of cell death (BAD) with three serine to alanine mutations (S75A, S99A, S118A) in MCF10A cell culture stably expressing BAD-miniTurbo. \n\n2D cell culture: 20220805; sample: BAD3SA-turbo-biotin; control: BAD3SA-turbo (n=3); other raw files in the experiment (BAD-turbo-biotin, BAD-biotin, turbo-biotin, BAD-turbo) are found under the identifier MSV000093357. The file \"20230921-2D-miniTurbo-BAD3SA-low-abundance-imputation.pdResult\" contains the Proteome Discoverer search result for the full 2D miniTurbo experiment.\n\n3D cell culture: 20230710; sample: BAD3SA-biotin (n=4); other raw files (BAD-turbo-biotin, turbo-biotin) in the experiment are found under the identifier MSV000093358. The file \"20230921-3D-miniTurbo-BAD3SA-low-abundance-sampling.pdResult\" contains the Proteome Discoverer search result for the full 3D miniTurbo experiment.","fileCount":"13","fileSizeKB":"59818750","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"BioID;miniTurbo;3D cell culture;BAD;DatasetType:Proteomics","pi":[{"name":"Ing Swie Goping","email":"igoping@ualberta.ca","institution":"University of Alberta","country":"Canada"},{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD071781","task":"68014d89f53a4904a47c99d1fe5c0c44","id":"14"}, {"dataset":"MSV000100161","datasetNum":"100161","title":"Acyl petrobactin, Bulbichelin, and related chemical species analyzed for metal binding","user":"redghoti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765300563000","created":"Dec. 9, 2025, 9:16 AM","description":"This dataset contains data on metal infusions of Fe, Zn, Co, Mn, Ni, and Cu mixed post-LC with sample in order to visualize potential metal-binding partners for variations of Acyl petrobactin and Bulbichelin.","fileCount":"80","fileSizeKB":"14746598","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Microbulbifer sp. CNSA002","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"petrobactin;metallophore;siderophore;promiscuity;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7d1cff7ffab0442ea689af52de9e3968","id":"15"}, {"dataset":"MSV000100158","datasetNum":"100158","title":"Dataset Workshop on Advanced Mass Spectometry 2025","user":"anaschiavo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765288103000","created":"Dec. 9, 2025, 5:48 AM","description":"LC-MS\/MS data of crude extracts produced by isolated bacteria recovered from Brazilian Rocas Atoll. Subset of MSV000083601 for use as an example dataset on the Workshop on Advanced Mass Spectometry 2025.","fileCount":"15","fileSizeKB":"506856","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Salinispora (NCBITaxon:168694);Streptomyces (NCBITaxon:1883);Bacillus","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"workshop;wams;DatasetType:Metabolomics","pi":[{"name":"Anelize Bauermeister","email":"anelize@iq.usp.br","institution":"Universidade de Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"be08cce295764f38bde15602f8bb7e5f","id":"16"}, {"dataset":"MSV000100150","datasetNum":"100150","title":"GNPS - Corals Metabolomic Profile to Establish Coral Cell Culture time-series experiment","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765222970000","created":"Dec. 8, 2025, 11:42 AM","description":"Samples from Pocillopora demicornis were collected by airbrushing, frozen, lyophilized and extracted with methanol-water (4:1). Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"600","fileSizeKB":"31195181","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pocillopora damicornis (NCBITaxon:46731)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coral;Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Nikki Traylor-Knowles","email":"ntraylorknowles@earth.miami.edu","institution":"University of Miami","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ade409f0546d4392b88856355069eb95","id":"17"}, {"dataset":"MSV000100146","datasetNum":"100146","title":"beta4-integrin affects prostate cancer progression by regulating the properties of nuclear envelope","user":"XIOLIU","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765202167000","created":"Dec. 8, 2025, 5:56 AM","description":"This dataset contains proximity-labeling mass spectrometry measurements generated to investigate how loss of bata4-integrin affects nuclear integrity, nuclear mechanics, lamin composition, and nuclear pore complex (NPC) organization in prostate epithelial cells. ","fileCount":"13","fileSizeKB":"19127834","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ITGB4;integrin;hemidesmosomes;nuclear mechanotransduction;nuclear pore complex;prostate cancer;DatasetType:Proteomics","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e7e6c7b2ad604ba1aaa8c39ba6b5d934","id":"18"}, {"dataset":"MSV000100141","datasetNum":"100141","title":"Reductive_amination_retention_time_matching","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765166469000","created":"Dec. 7, 2025, 8:01 PM","description":"MS\/MS fragmentation data of retention time matching rheumatoid arthristis acquired on Q Exactive - 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with\nchromatographic separation on a Phenomenex polar C18 column.\n","fileCount":"10","fileSizeKB":"860251","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"retention;time;matching;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"University of California-San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9ca97c5430644385940f4c8890f540e9","id":"20"}, {"dataset":"MSV000100138","datasetNum":"100138","title":"Reductive_amination_retention_matching","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765154852000","created":"Dec. 7, 2025, 4:47 PM","description":"MS\/MS fragmentation data of rheumatoid arthritis retention time matching acquired on Q Exactive - with\nchromatographic separation on a Phenomenex polar C18 column","fileCount":"10","fileSizeKB":"923333","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"retention time;matching;RA;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"University of California-San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1deb3a133bdc4bdba6a9cf0be101d426","id":"21"}, {"dataset":"MSV000100137","datasetNum":"100137","title":"Mammarenaviruses depend on endogenous fatty acid synthesis in cell culture systems","user":"kmhines5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765140452000","created":"Dec. 7, 2025, 12:47 PM","description":"Lassa virus (LASV) and lymphocytic choriomeningitis virus (LCMV) are Old World mammarenaviruses that, like all viruses, rely on host-derived biological molecules to complete their replication cycle. Identifying host factors essential for mammarenavirus replication may reveal novel targets for antiviral intervention. To this end, we found that replication of recombinant tri-segmented (r3) LCMV and an r3LCMV variant in which the LCMV glycoprotein complex (GPC) was replaced with that of LASV (r3LCMV LASV) was sensitive to reductions in both exogenously supplied and endogenously synthesized lipids. To explore the relationship between mammarenavirus replication and host lipid metabolism, we performed lipidomic analysis on mock infected and virus-infected VeroS cells. Infection with r3LCMV LASV increased the abundance of triacylglycerols (TG), phosphatidylcholine (PC), and phosphatidylglycerol (PG), while decreasing levels of ceramides, phosphatidylethanolamine (PE), and phosphatidylserine (PS). Although TG levels rose during infection, pharmacologic inhibition of TG synthesis did not impair viral replication. In contrast, inhibition of fatty acid synthase (FASN), a key enzyme upstream of TG synthesis, significantly reduced r3LCMV LASV and r3LCMV spread. FASN inhibition suppressed both viral genome replication and viral budding. The addition of oleic acid, but not palmitic acid (the principal product of FASN), rescued the inhibitory effect of FASN blockade. Dependence on FASN activity was also observed for ML29, a Mopeia LASV chimeric virus, as well as the New World mammarenaviruses Tacaribe and Junin Candid #1. Moreover, the FASN dependency was conserved across multiple cell types, including human and murine hepatocellular carcinoma cells (Huh7 and Hepa1 6) and human respiratory epithelial (A549) cells.","fileCount":"690","fileSizeKB":"23930800","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lassa mammarenavirus (NCBITaxon:11620)","instrument":"Synapt XS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipidomics;viral replication;fatty acid synthesis;DatasetType:Metabolomics","pi":[{"name":"Kelly M. Hines","email":"kelly.hines@uga.edu","institution":"University of Georgia","country":"USA"},{"name":"Melinda A. Brindley","email":"mbrindle@uga.edu","institution":"University of Georgia","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6cdd9ca8d4a2465195a8b355da4af5c2","id":"22"}, {"dataset":"MSV000100133","datasetNum":"100133","title":"Effect of Processing and Microbial Inoculation on the Peptidomics of Goat Cheeses","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1765044073000","created":"Dec. 6, 2025, 10:01 AM","description":"The aim of these peptidomic study was to identify and characterize the peptides released after the in vitro digestion of goat cheeses, allowing the comparison of the effects of heat treatment (Raw versus Pasteurized) and the inoculation of Limosilactobacillus mucosae CNPC007 during their production. Mass spectrometry analysis provided precise mapping of the peptide sequences generated, including their size, composition, and structural properties. These data enabled the association of peptide profiles with potential biofunctional activities, positioning goat cheese as a promising functional matrix for the development of value added foods.","fileCount":"9","fileSizeKB":"11759638","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Limosilactobacillus mucosae ;Capra aegagrus (NCBITaxon:9923)","instrument":"Q-Exactive Thermo Fisher","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Goat cheese;Peptides;Limosilactobacillus mucosae inoculation;DatasetType:Other (Peptidomic)","pi":[{"name":"Adriane Elisabete Antunes de Moraes","email":"adriane@unicamp.br","institution":"Universidade Estadual de Campinas (UNICAMP)","country":"Brazil"},{"name":"Angela Matilde da Silva Alves ","email":"angela_matilde@hotmail.com","institution":"Universidade Estadual de Campinas (UNICAMP)","country":"Brazil"},{"name":"Bruno Cesar Rossini","email":"bruno.rossini@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brazil"},{"name":"Camila Neves Meireles Costa","email":"camilanevesmc@gmail.com","institution":"Universidade Federal da Paraiba (UFPB)","country":"Brazil"},{"name":"Ezequiel Ricardo Coscueta ","email":"ecoscueta@ucp.pt","institution":"Universidade Catolica Portuguesa","country":"Portugal"},{"name":"Fabiana Andrea Barrera Galland","email":"fabiana.pe@ital.sp.gov.br","institution":"Instituto de Tecnologia em Alimentos (ITAL)","country":"Brazil"},{"name":"Julia Mariano Caju de Oliveira","email":"juliacaju0@gmail.com","institution":"Universidade Federal da Paraiba (UFPB)","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brazil"},{"name":"Manuela Machado","email":"mmachado@ucp.pt","institution":"Universidade Catolica Portuguesa","country":"Portugal"},{"name":"Maria Elieidy Gomes de Oliveira","email":"elieidynutri@yahoo.com.br","institution":"Universidade Federal da Paraiba (UFPB)","country":"Brazil"},{"name":"Maria Manuela Pintado ","email":"mpintado@ucp.pt","institution":"Universidade Catolica Portuguesa","country":"Portugal"},{"name":"Maria Teresa Bertoldo Pacheco","email":"mtb@ital.sp.gov.br","institution":"Instituto de Tecnologia em Alimentos (ITAL)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3b24139ea5334fdfb3b454afe3dce1b5","id":"23"}, {"dataset":"MSV000100129","datasetNum":"100129","title":"CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis","user":"JustinMcKetney","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764976074000","created":"Dec. 5, 2025, 3:07 PM","description":"Aggregation of the protein tau defines tauopathies, the most common age-related neurodegenerative diseases, which include Alzheimers disease and frontotemporal dementia. Specific neuronal subtypes are selectively vulnerable to tau aggregation, subsequent dysfunction, and death. However, molecular mechanisms underlying cell type-selective vulnerability are unknown. To systematically uncover the cellular factors controlling the accumulation of tau aggregates in human neurons, we conducted a genome-wide CRISPRi screen in iPSC-derived neurons. The screen uncovered both known and unexpected pathways, including UFMylation and GPI anchor biosynthesis, that control tau oligomer levels. We discovered that the E3 ubiquitin ligase CUL5SOCS4 controls tau levels in human neurons, ubiquitinates tau, and is correlated with resilience to tauopathies in human disease. Disruption of mitochondrial function promotes proteasomal misprocessing of tau, generating disease-relevant tau proteolytic fragments and changes tau aggregation in vitro. These results systematically reveal principles of tau proteostasis in human neurons and suggest potential therapeutic targets for tauopathies.","fileCount":"51","fileSizeKB":"27571425","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"CRISPR;Neurons;Tau protein;Neurodegeneration;Proteostasis;CUL5;Ubiquitination;Aggregation;Proteasome;DatasetType:Proteomics","pi":[{"name":"Danielle Swaney","email":"danielle.swaney@gladstone.ucsf.edu","institution":"UCSF","country":"United States"},{"name":"Martin Kampmann","email":"martin.kampmann@ucsf.edu","institution":"University of California San Francisco","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD071655","task":"bc4b811719af4447ae86f2bbb7a53957","id":"24"}, {"dataset":"MSV000100122","datasetNum":"100122","title":"Periodic fasting and refeeding re-shapes lipid saturation, storage and distribution in brown adipose tissue","user":"tjiang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764959018000","created":"Dec. 5, 2025, 10:23 AM","description":"Raw data of mass spec imaging of lipids in mouse brown fat tissue to study effect of periodic fasting and refeeding.","fileCount":"4","fileSizeKB":"168184432","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"NA","keywords":"mass spec imaging, lipids;DatasetType:Other (Mass spec imaging)","pi":[{"name":"Meilian Liu","email":"MeilianLiu@salud.unm.edu","institution":"UNM","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8bffade7af184990bbf812e6e090d8e1","id":"25"}, {"dataset":"MSV000100119","datasetNum":"100119","title":"Metabolomics-The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification","user":"Leo_001","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764944556000","created":"Dec. 5, 2025, 6:22 AM","description":"\tGlioblastoma Multiforme (GBM) is one of the most malignant tumors, characterized by high treatment costs and poor outcomes, thus urgently necessitating the development of new therapeutic approaches. Recent studies have found that intermittent fasting (IF) not only can suppress GBM among various tumors but also can reconstruct the gut microbiome and alter metabolism. However, the mechanism by which IF inhibits GBM is not yet fully understood. Using animal models, I discovered that IF can effectively suppress GBM and alter the gut microbiome.Furthermore, microbial metabolites such as methionine, m6A, and the m6A-targeted oncogene TGFB2 were also downregulated. Therefore, we hypothesize that IF, by reconstructing the gut microbiome, reduces the levels of microbial metabolite methionine, subsequently decreasing m6A in GBM, leading to the downregulation of the m6A-targeted oncogene TGFB2, thereby inhibiting the development of GBM.","fileCount":"49","fileSizeKB":"9041943","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"LS-MS\\\/MS","modification":"MOD:00085 - \\\"A protein modification that effectively converts an L-lysine residue to N6-methyl-L-lysine.\\\"","keywords":"gbm;IF;DatasetType:Metabolomics","pi":[{"name":"Sanqi An","email":"ansanqi@sr.gxmu.edu.cn","institution":"Guangxi Medical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c6159b958a054158a57e733bb2fb921f","id":"26"}, {"dataset":"MSV000100113","datasetNum":"100113","title":"Rapid Target Engagement of KRAS G12C Tricomplex Inhibitor RO3903 Overcomes Resistance and Drives Durable Tumor Regression","user":"Zhenze","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764914786000","created":"Dec. 4, 2025, 10:06 PM","description":"Cysteine chemoproteomics data for paper \"Rapid Target Engagement of KRAS G12C Tricomplex Inhibitor RO3903 Overcomes Resistance and Drives Durable Tumor Regression\"","fileCount":"13","fileSizeKB":"8473966","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"KRAS;covalent;KRAS G12C;chemoproteomics;activity-based proteome profiling;DatasetType:Proteomics","pi":[{"name":"Zhenze Jiang","email":"zhenze.jiang@roche.com","institution":"Roche","country":"China"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"94f76c0139964486a3ed876f218e522d","id":"27"}, {"dataset":"MSV000100109","datasetNum":"100109","title":"GNPS - eDNAID Thrust 3 test samples M01","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764892193000","created":"Dec. 4, 2025, 3:49 PM","description":"Water samples (ocean and river) as tests for eDNAID Thrust study (part of Qiita ID 16188). 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The aim of this experiment is to identify the impact of the carbon sequestration technique ocean alkalinity enhancement on the microbiome and metabolome of the coral holobiont and the surrounding water column.Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1585","fileSizeKB":"97786372","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Montipora (NCBITaxon:46703);Pocilloporidae (NCBITaxon:46729)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Coral tissue;Dissolved Organic Matter;DatasetType:Metabolomics;MSCollaboratory","pi":[{"name":"Craig Nelson","email":"craig.nelson@hawaii.edu","institution":"University of Hawaii","country":"USA"},{"name":"Rayna McClintock","email":"raynamcc@hawaii.edu","institution":"University of Hawai'i at Manoa","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8fc001113e77490dbf6ce66ff9fb5496","id":"33"}, {"dataset":"MSV000100088","datasetNum":"100088","title":"Checking Fractions from HPLC Separation Work for Metallophores Run 2","user":"redghoti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764787962000","created":"Dec. 3, 2025, 10:52 AM","description":"This dataset simply looks at various fractions pulled from an HPLC run to separate metabolites and ideally find fraction(s) that contain our metallophore(s) of interest. 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We performed comprehensive interactomics analyses on both wild type POP5 and selected disease associated POP5 mutants. POP5 constructs were generated with N and C terminal MAC tags to enable affinity purification and proximity labeling. Stable HEK293 cell lines expressing the POP5 variants were established using the MAC tag system, followed by doxycycline inducible expression where applicable.\r\nFor interactome mapping, we employed affinity purification\u2013mass spectrometry (AP MS) and BioID based proximity labeling to capture both stable and transient interaction partners. Purified protein complexes were analyzed using high resolution LC MS\/MS, and interaction networks were constructed using SAINT, CRAPome filtering, and STRING based functional clustering. 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Experiments were performed from mammary glands organoids derived from mouse and the MS files were acquired on Orbitrap Fusion mass spectrometer. For questions, please contact Etienne Audet-Walsh (Etienne.Audet-Walsh@crchudequebec.ulaval.ca).","fileCount":"17","fileSizeKB":"14574818","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"DatasetType:Proteomics;organoids;mTOR;mammary gland;rapamycin;torin;estrogens","pi":[{"name":"Etienne Audet-Walsh","email":"Etienne.Audet-Walsh@crchudequebec.ulaval.ca","institution":"Universite Laval","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5f87d28fa6a84ea187736a64a02237d2","id":"38"}, {"dataset":"MSV000100060","datasetNum":"100060","title":"LCMS Analysis of V5-KEAP1 +\/- Drug, Wood Lab","user":"es3064","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1764598173000","created":"Dec. 1, 2025, 6:09 AM","description":"Coomassie stained SDS-PAGE bands were subjected to standardized in-gel trypsin digestion in which gel bands were subjected to reduction with 10 mM dithiolthreitol, alkylated with 20 mM iodoacetamide, and digested with 100ng of sequencing grade modified trypsin (Promega). 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The instrument was set to acquire a precursor MS scan from m\/z 200-1500 in the Orbitrap at r=120,000 with MS\/MS spectra acquired in the Ion Trap with AGC setting of 1e4 and 100ms. 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Data was acquired using UHPLC-MS\/MS method, samples resuspended in 50-50 MeOH\/H2O.","fileCount":"145","fileSizeKB":"15403962","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No Species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Stool;Dino;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cf4b12c452f149a981bba7380b75b693","id":"57"}, {"dataset":"MSV000099991","datasetNum":"99991","title":"GNPS - Mashua_Tropaeolum tuberosum_pilot data set","user":"Desolis","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763792724000","created":"Nov. 21, 2025, 10:25 PM","description":"This dataset contains a pilot LC-MS\/MS analysis of Tropaeolum tuberosum (mashua) tuber extracts acquired using a Q Exactive system. The purpose of this pilot run is to evaluate extraction performance and chromatographic conditions prior to generating the full dataset. Samples were acquired in positive ion mode.\n","fileCount":"207","fileSizeKB":"24056555","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Tropaeolum tuberosum (NCBITaxon:147035)","instrument":"Q Exactive","modification":"none","keywords":"metabolomic;mashua;plant metabolomic;Tropaeolum tuberosum;DatasetType:Metabolomics","pi":[{"name":"Deyvis Solis","email":"deyvisfarmacia@gmail.com","institution":"Universidad Nacional del Santa","country":"Peru"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a0ff1a1c55a64f24afcee692a632d194","id":"58"}, {"dataset":"MSV000099988","datasetNum":"99988","title":"Identification of LA1 as associated with the Arabidopsis thaliana telomerase complex by AP\/MS","user":"OpheliaP","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763755207000","created":"Nov. 21, 2025, 12:00 PM","description":"Label free quantification of proteins associated with Arabidopsis thaliana core telomerase complex using AP\/MS from plants overexpressing TwinStrep tagged TERT and TR vs control plants mu. Data were collected for four biological replicates of overexpressing lines vs tert mutant lines. For 2 biological replicates the data was single injections collected on a an Orbitrap Fusion Lumos instrument, and for the other 2 biological replicates data comprised 3 injections each on an Orbitrap Fusion instrument.","fileCount":"58","fileSizeKB":"68299789","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion Lumos;Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"telomerase, TERT, Arabidopsis thaliana, LA1, TR, AP\/MS;DatasetType:Proteomics","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD071051","task":"7d64de9dcb9d4f9b9cd78c15ad772544","id":"59"}, {"dataset":"MSV000099979","datasetNum":"99979","title":"SILAC-iTRAQ-TAILS - Monitoring matrix metalloproteinase activity at the epidermal-dermal interface by SILAC-iTRAQ-TAILS","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763703354000","created":"Nov. 20, 2025, 9:35 PM","description":"Secreted proteases act on interstitial tissue secretomes released from multiple cell types. Thus, substrate proteins might be part of higher molecular complexes constituted by many proteins with diverse and potentially unknown cellular origin. In cell culture these might be reconstituted by mixing native secretomes from different cell types prior to incubation with a test protease. Although current degradomics techniques could identify novel substrate proteins in these complexes, all information on the cellular origin would be lost. To address this limitation we combined iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (iTRAQ-TAILS) with stable isotope labeling by amino acids in cell culture (SILAC) to assign proteins to a specific cell type by MS1- and their cleavage by MS2-based quantification in the same experiment. We demonstrate the power of our newly established workflow by monitoring matrix metalloproteinase (MMP) 10-dependent cleavages in mixtures from heavy labeled fibroblast and light labeled keratinocyte sectretomes. This analysis correctly assigned extracellular matrix components, such as laminins and collagens, to their respective cellular origins and revealed their processing in an MMP10-dependent manner. Hence, our newly devised degradomics workflow facilitates deeper insights into protease activity in complex intercellular compartments like the epidermal-dermal interface by integrating multiple modes of quantification with positional proteomics.","fileCount":"35","fileSizeKB":"11386831","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MOD:00587 - \\\"A protein modification that effectively converts an L-arginine residue to 6x(13)C, 4x(15)N labeled L-arginine.\\\";MOD:01499 - \\\"A protein modification that effectively replaces a hydrogen atom of a residue with the Applied Biosystems iTRAQ4plex-116 reporter+balance group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Skin;Basement membrane;Tails;Silac;Itraq;Mmp;DatasetType:Proteomics","pi":[{"name":"Ulrich auf dem Keller","email":"ulrich.aufdemkeller@biol.ethz.ch","institution":"ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD001643","task":"12e1b3c2d43147728b0c590492e30087","id":"60"}, {"dataset":"MSV000099978","datasetNum":"99978","title":"GNPS-Lizards_samples_Panama_retention_time_matching","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763698355000","created":"Nov. 20, 2025, 8:12 PM","description":"MS\/MS fragmentation data of Lizard samples acquired on Q Exactive - with\r\nchromatographic separation on a Phenomenex polar C18 column","fileCount":"16","fileSizeKB":"1109579","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Retention;matching;time;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"University of California-San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0d0b658dc59e4d8883226e6e8e581b97","id":"61"}, {"dataset":"MSV000099975","datasetNum":"99975","title":"The nature and extent of contributions by defective ribosome products to the HLA peptidome","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763669584000","created":"Nov. 20, 2025, 12:13 PM","description":"MHC class I peptides are products of endogenous cellular protein degradation. Their prompt presentation, after rapid degradation of their newly synthesized source proteins, is needed to alert the immune system during pathogen infection. A possible source for such rapidly degrading proteins can be defective ribosome products (DRiPs), which include polypeptides produced as part of the pioneer round of translation, premature translation termination, and proteins failing to fold properly or to assemble into their multisubunit protein complexes. However, the identities and relative contribution to the MHC peptidome of these mature or newly synthesized and rapidly degraded cellular proteins is not well understood. To clarify these issues, we used dynamic stable isotope labeling by amino acids in cell culture to define the relative rates of synthesis of the HLA class I peptidomes and the source proteomes of three cultured human hematopoietic cell lines. Large numbers of HLA class I peptides were observed to be derived from DRiPs, defined here as HLA peptides that shift from their light to heavy isotope forms, faster than their source proteins. Specific groups of proteins, such as ribosomal and T-complex protein 1 (TCP-1), contributed a disproportionately large number of DRiPs to the HLA peptidomes. Furthermore, no significant preference was observed for HLA peptides derived from the amino terminal regions of the proteins, suggesting that the contribution of products of premature translation termination was minimal. Thus, the most likely sources of DRiPs-derived HLA peptides are full-sized, misassembled, and surplus subunits of large protein complexes.","fileCount":"72","fileSizeKB":"65039068","spectra":"1277946","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;LTQ Orbitrap","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Dripome;Dynamic silac;Immunopeptidome;DatasetType:Proteomics","pi":[{"name":"Arie Admon","email":"admon@technion.ac.il","institution":"Deprtment of Biology, Technion - Israel Institue of Technology, Haifa, Israel","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD009801","task":"2c4bfe78d3c743ab81cc1c533cefcc0c","id":"62"}, {"dataset":"MSV000099974","datasetNum":"99974","title":"Acute in vivo proximity labeling for membrane targeted proteomics in neuronal circuits","user":"brettsp1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763668817000","created":"Nov. 20, 2025, 12:00 PM","description":"The field of molecular systems neuroscience aims to bridge neuronal circuit activity patterns with changes in protein expression and localization in the context of specific animal behaviors. However, there are limited tools for capturing changes in subcellulary-defined proteomes within neuronal circuits during activity-gated timescales in vivo. Here, we engineered targeted versions of the proximity labeling enzyme TurboID, to tag proteins at the neuronal membrane during a user-delivered biotin injection. We optimized a labeling strategy that enables a one-to-two-hour labeling window to tag proteins in prefrontal cortex (PFC) cell bodies and corresponding axons in two downstream projections. We performed proteomics to identify proteins enriched across different projections, and identified membrane associated proteins in the PFC cell bodies that are enriched at the membrane following an acute cocaine injection. These advancements enable the detection of proteins at the subcellular level within short labeling windows, allowing identification of stimulus-specific proteomes in behaving mice.","fileCount":"237","fileSizeKB":"27210152","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF HT;Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"proximity labeling, TurboID, subcellular proteomics, medial prefrontal cortex, neuronal circuit projections, cocaine, axonal proteomics;DatasetType:Proteomics","pi":[{"name":"Christina K. Kim1","email":"ckk@princeton.edu","institution":"Princeton","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD071005","task":"d8ddcfdb7d124e6ca9654997c07f9203","id":"63"}, {"dataset":"MSV000099973","datasetNum":"99973","title":"The effect of proteasome inhibition on the HLA peptidome","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763666781000","created":"Nov. 20, 2025, 11:26 AM","description":"The Major histocompatibility complex (MHC) class I peptidome is thought to be generated mostly through proteasomal degradation of cellular proteins, a notion that is based on the alterations in presentation of selected peptides following proteasome inhibition. We evaluated the effects of proteasome inhibitors, epoxomicin and bortezomib, on human cultured cancer cells. Since the inhibitors did not reduce the level of presentation of the cell surface human leukocyte antigen (HLA) molecules, we followed their effects on the rates of synthesis of both HLA peptidome and proteome of the cells, using dynamic stable isotope labeling in tissue culture (dynamic-SILAC). The inhibitors reduced the rates of synthesis of most cellular proteins and HLA peptides, yet the synthesis rates of some of the proteins and HLA peptides was not decreased by the inhibitors and of some even increased. Therefore, we concluded that the inhibitors affected the production of the HLA peptidome in a complex manner, including modulation of the synthesis rates of the source proteins of the HLA peptides in addition to their effect on their degradation. The collected data may suggest that the current reliance on proteasome inhibition may overestimate the centrality of the proteasome in the generation of the MHC peptidome. It is therefore suggested that the relative contribution of the proteasomal and non-proteasomal pathways to the production of the MHC peptidome should be revaluated in accordance with the inhibitors effects on the synthesis rates of the source proteins of the MHC peptides. Bioinformatics & data processing: Peptides were identified and the dynamic-SILAC data were quantified using the MaxQuant and the Proteome Discoverer software tools. Graphical representation of the bioinformatics results was performed with Perseus, version 1.3.0.4. MaxQuant [54] version 1.3.0.5 was used with the Andromeda search engine [55] and the human section of Nov 2011 of UniProt containing 20257 entries and mass tolerance of 6 ppm for the precursor masses and 0.5 Da for the fragments. Methionine oxidation was accepted as variable modification for both tryptic and HLA peptides. Carbamidomethyl cysteine and n-acetylation were accepted as modification for the proteomics analyses. Minimal peptide length was set to 7 amino acids and a maximum of two missed cleavages was allowed for tryptic peptides. The false discovery rate (FDR) was set for tryptic peptides to 0.01 for protein identifications, and 0.05 for the MHC peptides. The resulting identified protein tables were filtered to eliminate the identifications derived from the reverse database, as well as common contaminants. Proteome Discoverer version 1.3 (Thermo-Fisher) was used with UniProt of April 2012 for the Sequest search (containing 20220 entries) and July 2012 for the Mascot search (containing 20306 entries). Masses tolerance was set to 6 ppm for the precursors and 0.5 Da for the fragments. Methionine oxidation and n-acetylation were accepted as variable modification for both tryptic and HLA peptides. Carbamidomethyl cysteine was set as fixed modification for the proteomics analyses. Mass range of 350-5000 Da was used for tryptic peptides and mass range of 750-2500 Da was used for the MHC peptides. For both tryptic and MHC peptides the PSMs were filtered with at least 0.05 FDR (medium confidence), peptide maximum rank was set to 1. Minimal number of identified peptides per proteins was set to 2.","fileCount":"200","fileSizeKB":"101072610","spectra":"1249101","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Hla peptidome;Proteasome inhibitors;Dynamic silac;DatasetType:Proteomics","pi":[{"name":"Arie Admon","email":"admon@technion.ac.il","institution":"Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000171","task":"62e80c46ea504f32ad2a4716d3eac7a4","id":"64"}, {"dataset":"MSV000099968","datasetNum":"99968","title":"PCI-DB: A novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763599968000","created":"Nov. 19, 2025, 4:52 PM","description":"Various cancer immunotherapies rely on the T cell recognition of peptide antigens presented on human leukocyte antigens (HLA). However, the identification and selection of naturally presented peptide targets for the development of personalized as well as off-the-shelf immunotherapy approaches remains challenging. Here, we introduce the open-access Peptides for Cancer Immunotherapy Database (PCI-DB, https:\/\/pci-db.org\/), a comprehensive resource of immunopeptidome data originating from various malignant and benign primary tissues that provides the research community with a convenient tool to facilitate the identification of peptide targets for immunotherapy development. The PCI-DB includes > 6.6 million HLA class I and > 3.4 million HLA class II peptides from over 40 tissue types and cancer entities analyzed uniformly using high-sensitive nf-core bioinformatics pipelines and applying a global peptide false discovery rate (FDR) approach. First application of the database provided insights into the representation of cancer-testis antigens (CTA) across malignant and benign tissues and enabled the identification and characterization of the cross-tumor entity and entity-specific tumor-associated antigens as well as naturally presented neoepitopes from frequent cancer mutations. Further, we used the PCI-DB to design personalized peptide vaccines for two patients suffering from metastatic cancer. PCI-DB enabled the composition of both a multi-peptide vaccine comprising non-mutated, highly frequent tumor-associated antigens matching the immunopeptidome of the individual patient´s tumor and a neoepitope-based vaccine matching the mutational profile of the cancer patient. Both vaccine approaches induced potent and long-lasting T-cell responses, accompanied by long-term survival of these advanced cancer patients. In conclusion, the PCI-DB provides a highly versatile tool to broaden the understanding of cancer-related antigen presentation and, ultimately, supports the development of novel immunotherapies.","fileCount":"36","fileSizeKB":"13911570","spectra":"371668","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Orbitrap Fusion Lumos;timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human;Lc-msms;Synthetic peptides;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. med. 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Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). 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The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi-) personalized strategies.","fileCount":"847","fileSizeKB":"220176226","spectra":"2885182","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap XL","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hpv;Hla;Tumor-associated antigen;Oropharyngeal squamous cell carcinoma;Mass spectrometry;Opscc;Immunopeptidome;Immunopeptidomics;DatasetType:Proteomics","pi":[{"name":"Simon Laban","email":"simon.laban@uniklinik-ulm.de","institution":"Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD033383","task":"dedf648b650840efb00548cd35d9731f","id":"71"}, {"dataset":"MSV000099946","datasetNum":"99946","title":"The transmembrane protein disulfide isomerase TMX3 potentiates platelet aggregation and arterial thrombosis in mice","user":"fengwu_chen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763500822000","created":"Nov. 18, 2025, 1:20 PM","description":"To identify the specific disulfide bonds in alphaIIbbeta3 catalyzed by TMX3, alphaIIbbeta3 protein was incubated with GSH (group 1), GSH plus TMX3 (group 2), or DTT (group 3). After incubation, free thiols were labeled with IAM, excess IAM was removed by Zeba column, and the remaining disulfide bonds were subsequently reduced by DTT and labeled with NEM, excess NEM was removed by Zeba column. The abundance of Cys-IAM was then quantified by mass spectrometry.","fileCount":"17","fileSizeKB":"27168409","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00483 - \\\"A protein modification that is produced by reaction with N-ethylmaleimide.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"TMX3, alphaIIbbeta3, disulfide bond;DatasetType:Proteomics","pi":[{"name":"Fengwu Chen","email":"fengwu_chen@126.com","institution":"Tsinghua University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD070905","task":"938c4cc91f584dc38275442ed848ac7e","id":"72"}, {"dataset":"MSV000099945","datasetNum":"99945","title":"GNPS - Unraveling Environmental Drivers of Pseudo-nitzschia Harmful Algal Blooms","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1763500725000","created":"Nov. 18, 2025, 1:18 PM","description":"This research aims to identify and describe molecular indicators of domoic acid events specific to the Santa Barbara Channel. 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Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).\n","fileCount":"3820","fileSizeKB":"253633679","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;Dissolved Organic Matter (DOM);DatasetType:Metabolomics","pi":[{"name":"Andrew Allen","email":"aallen@ucsd.edu","institution":"University of California San Diego","country":"USA"},{"name":"Bradley S. 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However, these approaches often introduce functional disruptions or ligand-associated biological effects. Herein, we address these challenges by developing covalent fluorescent probes for endogenous tubulin, a critical cytoskeletal protein involved in processes such as cell movement, division, and biomolecule trafficking. Using well-known tubulin binder cabazitaxel and cell permeable fluorophore silicon-rhodamine as a basis, we introduce a novel biocompatible cleavable linker containing a sulfonium center. This allowed the construction of the optimized probe, 6-SiR-o-C9-CTX, demonstrating excellent cell permeability, fluorogenic properties, and the ability to covalently label tubulin across various human cell lines. Importantly, the targeting moiety could be washed out while preserving tubulin staining, ensuring minimal disruption of tubulin function. 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Search for the DDA data was performed using MaxQuant, following the label-free quantification and match between runs (LFQ-MBR) workflow. The DIA data was searched with FragPipe\/DIA-NN. 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Mid-log cells (OD600 0.3) were lysed (urea\/thiourea\/TEAB buffer), reduced\/alkylated, barocycled, digested, TMT-labeled, and analyzed on an Orbitrap Eclipse using HCD. Raw files and search results (Proteome Discoverer; UniProt S. aureus pan-proteome UP000008816 plus common contaminants) are included. The dataset supports the mBio study Commensal-derived short-chain fatty acids disrupt membrane lipid homeostasis in Staphylococcus aureus (Fletcher et al.) and enables assessment of global protein abundance changes elicited by SCFAs that converge on lipid\/branched-chain fatty acid metabolism, cell envelope homeostasis, and virulence regulation. Differential proteins highlighted in the manuscript include induction of acetolactate synthase components (BudA\/AlsS) and NanA in propionate, increased dihydropicolinate synthases (DapA\/B\/H) in butyrate, and decreased RecR and NrdI in both conditions. 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On days 5, 10, 15, and 20, we returned to each deployment site and collected two decomposing leaves from each leaf pack to describe how the metabolome profile from Home and Away leaves change throughout decomposition. In addition, microbial decomposer communities were collected at each time point to test how each successional community originating from Home and Away leaves utilized fresh leaf metabolites which were extracted as described above. All decomposing leaves were lyophilized for 24 hours at -55C and 0.22m Bar using a Labconco FreeZone lyophilizer. From fresh and decomposing leaves, we then extracted 5mg of plant tissue in 1mL of 70% LC-MS grade methanol with 1 uM sulfadimethoxine using a Qiagen TissueLyser II (Qiagen, Hilden, Germany) set to 25 Hz for 5 minutes at ambient temperature. Sample extractions were then centrifuged at 15,000 rpm for 5 minutes at room temperature, where 400 uL of supernatant was transferred into a 96 deep well plate. Samples were then concentrated in a Labconco centrivap system for 24 hours at 25 oC. Afterwards, samples were resuspended in 200 uL 70% methanol with 1 uM sulfachloropyridazine, sealed, and stored in -80C until liquid chromatography tandem mass spectrometry (LC-MS\/MS) analysis. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Q Exactive (Thermo Fisher Scientific, Bremen, Germany). 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Inherited mutations in genes encoding ubiquitous RNases are associated with human diseases, primarily affecting the nervous system. Recessive mutations in genes encoding the evolutionarily conserved RNA exosome, an RNase complex, cause syndromic neurodevelopmental disorders, such as Pontocerebellar Hypoplasia Type 1b (PCH1b), characterized by progressive neurodegeneration. Here, we establish a CRISPR\/Cas9-engineered Drosophila model of PCH1b to investigate the cell-type-specific post-transcriptional regulatory functions of the RNA exosome complex in vivo. Pathogenic variants in Rrp40, a subunit of the complex, disrupt RNA exosome activity, leading to widespread transcriptomic dysregulation in brain-enriched cell populations, including defective rRNA processing. These molecular defects coincide with progressive neurodegeneration and behavioral impairments that track with allele severity. 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Plant seeds as specified in file name and metadata were collected. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m\/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL acetonitrile-water-formic acid (50%\/48%\/2%, v\/v\/v), ground another 20 s at 6 m\/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. The extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, transferred to a glass vial (12x75 mm) and dried in a speedvac (3 h at 45 celsius at 500 mtorr). Dried supernatant was resuspended in 80% methanol, transferred to 2mL tubes, centrifuged for 5 min at 16,000 x g and filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS\/MS on an Thermo QExactive orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL\/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50 ms, mass range 150-500 m\/z (lowmz method) or 450-1,500 m\/z (highmz method), dd-MS2 (data-dependent MS\/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m\/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.","fileCount":"701","fileSizeKB":"42273155","spectra":"2050157","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plants, metabolomics, seeds;DatasetType:Metabolomics","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan, Ann Arbor","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5d4b4dc85c304f04aa10cb99ec8c8c88","id":"127"}, {"dataset":"MSV000099792","datasetNum":"99792","title":"GNPS - plantMASST submission - seedling extracts","user":"wenjieliCOP","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762537910000","created":"Nov. 7, 2025, 9:51 AM","description":"Plant metabolic extracts. Plant seedlings were grown in Premier Horticulture Pro Mix HP High Porosity with Mycorrhizae for plant growth under plant growth lights with a 16 h light\/8 h dark cycle for 6-8 weeks at room temperature. Plant tissue samples were collected as specified in file name and metadata. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m\/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL 80% methanol, ground another 20 s at 6 m\/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. Methanol extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, and filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS\/MS on an Thermo QExactive orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex\r\n2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL\/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50\r\nms, mass range 150-500 m\/z (lowmz method) or 450-1,500 m\/z (highmz method), dd-MS2 (data-dependent MS\/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m\/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.","fileCount":"1160","fileSizeKB":"62274095","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plantMASST, metabolomics, plants, seedling;DatasetType:Metabolomics","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6f093b73f0a4435bb1dfc04cc2926981","id":"128"}, {"dataset":"MSV000099790","datasetNum":"99790","title":"GNPS - plantMASST data submission - additional plant families","user":"Rolandoo1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762537747000","created":"Nov. 7, 2025, 9:49 AM","description":"Plant metabolic extracts. Plant seeds and plant tissues as specified in file name and metadata were collected. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m\/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL 80% methanol, ground another 20 s at 6 m\/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. Methanol extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, and filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS\/MS on an Thermo QExactive orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL\/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50 ms, mass range 150-500 m\/z (lowmz method) or 450-1,500 m\/z (highmz method), dd-MS2 (data-dependent MS\/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m\/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.","fileCount":"289","fileSizeKB":"17189704","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plants, metabolomics;DatasetType:Metabolomics","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan, Ann Arbor","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"34ba04acb0674a54b52c71e614111084","id":"129"}, {"dataset":"MSV000099788","datasetNum":"99788","title":"GNPS - plantMASST submission - seed extracts","user":"wenjieliCOP","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762536877000","created":"Nov. 7, 2025, 9:34 AM","description":"Plant metabolic extracts. Plant seeds as specified in file name and metadata were collected. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m\/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL acetonitrile-water-formic acid (50%\/48%\/2%, v\/v\/v), ground another 20 s at 6 m\/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. The extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, transferred to a glass vial (12x75 mm) and dried in a speedvac (3 h at 45 celsius at 500 (m)torr). Dried supernatant was resuspended in 80% methanol, transferred to 2mL tubes, centrifuged for 5 min at 16,000 x g filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS\/MS on an Thermo QExactive\r\norbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL\/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50 ms, mass range 150-500 m\/z (lowmz method) or 450-1,500 m\/z (highmz method), dd-MS2 (data-dependent MS\/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m\/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.","fileCount":"468","fileSizeKB":"28375257","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plantMASST;metabolomics;plants;seeds;DatasetType:Metabolomics","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d1af4d2ceacb41babe91c7eeca72337d","id":"130"}, {"dataset":"MSV000099783","datasetNum":"99783","title":"GNPS-HNRC_lithocholic_acid_n-acetylcadaverine_rt_matching","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762512931000","created":"Nov. 7, 2025, 2:55 AM","description":"MS\/MS fragmentation data of HNRC fecal samples acquired on Q Exactive - with\r\nchromatographic separation on a Phenomenex polar C18 column","fileCount":"7","fileSizeKB":"361228","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Custom Species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"retention time;matching;biological;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"University of California- San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7a11944f37a344cca3bba7c6d1007b54","id":"131"}, {"dataset":"MSV000099779","datasetNum":"99779","title":"GNPS - Aplysia dactylomela - Vzla 2025","user":"Darrieche","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762460204000","created":"Nov. 6, 2025, 12:16 PM","description":"Ethanolic extracts from Aplysisa dactylomela from Venezuela","fileCount":"7","fileSizeKB":"26588","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aplysia dactylomela (NCBITaxon:144766)","instrument":"Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Aplysia;Marine Natural Products;Marine Mollusk;DatasetType:Metabolomics","pi":[{"name":"Dioni Antonio Arrieche","email":"dioniarrieche@gmail.com","institution":"Universidad Tecnica Federico Santa Maria","country":"Chile"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"762bf001679f43749781a036bfbe67af","id":"132"}, {"dataset":"MSV000099777","datasetNum":"99777","title":"Metabolites production under varying soluble\/insoluble La","user":"redghoti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762449123000","created":"Nov. 6, 2025, 9:12 AM","description":"This run looked at changes in metabolite production under varying conditions of soluble v insoluble lanthanum (and a no additive condition). This dataset is intended to be compared with samples pulled at the same time for RT-qPCR analysis.","fileCount":"41","fileSizeKB":"3527424","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Methylobacterium aquaticum (NCBITaxon:270351)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gram-negative;methylobacteria;metallophore;lanthanophore;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7f6705c8a0064180abb6a25e3c617819","id":"133"}, {"dataset":"MSV000099770","datasetNum":"99770","title":"GNPS-Chroh's_and_Colitis_fecal_samples","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762386382000","created":"Nov. 5, 2025, 3:46 PM","description":"MS\/MS fragmentation data of CCFA biological samples acquired on Q Exactive - with\r\nchromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"10","fileSizeKB":"516436","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Custom Species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"retention time matching;synthesized standards;biological samples;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"University of California-San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"60850a3fede347088e50f52585e161c1","id":"134"}, {"dataset":"MSV000099768","datasetNum":"99768","title":"Magnesium modulates the stress response of oral streptococci to environmental and antibiotic challenges by altering cell envelope and nutrient transport pathways ","user":"Tina_2025","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762377204000","created":"Nov. 5, 2025, 1:13 PM","description":"Magnesium supplementation increases the tolerance of various Streptococcus species to environmental stressors, specifically osmotic and Zn-excess. In order to understand the mechanism of Mg-dependent stress tolerance, a putative Mg2+-efflux pump gene, hlyX, has been deleted in Streptococcus mutans. The effects of Mg2+ supplementation on wild-type and Delta-hlyX strains regarding growth, stress tolerance, and intracellular metal concentrations were compared to elucidate the role of HlyX in Mg2+ efflux. Proteomic and lipidomic analyses of the wild-type and Delta-hlyX strains in the presence of 25 mM MgCl2 were compared with those grown in unsupplemented media. Proteomic and lipidomic analyses revealed altered levels of amino acid transporters, cell envelope proteins, and an increase in long-chain unsaturated fatty acids. Furthermore, modulating intracellular Mg2+ concentration, either by MgCl2 supplementation or by eliminating HlyX, impacted the efficacy of multiple cell wall-targeting antibiotics. ","fileCount":"53","fileSizeKB":"28347746","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ULTIMATE 3000 nano UHPLC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"human, liver, plasma, LC-MSMS;DatasetType:Proteomics","pi":[{"name":"Surabhi Mishra","email":"sumishr@iu.edu","institution":"Dept. of Biomedical and Applied Sciences Indiana School of Dentistry","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD070376","task":"882594b825464bafab0553331161b1bf","id":"135"}, {"dataset":"MSV000099764","datasetNum":"99764","title":"CMMC_5_asa_bile_acid_3_hydroxyantharanilic_acid","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762371626000","created":"Nov. 5, 2025, 11:40 AM","description":"MS\/MS fragmentation data of reaction mixture was acquired on Q Exactive - with\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"7","fileSizeKB":"538313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CMM;drugs;bile acid;5-aminosalicylic acid;multiplex synthesis;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a42e9be9c5bf43bdaa66cbe3159cd9cc","id":"136"}, {"dataset":"MSV000099762","datasetNum":"99762","title":"Trial1____________________________________________________________","user":"harpersk","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762368036000","created":"Nov. 5, 2025, 10:40 AM","description":"dddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddd","fileCount":"622","fileSizeKB":"84093301","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"latrunculia austini","instrument":"qtof","modification":"None","keywords":"None;DatasetType:Proteomics","pi":[{"name":"none","email":"none@gmail.com","institution":"none","country":"none"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD070367","task":"ecc250205213417bb9c16df72c01206b","id":"137"}, {"dataset":"MSV000099757","datasetNum":"99757","title":"The lactate sensor NDRG3 decelerates ER-to-Golgi transport through interaction with the long isoform of syntaxin-5_2025","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762300201000","created":"Nov. 4, 2025, 3:50 PM","description":"Authors:\nPia E. Ferle, Niklas Krause, Judith Koliwer, Joern Michael Voelker, Fabia Becker, Alexander Hillebrand, Leonie F. Schroeder, Stefanie Jaeger, Seby Edassery, Dali Liu, Nevan Krogan, Jeffrey N. Savas, Gabriele Fischer von Mollard and Michael Schwake\n","fileCount":"64","fileSizeKB":"20706925","spectra":"0","psms":"141401","peptides":"26694","variants":"26694","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1001460 - This term should be given if the modification was unknown.;UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Hypoxia, Syntaxin5, SNARE, progressive myoclonus epilepsy, congenital muscular dystrophy, lactate;DatasetType:Proteomics","pi":[{"name":"Michael Schwake","email":"Michael.schwake@uni-bielefeld.de","institution":"University of Bielefeld","country":"Germany"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD070322","task":"1e8be58c25af42f7b6a59228fde2b9e4","id":"138"}, {"dataset":"MSV000099751","datasetNum":"99751","title":"Elucidation of genomic context for a non pyl monomethyamine methyltransfersae ","user":"Methanogen123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762284668000","created":"Nov. 4, 2025, 11:31 AM","description":"This study identifies and characterizes the first non pyrrolysine monomethylamine methyltransferase supporting quaternary amine dependent methanogenesis in Methanococcoides methylutens Q3c","fileCount":"127","fileSizeKB":"10093667","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Methanococcoides methylutens (NCBITaxon:2226)","instrument":"LTQ Orbitrap XL","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Quaternary amine, Methanogen;DatasetType:Proteomics","pi":[{"name":"DJ Ferguson","email":"fergusdj@miamioh.edu","institution":"Miami Unviersty","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4f38cbd7a4f0472e8008efde8424a0b7","id":"139"}, {"dataset":"MSV000099743","datasetNum":"99743","title":"Global, phosphoproteome and acetylome of rice genotypes against Magnaporthe oryzae infection","user":"PAuler","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762262122000","created":"Nov. 4, 2025, 5:15 AM","description":"In this study, we examine the complex rice-Magnaporthe oryzae pathosystem. Specifically, we use quantitative proteomics to compare the proteome, phosphoproteome, and acetylome of two rice genotypes that differ in resistance to M. oryzae.","fileCount":"88","fileSizeKB":"95674973","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Oryza sativa (NCBITaxon:4530)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:260 - \\\"Thiophosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Oryza sativa;Magnaporthe oryzae;disease;rice genotypes;multiproteomics;DatasetType:Proteomics","pi":[{"name":"Justin Walley","email":"jwalley@iastate.edu","institution":"Iowa State University","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD070288","task":"1b0d07fd3cca46fc9e0ededa86794c61","id":"140"}, {"dataset":"MSV000099738","datasetNum":"99738","title":"GNPS - Lahaina wildfire Project","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762220656000","created":"Nov. 3, 2025, 5:44 PM","description":"This dataset includes samples from coral tissues collected along the coast of Maui following the Lahaina wildfire. These samples were collected by Dr. Craig E. Nelson, Sean Swift, and Justin Berg. This project was supported by NSF-Rapid grant #2345201 to Dr. Craig E. Nelson and Dr. Andrea Kealoha. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1358","fileSizeKB":"75975402","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Several","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;Metabolomics;Coral;Lahaina wildfire;DatasetType:Metabolomics","pi":[{"name":"Craig Nelson","email":"craig.nelson@hawaii.edu","institution":"University of Hawaii","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d164cb12932c49ce952bd8a53e918346","id":"141"}, {"dataset":"MSV000099737","datasetNum":"99737","title":"GNPS - Crustose coralline algae (CCA)","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762220266000","created":"Nov. 3, 2025, 5:37 PM","description":"This dataset includes two species of the encrusting red algae, Crustose coralline algae (CCA) collected from Kaneohe Bay Oahu and Moorea, French Polynesia by Dr. Raphael Ritson Williams and Dr. Zachary A. Quinlan. The majority of the samples were visually identified under direction scope as Hydrolithon reinboldii, while three samples were Titanoderum sp. Tissues were extracted in 80% LC MS\/MS methanol and frozen at -80 Celsius degrees. A portion of this study was funded by NSF-OCE PRF grant #2308400 and NSF-OCE grant 2516814. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"303","fileSizeKB":"17633428","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hydrolithon reinboldii (NCBITaxon:389195);Titanoderum sp.","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;Metabolomics;Crustose coralline algae (CCA);DatasetType:Metabolomics","pi":[{"name":"Zachary A. 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The metabolomics data are generated through a RapidFire+6560 combination. 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Despite the essential role of lactation in maternal nutritional support, the influence of epigenetic factors on lactation and postnatal growth remains poorly understood. Zinc-finger protein 57 (ZFP57), is an epigenetic regulator of genomic imprinting, a process that directs gene expression based on parental origin, playing a vital role in mammalian prenatal growth. Here, we identify a novel function of ZFP57 in the mammary gland, where it serves as a key modulator of postnatal resource control, independently of imprinted genes. ZFP57 regulates multiple aspects of mammary gland functions, including ductal branching and cellular homeostasis. Its absence leads to significant differential gene expression, related to alveologenesis, lactogenesis and milk synthesis, associated with delayed lactation and altered milk composition. This results in life-long impacts on offspring including the development of metabolic syndrome. Cross-fostering reveals intricate dynamics between mother and offspring during lactation. Pups raised by a dam of a different genotype than their birth-mother exhibit exacerbated metabolic features in adulthood. This study shows a novel mechanism responsible for the programming of offspring long-term health by maternal context.","fileCount":"101","fileSizeKB":"4189069","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipids;DatasetType:Metabolomics","pi":[{"name":"Albert Koulman","email":"ak675@cam.ac.uk","institution":"University of Cambridge","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5aa276940c2047d1a12be0c4a529c5de","id":"145"}, {"dataset":"MSV000099717","datasetNum":"99717","title":"Monitoring the effect of Calmodulin binding to eEF2K_70-724 by HDX mass-spectroscopy","user":"apiserchio","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1762035138000","created":"Nov. 1, 2025, 3:12 PM","description":"A study of the effects of Calmodulin binding on eEF2K_70-725 monitored by hydrogen deuterium exchange mass spectroscopy. 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Aliquot was thawed, 100ul applied to the 50ul bed volume drug resin (124) or control resin lacking the drug ligand (74) and incubated for 1hr at room temperature followed by 100 bed volumes of wash with column buffer. Free drug at 200uM in column buffer was used to elute bound proteins, and the drug resin stripped with 8M urea to remove proteins that may have stuck after elution. Samples 16-18 were the bands observed in the control resin. Samples 4-14 were the bands observed in the drug resin. Samples 1-3 were the bands observed in the 8M urea stripping of the drug resin and not observed upon similar stripping the control resin. ","fileCount":"78","fileSizeKB":"38213","spectra":"0","psms":"204","peptides":"108","variants":"114","proteins":"59","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sus scrofa (NCBITaxon:9823)","instrument":"sciex","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Protein assembly modulation, allosteric site, small molecule, pig brain, Alzheimers Disease;DatasetType:Proteomics","pi":[{"name":"Vishwanath R. 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The assay was conducted using Pseudomonas putida A514 harboring a FLAG tagged DypB2985 vector, with A514 carrying the empty FLAG tagged vector serving as the control.","fileCount":"7","fileSizeKB":"1238407","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas putida (NCBITaxon:303)","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS\/MS;DatasetType:Metabolomics","pi":[{"name":"Congying Liang","email":"cyliang0819@163.com","institution":"Shandong University","country":"china"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a63037e35de54e2087258a7d330b7f07","id":"148"}, {"dataset":"MSV000099702","datasetNum":"99702","title":"Aspergillus fumigatus metabelomics after rice straw treatment","user":"scimohamednasr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1761900162000","created":"Oct. 31, 2025, 1:42 AM","description":"This metabolomic dataset investigates the effect of HBC-HA on Aspergillus fumigatus AF01 during rice straw degradation. It includes data from four experimental conditions: fungus with substrate, with substrate and HBC-HA, and relevant controls.","fileCount":"80","fileSizeKB":"10564130","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus fumigatus (NCBITaxon:746128);environmental samples (NCBITaxon:33858)","instrument":"UHPLC-Exploris240 system with an ACQUITY HSS T3 column.","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Aspergillus fumigatus;Rice straw;DatasetType:Metabolomics","pi":[{"name":"Mohamed N. 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Experiment is five biological replicates per condition, each LC-MS run is a single biological replicate.","fileCount":"12","fileSizeKB":"6861686","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"signaling;proximity labeling;DatasetType:Proteomics","pi":[{"name":"John D Scott","email":"scottjdw@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD070113","task":"6d52a3ceeb3345bbb6fcc06408b78e3e","id":"150"}, {"dataset":"MSV000099697","datasetNum":"99697","title":"Deoxyhypusine synthase, an essential enzyme for hypusine biosynthesis, is required for proper exocrine pancreas development","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1761845552000","created":"Oct. 30, 2025, 10:32 AM","description":"Pancreatic diseases including diabetes and exocrine insufficiency would benefit from therapies that reverse cellular loss and\/or restore cellular mass. The identification of molecular pathways that influence cellular growth is therefore critical for future therapeutic generation. Deoxyhypusine synthase (DHPS) is an enzyme that post-translationally modifies and activates the mRNA translation factor eukaryotic initiation factor 5A (eIF5A). Previous work demonstrated that the inhibition of DHPS impairs zebrafish exocrine pancreas development; however, the link between DHPS, eIF5A, and regulation of pancreatic organogenesis remains unknown. Herein we identified that the conditional deletion of either Dhps or Eif5a in the murine pancreas results in the absence of acinar cells. Because DHPS catalyzes the activation of eIF5A, we evaluated and uncovered a defect in mRNA translation concomitant with defective production of proteins that influence cellular development. Our studies reveal a heretofore unappreciated role for DHPS and eIF5A in the synthesis of proteins required for cellular development and function.\n\n ","fileCount":"43","fileSizeKB":"95363880","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"DHPS;hypusine;eIF5A;embryonic pancreas;exocrine;on demand translation;DatasetType:Proteomics","pi":[{"name":"Amber L. 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Two samples are from flowers, the other 143 came from leaves.","fileCount":"148","fileSizeKB":"35792320","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"See metadata","instrument":"Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"crude extracts;medicinal plants;DatasetType:Metabolomics","pi":[{"name":"Tomas Pluskal","email":"tomas.pluskal@uochb.cas.cz","institution":"Institute of Organic Chemistry and Biochemistry of the CAS","country":"Czech Republic"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"411cc2cad9b74c9ea7efe0e26c899b6b","id":"152"}, {"dataset":"MSV000099691","datasetNum":"99691","title":"Whole saliva baseline proteome profile - head and neck cancer","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1761789554000","created":"Oct. 29, 2025, 6:59 PM","description":"Oral mucositis (OM) is a common, painful and often treatment-limiting side effect of radiotherapy (RT) for head and neck cancer (HNC) patients. Unstimulated saliva was collected before the first radiotherapy application in 50 HNC patients. 41 out of 50 patients developed OM (grade III) during radiotherapy, of which 14 patients even displayed an early OM (grade III) at low radiation dose of 30 Gy. Nine patients did not develop OM (grade III). Using an LC-MS\/MS approach 5,323 tryptic peptides were assigned to 487 distinct proteins (?2 peptides) in the data set. The levels of 48 proteins differed significantly (p<0.05) between patients developing OM or not. 17 proteins displayed increased levels (?1.3-fold) and 31 proteins decreased in level in OM, respectively. Furthermore, using partial least square analysis proteins patterns could be used to distinguish subjects which did not develop grade III OM even after 70 Gy total dose (n=9) and those displaying early OM (grade III at <30 Gy total dose, n=14). 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An N1-aminopropylagmatine concentration gradient was included for absolute quantification. Data were used for the preparation of Figure 2H and SFig. 7A in Nauta et al 2025: \"A noncanonical polyamine from bacteria antagonizes host mitochondrial function\". 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Through metabolomics analyses, we aim to identify the presence\/absence of key metabolites observed in experimental treatments. \r\nSpecific aim. Experimental characterization of root colonization mechanisms. Brachypodium seeds will be surface sterilized and plated agar plates and left at 4oC for approximately 48 hours to allow for stratification. Two seedlings will be added to ecoBoxes and let to grow for 1-2 weeks with 60 ml 1\/5 MS media (pH adjusted to ~ 5.7). Pseudomonas simiae WCS417 fluorescent strain, SB642 will be added to \u2018with bacterium\u2019 treatment and ?? mutant strains will be added to ?? treatments. All samples will be subsequently collected at ~ 4 weeks. Each treatment will have 5 corresponding replicates. Exudate media will be processed for metabolomic analysis (20 samples total).\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008794) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"177","fileSizeKB":"16469480","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brachypodium microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plant microbiome;root colonization;fabricated ecosystems;rhizobacterium;DatasetType:Metabolomics","pi":[{"name":"Jonelle Basso","email":"JBasso@lbl.gov","institution":"Lawrence Berkeley National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"786bf58fca8148d4a9d0f8dd07d0e39b","id":"166"}, {"dataset":"MSV000099654","datasetNum":"99654","title":"A noncanonical polyamine from bacteria antagonizes host mitochondrial function - 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The T-DNA insertion mutants of AOP3 (SALK_001655C) and the WT were sowed directly in fertilized soil. Plants were grown in optimal conditions (control) in a growth chamber with long day photoperiod (16h light\/21 celsius degrees - 8h dark\/19 celsius degrees). Watering was made with water. At the onset of flowering (occurring between 5 and 6 weeks after seed sowing), high temperature (HT) was applied to half of the plants of the corresponding experiment by transferring them to another growth chamber (SANYO, Thermo Fisher Scientific) displaying high temperature conditions (16h of light\/27 celsius degrees - 8h of dark\/24 celsius degrees). The other half of the plants, constituting control plants, remained in the initial growth chamber with control temperature conditions. Flower bud tagging was used to harvest seeds at precise developmental stages: Globular, Transition, Torpedo, Bent cotyledon, Mature green and Dry seed. Furthermore, rosette leaves were also harvested. 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Through the combination of RTsum with diagonal-PASEF, we demonstrate that this strategy yields higher signal-to-noise ratios while retaining the peak shape for analytes of interest ultimately improving overall number of peptide and protein identifications of diagonal-PASEF. Importantly, combining RTsum with diagonal-PASEF improved overall identifications and quantitative precision when compared to dia-PASEF with variable quadrupole isolation widths and across different input amounts for cell line injections. We also tested the performance of diagonal-PASEF in controlled quantitative experiments where diagonal-PASEF outperformed dia-PASEF in the overall number of retained candidates below 1% or 5% error-rate, quantitative precision and identifications on peptide level and protein level. These data indicate that RTsum demonstrates a positive use case of the high sampling rate of diagonal-PASEF and might therefore be a valuable addition to existing analysis pipelines. 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This study presents a high-resolution proteotyping workflow integrating whole-cell MALDI-TOF MS, nanoLC-MS\/MS, and comparative genomics to distinguish H. influenzae and H. aegyptius. We identified 31 robust protein biomarkers validated by LC-MS\/MS peptide mapping and comparative genomics, providing enhanced diagnostic resolution for closely related pathogens.\n","fileCount":"2933","fileSizeKB":"75307","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Haemophilus influenzae (NCBITaxon:727);Haemophilus aegyptius (NCBITaxon:197575)","instrument":"MALDI Biotyper","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"proteotyping;MALDI-TOF MS;LC-MS\/MS;Haemophilus influenzae;Haemophilus aegyptius;biomarker discovery;clinical microbiology;DatasetType:Proteomics","pi":[{"name":"Roger Karlsson","email":"roger.karlsson@gu.se","institution":"Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg; 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Nasopharyngeal (NP) swabs are widely used for diagnostic and research applications, but their collection can be uncomfortable, particularly in children, and their suitability for close-interval sequential sampling is limited. Synthetic absorptive matrices (SAMs) represent a minimally invasive alternative, but their performance in untargeted, deep proteomic applications has not been systematically evaluated.\n\nHere, we directly compared proteomes obtained from paired NP and SAM samples collected from healthy adults, each separately eluted in different buffer chemistries: Qiagen RLT and urea-triethylammonium bicarbonate. High-performance liquid chromatography tandem mass spectrometry identified thousands of proteins in each sampling condition, spanning a dynamic range of more than five orders of magnitude. SAM and NP yielded broadly comparable proteome depth, with similar distributions of high-, intermediate-, and low-abundance proteins. Immune-relevant proteins, including soluble mediators, complement components, antimicrobial peptides, immunoglobulin transporters, oxidative stress proteins, markers of epithelial integrity, and interferon-stimulated gene products, were consistently recovered by both methods. Buffer chemistry introduced modest shifts in overall abundance distributions but generally preserved the relative differences between donors.\n\nThese results establish that SAM sampling, in combination with either RLT or urea extraction, provides an acceptable and well-tolerated alternative to NP swabs for airway proteomics. This approach enables minimally invasive profiling of the human nasopharyngeal proteome and supports its application in studies of airway immunity and infection.","fileCount":"25","fileSizeKB":"25022855","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Nasopharynx, airway proteomics, synthetic absorptive matrix, nasopharyngeal swab, label-free quantification, mucosal immunity, mass spectrometry, sampling methods;DatasetType:Proteomics","pi":[{"name":"Prof. Charles J. 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Data were acquired in negative ion mode and processed using MS-DIAL software. Feature detection, deconvolution, and alignment were performed, and metabolites were annotated using public MSP spectral libraries. Quality control included pooled QC samples, solvent blanks, and mock-treated controls. 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While native ion-exchange chromatography (IEC) hyphenated with native mass spectrometry (nMS) is a powerful method for resolving protein charge variants under non-denaturing conditions, its application to complex proteome samples is still limited. Two key limitations constrain the analysis: (i) the restricted availability of volatile buffer systems, which frequently leads to non-linear pH gradients and subsequent co-elution of proteoforms; and ii) reliance on a single ion-exchange mode (either anion or cation exchange), which provides insufficient resolving power for complex protein mixtures spanning a broad range of isoelectric points. To address these challenges, we developed a novel online nanoflow dual IEC-nMS platform. Mobile phases for strong anion-exchange (SAX) and strong cation-exchange (SCX) were first optimized with various volatile salts through analytical-scale chromatographic separations. This enabled methods with wide linear pH ranges spanning from 2.6 to 5.0 for SAX and 5.0 to 8.5 for SCX. Subsequently, nanoflow SAX- and SCX-nMS were developed using self-packed capillary columns operated at a flow rate of 500 nL\/min. To facilitate the highly efficient and simultaneous analysis of both acidic and basic proteoforms, we created a double-barrel setup that integrates the nanoSAX and nanoSCX in a non-interfering manner. The enhanced sensitivity and selectivity of the developed methods allowed for the detection of more than 1,000 proteoforms in a complex E. coli cell lysate, with molecular weights ranging from 10 to 150 kDa.","fileCount":"20","fileSizeKB":"1655398","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteins","instrument":"Q Exactive Plus","modification":"No","keywords":"cation exchange chromatography;anion exchange chromatography;nanoflow rate;native mass spectrometry;intact proteins;proteoform separation;DatasetType:Other (Intact proteins)","pi":[{"name":"Ziran Zhai","email":"z.zhai@uva.nl","institution":"University of Amsterdam","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a884157cd01f407ba6323eec397622d7","id":"242"}, {"dataset":"MSV000099510","datasetNum":"99510","title":"GNPS - Dataset Created via Quickstart","user":"gordana1988","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760600755000","created":"Oct. 16, 2025, 12:45 AM","description":"Metabolomics dataset of DD27 extract analyzed by LC-MS\/MS (positive mode).","fileCount":"4","fileSizeKB":"286036","spectra":"2370","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Euphorbia lucida (NCBITaxon:756625)","instrument":"6510 Quadrupole Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"diterpenoides;DatasetType:Metabolomics","pi":[{"name":"Gordana Krstic","email":"gkrstic@chem.bg.ac.rs","institution":"University Of Belgrade - Faculty Of Chemistry","country":"Serbia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3f3848c3bd114846a5f456c1bfafb455","id":"243"}, {"dataset":"MSV000099509","datasetNum":"99509","title":"GNPS-Reductive_amination_synthesis_5-ASA_conjugates","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760596391000","created":"Oct. 15, 2025, 11:33 PM","description":"MS\/MS fragmentation data of synthetic standards acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"76","fileSizeKB":"7833358","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Custom Species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;synthesis;standards;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@health.ucsd.edu","institution":"Univer of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"964cc1bba620486dbe1326fcfc6b9a8e","id":"244"}, {"dataset":"MSV000099506","datasetNum":"99506","title":"4EHP and NELF-E regulate physiological ATF4 induction and proteostasis in disease models of Drosophila","user":"KanshinED1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760570967000","created":"Oct. 15, 2025, 4:29 PM","description":"Cells adapt to proteostatic and metabolic stresses, in part, by triggering the phosphorylation of eIF2a and the synthesis of ATF4. eIF2a phosphorylation facilitates ATF4 translation through regulatory elements at ATF4 mRNAs 5 leader. In addition to eIF2a, ATF4 induction requires other regulators that remain poorly understood. Here, we report an ATF4 regulatory network consisting of eIF4E-Homologous Protein (4EHP), NELF-E, the 40S ribosome, and eIF3 subunits. Specifically, we found that the mRNA cap-binding protein, 4EHP, was required for ATF4 signaling in the Drosophila larval fat body and in disease models associated with abnormal ATF4 signaling. NELF-E mRNA, encoding a regulator of pol II-mediated transcription, was identified as a top interactor of 4EHP in a TRIBE (Targets of RNA Binding through Editing) screen. Quantitative proteomics analysis revealed that the knockdown of NELF-E or 4EHP commonly reduced several subunits of the 40S ribosome (RpS) and the eIF3 translation initiation factor. Moreover, reduction of NELF-E, 4EHP, RpS12, eIF3l, or eIF3h suppressed the expression of ATF4 and its target genes. These results uncover a previously unrecognized ATF4 regulatory network consisting of 4EHP and NELF-E that impacts proteostasis during normal development and in disease models.","fileCount":"7","fileSizeKB":"17896963","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"Q Exactive HF-X","modification":"UNIMOD:736 - \\\"Dithiothreitol (DTT) on Cys.\\\";UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\"","keywords":"eIF2a;NELF-E;ATF4;Drosophila;DatasetType:Proteomics","pi":[{"name":"Beatrix M Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"NYU Langone Grossman School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"61d55c8e4a5c45f2ae769316a4ab0ece","id":"245"}, {"dataset":"MSV000099504","datasetNum":"99504","title":"syntheis_prm_data_confirmation_test_10152025","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760565810000","created":"Oct. 15, 2025, 3:03 PM","description":"MS\/MS fragmentation data of reaction acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"4","fileSizeKB":"209317","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CMMC;bile acid;modifications;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"591400a05857429088b3dede6e981a61","id":"246"}, {"dataset":"MSV000099501","datasetNum":"99501","title":"YSB-phosphoproteomics cryptococcus using high resolution mass spectrometry, Yadav and Heitman","user":"es3064","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760549943000","created":"Oct. 15, 2025, 10:39 AM","description":"Quantitative LC\/MS\/MS was performed using an EvoSep One UPLC coupled to a Thermo Orbitrap Astral high resolution accurate mass tandem mass spectrometer (Thermo). 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Taken together, these findings highlight the novelty and efficacy of asymmetric biphasic stimulation in generating more physiologically relevant in vitro cardiac models, providing a promising alternative to standard ES protocols.","fileCount":"19","fileSizeKB":"38834518","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"electrical stimulation, monophasic waveform, biphasic waveform, asymmetric biphasic waveform, cardiac tissue engineering;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069476","task":"b1dec51ab538444fac4213d62127424d","id":"248"}, {"dataset":"MSV000099488","datasetNum":"99488","title":"Jagged1 proximity labeling with APEX2 under shear stress in endothelial cells","user":"ostassen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760480823000","created":"Oct. 14, 2025, 3:27 PM","description":"Morphogenesis of the cardiovascular system is responsive to hemodynamic cues sensed by endothelial cells. 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Current diagnosis often involves Congo red staining, but it has limitations in quantification and specificity. A novel method called iprm-PASEF exploits MALDI imaging and offers a faster, spatially resolved, antibody-independent technique for identifying peptides while preserving tissue structure. In this study, iprm-PASEF was used to further evaluate its applicability on amyloidosis. FFPE slides of an amyloidosis TMA including biopsies of 18 amyloidosis positive tissues were prepared for tryptic peptide MALDI imaging. An initial MALDI TIMS MS1 measurement was performed, followed by the manual generation of a precursor list containing mass-to-charge ratios and ion mobility windows. In a second iprm-PASEF measurement, the selected precursors are analyzed in a multiplexed MALDI MS\/MS mode. Peptide identification was achieved through peptide-to-spectrum matching using MASCOT. Within the course of this study, we characterized an amyloidosis TMA consisting of AA, AL and ATTR amyloidosis diseased tissue with MALDI imaging of tryptic peptides. We successfully identified eight amyloidosis related peptides derived from serum amyloid A, vitronectin, apolipoprotein E, serum amyloid P component and transthyretin receptor in one single iprm-PASEF measurement. Peptide signals mapped to amyloidogenic plaques determined in a Congo red staining. Some of these peptides were specifically found in ATTR and AA amyloidosis. This represents a significant step towards integrating MALDI imaging into the diagnostic process for amyloidosis. All Datasets are uploaded separateley. 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Diagnosing amyloidosis is difficult due to its many subtypes (e.g. AA, AL, ATTR), with varying symptoms. Current diagnosis often involves Congo red staining, but it has limitations in quantification and specificity. A novel method called iprm-PASEF exploits MALDI imaging and offers a faster, spatially resolved, antibody-independent technique for identifying peptides while preserving tissue structure. In this study, iprm-PASEF was used to further evaluate its applicability on amyloidosis. FFPE slides of an amyloidosis TMA including biopsies of 18 amyloidosis positive tissues were prepared for tryptic peptide MALDI imaging. An initial MALDI TIMS MS1 measurement was performed, followed by the manual generation of a precursor list containing mass-to-charge ratios and ion mobility windows. In a second iprm-PASEF measurement, the selected precursors are analyzed in a multiplexed MALDI MS\/MS mode. Peptide identification was achieved through peptide-to-spectrum matching using MASCOT. Within the course of this study, we characterized an amyloidosis TMA consisting of AA, AL and ATTR amyloidosis diseased tissue with MALDI imaging of tryptic peptides. We successfully identified eight amyloidosis related peptides derived from serum amyloid A, vitronectin, apolipoprotein E, serum amyloid P component and transthyretin receptor in one single iprm-PASEF measurement. Peptide signals mapped to amyloidogenic plaques determined in a Congo red staining. Some of these peptides were specifically found in ATTR and AA amyloidosis. This represents a significant step towards integrating MALDI imaging into the diagnostic process for amyloidosis. All Datasets are uploaded separateley. This file contains the dataset for amyloidosis MS1 data.\n","fileCount":"124","fileSizeKB":"17067919","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"MALDI imaging;TIMS;peptides;iprm-PASEF;MALDI TIMS MS\/MS Imaging;spatial Proteomics;Amyloidosis;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Oliver Schilling","email":"oliver.schilling@uniklinik-freiburg.de","institution":"Medical Center - University of Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"42744a219dff4f9d909277c19ecb879e","id":"252"}, {"dataset":"MSV000099478","datasetNum":"99478","title":"Proteomics analysis of mouse aorta samples","user":"kallogergo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760426998000","created":"Oct. 14, 2025, 12:29 AM","description":"Proteomics analysis of mouse abdominal aorta were performed. The oxidation of hemoglobin was investigated.","fileCount":"592","fileSizeKB":"23112754","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:345 - \\\"Cysteine oxidation to cysteic acid.\\\"","keywords":"mouse;aorta;oxidation;DatasetType:Proteomics","pi":[{"name":"Gergo Kallo","email":"kallo.gergo@med.unideb.hu","institution":"University of Debrecen","country":"Hungary"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069426","task":"84bdc72841d047438d18b43a9d813284","id":"253"}, {"dataset":"MSV000099477","datasetNum":"99477","title":"Proteomics analysis of human aorta samples","user":"kallogergo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760426641000","created":"Oct. 14, 2025, 12:24 AM","description":"Proteomics analysis of healthy human aourta and ruptured lesions were performed. The oxidation of hemoglobin was investigated.","fileCount":"978","fileSizeKB":"56490950","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:345 - \\\"Cysteine oxidation to cysteic acid.\\\"","keywords":"aorta;aneurism;oxidation;DatasetType:Proteomics","pi":[{"name":"Gergo Kallo","email":"kallo.gergo@med.unideb.hu","institution":"University of Debrecen","country":"Hungary"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069425","task":"bdf64a140fbe4dddb1cfb41265cc6b05","id":"254"}, {"dataset":"MSV000099474","datasetNum":"99474","title":"caroline_proteomics_data_syntheis_library","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760399765000","created":"Oct. 13, 2025, 4:56 PM","description":"MS\/MS fragmentation data of Reaction was acquired on Q Exactive - with\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"37","fileSizeKB":"4201682","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no specie","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"syntheis;CMMC;small molecules;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3cbf0d0901364decad400b659bdc26d6","id":"255"}, {"dataset":"MSV000099464","datasetNum":"99464","title":"Cneo-CN-phospho cryptococcus using high resolution mass spectrometry, Yadav and Heitman","user":"es3064","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760362495000","created":"Oct. 13, 2025, 6:34 AM","description":"Quantitative LC\/MS\/MS was performed using an EvoSep One UPLC coupled to a Thermo Orbitrap Astral high resolution accurate mass tandem mass spectrometer (Thermo). Briefly, each sample loaded EvoTip was eluted onto a 1.5 um EvoSep 150um ID x 15cm performance (EvoSep) column using the SPD30 gradient at 55C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (m\/z 200) full MS scan from m\/z 380-1080 in the OT with a target AGC value of 4e5 ions. Fixed DIA windows of 5 m\/z from m\/z 380 to 1080 DIA MS\/MS scans were acquired in the Astral with a target AGC value of 5e4 and max fill time of 8 ms. HCD collision energy setting of 27% was used for all MS2 scans. The total analysis cycle time for each sample injection was approximately 40 min.","fileCount":"74","fileSizeKB":"849256915","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cryptococcus (NCBITaxon:5415)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"label free, turbo id, astral;DatasetType:Proteomics","pi":[{"name":"Joseph Heitman, MD PhD","email":"heitm001@duke.edu","institution":"Duke University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069393","task":"f2b47f40b3024515b72b3ca56310e8e0","id":"256"}, {"dataset":"MSV000099462","datasetNum":"99462","title":"LC-MS data of dithiocladospolide derived from a fungal PKS and a bacterial NRPS by cocultivation","user":"lishasha","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760355096000","created":"Oct. 13, 2025, 4:31 AM","description":"A new macrolide dimer, dithiocladospolide was identified from the co-cultures of the marine-derived Cladosporium sp. with Escherichia coli. 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The T-DNA insertion mutants of AOP3 (SALK_022752C), the WT were sowed directly in fertilized soil. Plants were grown in optimal conditions (control) in a growth chamber with long day photoperiod (16h light\/21 celsius degrees - 8h dark\/19 celsius degrees). Watering was made with water. At the onset of flowering (occurring between 5 and 6 weeks after seed sowing), high temperature (HT) was applied to half of the plants of the corresponding experiment by transferring them to another growth chamber (SANYO, Thermo Fisher Scientific) displaying high temperature conditions (16h of light\/27 celsius degrees - 8h of dark\/24 celsius degrees). The other half of the plants, constituting control plants, remained in the initial growth chamber with control temperature conditions. Dry seeds were harvested. Untargeted metabolomics (LC-MS\/MS) were performed with those samples","fileCount":"89","fileSizeKB":"20350112","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II;Ultimate 3000 (Thermo Fischer Scientific - HPLC)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis thaliana;Seed coat & endosperm;Seed embryo;High temperature;DatasetType:Metabolomics","pi":[{"name":"Massimiliano CORSO","email":"massimiliano.corso@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"309dca87567a4eaa9526fa9330b0081b","id":"260"}, {"dataset":"MSV000099457","datasetNum":"99457","title":"Proteomic analysis of secretomes from WM9\/Hs294T melanoma cells resistant and non-resistant to BRAF\/MEK and from their co-cultures with adipocytes","user":"msurman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760345628000","created":"Oct. 13, 2025, 1:53 AM","description":"Treatment based on BRAF\/MEK kinase inhibitors is currently one of the most commonly used methods in melanoma therapy. Unfortunately, in the case of advanced melanoma, patients often develop resistance to treatment at an early stage of the treatment. A thorough understanding of the causes and mechanisms may contribute to the development of new, more effective treatments. One of the ways in which treatment-resistant cells can affect other cancer cells and the tumor microenvironment is through the factors they secrete. Therefore, this study aimed to examine the protein composition of the secretome of cells resistant to vemurafenib (BRAF inhibitor) and cobimetinib (MEK inhibitor) and compare it with the secretome of non-resistant cells. Proteomic analysis, followed by gene ontology (GO) analysis, identified many differences in resistant melanoma cells' secretomes compared to controls (non-resistant) in terms of cellular compartment, molecular function, biological processes, and reactome pathways. Proteins unique to the secretomes of resistant cells were associated with, among others, integrin binding and interactions, and the extracellular matrix organization. Other interesting groups of proteins, i.e., up- or downregulated in secretomes of resistant melanoma cells vs their non-resistant variants, were directly related to cancer progression and associated with cell adhesion, actin cytoskeleton organization, matrix proteolysis, and drug resistance. Proteins included in these groups, once secreted by resistant melanoma cells, can undoubtedly influence the surrounding microenvironment in a way that promotes the formation of a pro-tumor niche.","fileCount":"44","fileSizeKB":"154732930","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"melanoma;drug resistance;secretome;BRAF inhibitor;vemurafenib;cobimetinib;MEK inhibitor;DatasetType:Proteomics","pi":[{"name":"Aleksandra Simiczyjew","email":"aleksandra.simiczyjew@uwr.edu.pl","institution":"Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw","country":"Poland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD069384","task":"0d12fe78b4384784ad1f6aab92ea98f4","id":"261"}, {"dataset":"MSV000099454","datasetNum":"99454","title":"Mitochondrial ABHD11 inhibition drives sterol metabolism to modulate T-cell effector function","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760264188000","created":"Oct. 12, 2025, 3:16 AM","description":"ABHD11 is a mitochondrial hydrolase that maintains the catalytic function of alpha-ketoglutarate dehydrogenase, and its expression in CD4+ T-cells has been linked to remission status in rheumatoid arthritis (RA). However, the importance of ABHD11 in regulating T-cell metabolism and function is yet to be explored. Here, we show that pharmacological inhibition of ABHD11 dampens cytokine production by human and mouse T-cells. Mechanistically, the anti-inflammatory effects of ABHD11 inhibition are attributed to increased 24,25-epoxycholesterol (24,25-EC) biosynthesis and subsequent liver X receptor (LXR) activation, which arise from a compromised TCA cycle. The impaired cytokine profile established by ABHD11 inhibition is extended to two patient cohorts of autoimmunity. Importantly, using murine models of accelerated type 1 diabetes (T1D), we show that targeting ABHD11 suppresses cytokine production in antigen-specific T-cells and delays the onset of diabetes in vivo in female mice. Collectively, our work provides pre-clinical evidence that ABHD11 is an encouraging drug target in T-cell-mediated inflammation.","fileCount":"51","fileSizeKB":"4746038","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;QTRAP 6500+;API 5000","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"T-cell;ABHD11;sterol;metabolism;DatasetType:Metabolomics","pi":[{"name":"Nicholas Jones","email":"N.Jones@Swansea.ac.uk","institution":"Institute of Life Science, Swansea University Medical School","country":"UK"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d7d5f93bef9c45c88f5f1263cabbfa42","id":"262"}, {"dataset":"MSV000099453","datasetNum":"99453","title":"Raw LC-MS data for actinobacteria strain Wu 15 for metabolomic profiling","user":"sam_321","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760209557000","created":"Oct. 11, 2025, 12:05 PM","description":"Raw LC-MS data for actinobacteria strain Wu 15 for metabolomic profiling ","fileCount":"12","fileSizeKB":"999351","spectra":"24937","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinobacteria (NCBITaxon:1760)","instrument":"Thermo Scientific Q-Exactive ","modification":"None","keywords":"Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Amit Jaisi","email":"amit.ja@wu.ac.th","institution":"Walailak University","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6aa736492ce54ce093964974edb22bad","id":"263"}, {"dataset":"MSV000099452","datasetNum":"99452","title":"5 actinobacteria strains 11-10-2025","user":"sam_321","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760207923000","created":"Oct. 11, 2025, 11:38 AM","description":"Raw spectratum data from actinobacteria sourced from the magroove environment in Thailand ","fileCount":"71","fileSizeKB":"7210511","spectra":"149178","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinobacteria (NCBITaxon:1760)","instrument":"LTQ Orbitrap","modification":"NONE","keywords":"actinobacteria;DatasetType:Metabolomics","pi":[{"name":"Amit Jaisi","email":"amit.ja@wu.ac.th","institution":"Walailak University","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069358","task":"26aa23f9f9b3456999ffe7d5de154880","id":"264"}, {"dataset":"MSV000099450","datasetNum":"99450","title":"Ruegeria pomeroyi knockout lipid extraction","user":"LuisePal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760147865000","created":"Oct. 10, 2025, 6:57 PM","description":"Lipid extraction of Ruegeria pomeroyi knockout strains SP00981 and SP002795.","fileCount":"9","fileSizeKB":"1864252","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruegeria pomeroyi (NCBITaxon:89184)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cysteinolic acid;Knockouts;DatasetType:Other (Lipidomics)","pi":[{"name":"Professor Spencer J Williams","email":"sjwill@unimelb.edu.au","institution":"Bio21 Institute Parkville, The University of Melbourne","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"40247f28a5684890ba5785096e7c4b68","id":"265"}, {"dataset":"MSV000099447","datasetNum":"99447","title":"Allosteric inhibition of human mitochondrial ClpP by hijacking the Dordaviprone (ONC201) binding site","user":"mgoncalves","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760115347000","created":"Oct. 10, 2025, 9:55 AM","description":"Continuous labelling HDX on WT ClpP, in apo, bortezomib-bound and OICR18704-bound states. 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Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1119","fileSizeKB":"39312772","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;U19;stool;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"32c74edfd97940cba6661cc2cb48c9de","id":"269"}, {"dataset":"MSV000099438","datasetNum":"99438","title":"202501009_Bigelow_Algae_Lib_Round_6_RAW_mzML","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1760036738000","created":"Oct. 9, 2025, 12:05 PM","description":"This dataset contains metabolomics samples (divided in supernatant and pellet) for an Algae Library from the Bigelow Laboratory, Maine. 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For targeted 13C flux analyses, isotopomers from ~140 polar molecules were targeted with a total of 460 SRM transitions. Samples were delivered to the mass spectrometer via hydrophilic interaction chromatography (HILIC). Gradients were run starting from 85% buffer B (HPLC grade acetonitrile) to 42% B from 0-5 minutes; 42% B to 0% B from 5-16minutes; 0% B was held from 16-24 minutes; 0% B to 85% B from 24 minutes; 85% B was held for 7 minutes to reequilibrate the column. Buffer A was comprised of 20 mM ammonium hydroxide\/20 mM ammonium acetate (pH=9.0) in 95:5 water:acetonitrile. Peak areas from the total ion current for each metabolite SRM transition were integrated using MultiQuant v3.2 software (AB\/SCIEX). Metabolites with CV<30% in pooled QC were used for the statistical analysis. The quality of integration for each metabolite peak was reviewed. 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Soluble lysates proceeded to anti-endogenous CRAF IP-MS with anti-CRAF antibody (BD Biosciences 610152; incubated at 4C overnight) and protein A\/G beads (Pierce 88802; incubated at RT for 1 h), and on-bead digestion with PreOmics sample cleanup kit. 200 ng of peptides were quantified and injected onto Orbitrap Eclipse with 60 min gradient using DIA.","fileCount":"11","fileSizeKB":"8611568","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Molecular glue;C-RAF;14-3-3;SFN;DatasetType:Proteomics","pi":[{"name":"Michelle Arkin","email":"Michelle.Arkin@ucsf.edu","institution":"UCSF","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069213","task":"29a090c822d941a589b3d01d4eaab2f7","id":"274"}, {"dataset":"MSV000099415","datasetNum":"99415","title":"MS sequencing of GFAP fragments from TBI patients CSF","user":"IWanner","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759876991000","created":"Oct. 7, 2025, 3:43 PM","description":"Protein Glial fibrillary acidic protein, GFAP fragment identification (breakdown products, BDPs) and their label free peptide\/ion quantification of GFAP immunoprecipitated from TBI patient's cerebrospinal fluid using a polyclonal anti-GFAP antibody. 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The proteome dataset of OSCC and normal tissues consisted of 5,123 protein groups, including 299 proteins with strong differential expression (p-value <0.01, fold change barrier to ?+2 and <-2, 205 upregulated and 94 down regulated) and 134 common proteins were also found out of total dataset of 4473 identified proteins of HNSCC cell line secretomes. Functional data analysis revealed that these differential proteins were significantly associated with multiple biological processes. Myogenesis, Fatty Acid Metabolism and KRAS Signaling DN were associated with the proteins downregulated in cancer tissues, while Protein Secretion, Unfolded Protein Response, Spliceosomal complex assembly, Protein localization to endosome and Interferon Gamma Response were enriched in the set of upregulated proteins and these regulated proteins may be classically or non-classically secreted. Furthermore, we found differential enrichment of Creb3L1, ESRRA, YY, ELF2, STAT1 and XBP transcription factors potentially regulating these major pathways.","fileCount":"219","fileSizeKB":"210502646","spectra":"4007209","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Head and neck carcinoma;Biomarkers.;Label-free;Secretome;Oral squamous cell carcinoma;DatasetType:Proteomics","pi":[{"name":"Connie Jimenez","email":"c.jimenez@amsterdamumc.nl","institution":"Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD025701","task":"1b70603c57464e3a937e5e11a47eb331","id":"276"}, {"dataset":"MSV000099412","datasetNum":"99412","title":"Specialized metabolome data of dry seeds from WT and aop3 genotypes developed under high temperatures","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759859276000","created":"Oct. 7, 2025, 10:47 AM","description":"Arabidopsis thaliana (thale cress) wild-type (WT) and transgenic lines were in the Columbia-0 (Col-0) background. The T-DNA insertion mutants of AOP3 (SALK_022752C), the WT were sowed directly in fertilized soil. Plants were grown in optimal conditions (control) in a growth chamber with long day photoperiod (16h light\/21 celsius degrees - 8h dark\/19 celsius degrees). Watering was made with water. At the onset of flowering (occurring between 5 and 6 weeks after seed sowing), high temperature (HT) was applied to half of the plants of the corresponding experiment by transferring them to another growth chamber (SANYO, Thermo Fisher Scientific) displaying high temperature conditions (16h of light\/27celsius degrees - 8h of dark\/24 celsius degrees). The other half of the plants, constituting control plants, remained in the initial growth chamber with control temperature conditions. Dry seeds were harvested. Untargeted metabolomics (LC-MS\/MS) were performed with those samples.","fileCount":"65","fileSizeKB":"16597062","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II;Ultimate 3000 (Thermo Fischer Scientific - HPLC)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis thaliana;seed development;High temperature;DatasetType:Metabolomics","pi":[{"name":"Massimiliano CORSO","email":"massimiliano.corso@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4269840835624081ad0918bdc5e6da14","id":"277"}, {"dataset":"MSV000099410","datasetNum":"99410","title":"Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759856813000","created":"Oct. 7, 2025, 10:06 AM","description":"The poor prognosis of head and neck cancer (HNC) is associated with metastasis within the lymph nodes (LNs). Herein, the proteome of 140 multisite samples from a 59-HNC patient cohort, including primary and matched LN-negative or -positive tissues, saliva, and blood cells, reveals insights into the biology and potential metastasis biomarkers that may assist in clinical decision-making. Protein profiles are strictly associated with immune modulation across datasets, and this provides the basis for investigating immune markers associated with metastasis. The proteome of LN metastatic cells recapitulates the proteome of the primary tumor sites. Conversely, the LN microenvironment proteome highlights the candidate prognostic markers. By integrating prioritized peptide, protein, and transcript levels with machine learning models, we identified nodal metastasis signatures in blood and saliva. We present a proteomic characterization wiring multiple sites in HNC, thus providing a promising basis for understanding tumoral biology and identifying metastasis-associated signatures. ","fileCount":"284","fileSizeKB":"209565806","spectra":"7244001","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Machine learning;Head and neck squamous cell carcinoma;Buffy coat;Saliva;Mouth neoplasms;Proteomics;Lymph node metastasis;Prognosis;Immune system;Biomarkers;DatasetType:Proteomics","pi":[{"name":"Adriana Franco Paes Leme","email":"adriana.paesleme@lnbio.cnpem.br","institution":"Laborat\uFFFDrio Nacional de Bioci\uFFFDncias - LNBio; Centro Nacional de Pesquisa em Energia e Materiais - CNPEM; Campinas; SP; 13083-100; Brazil","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD027780","task":"446720853e8b480880331cb4dc4d22e6","id":"278"}, {"dataset":"MSV000099408","datasetNum":"99408","title":"Specialized metabolome data of dry seeds from WT, aop3, scpl17 and bzo1 genotypes developed under high temperatures","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759851762000","created":"Oct. 7, 2025, 8:42 AM","description":"Arabidopsis thaliana (thale cress) wild-type (WT) and transgenic lines were in the Columbia-0 (Col-0) background. The T-DNA insertion mutants of AOP3 (SALK_001655C), BZO1 (two independent lines, SALK_094196 and GABI_565B09) and SCPL17 (two lines independent, SALK_075481 and SALK_126264) and the WT were sowed directly in fertilized soil. Plants were grown in optimal conditions (control) in a growth chamber with long day photoperiod (16h light\/21 celsius degrees - 8h dark\/19 celsius degrees). Watering was made with water. At the onset of flowering (occurring between 5 and 6 weeks after seed sowing), high temperature (HT) was applied to half of the plants of the corresponding experiment by transferring them to another growth chamber (SANYO, Thermo Fisher Scientific) displaying high temperature conditions (16h of light\/27 celsius degrees - 8h of dark\/24 celsius degrees). The other half of the plants, constituting control plants, remained in the initial growth chamber with control temperature conditions. Dry seeds were harvested. Untargeted metabolomics (LC-MS\/MS) were performed with those samples of dry seeds.","fileCount":"309","fileSizeKB":"74747593","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II;Ultimate 3000 (Thermo Fischer Scientific - HPLC)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"High temperature;Seeds;Glucosinolates;Arabidopsis thaliana;Seed development;DatasetType:Metabolomics","pi":[{"name":"Massimiliano CORSO","email":"massimiliano.corso@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"cd34f90c8ed7461e90027b084815b3e3","id":"279"}, {"dataset":"MSV000099405","datasetNum":"99405","title":"New Insights into the impact of Human Papillomavirus on Oral Cancer in Young Patients: Proteomic Approach Reveals a Novel Role for S100A8","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759790648000","created":"Oct. 6, 2025, 3:44 PM","description":"Human Papillomavirus (HPV) infection has been recently linked to a subset of cancers affecting the oral cavity. However, the molecular mechanisms underlying HPV-driven oral squamous cell carcinoma (OSCC) onset and\/ progression are poorly understood. Methods: We perform a MS-based proteomic profiling based on HPV status on OSCC in young patients, following biological characterization and cell assays to explore the proteome functional landscape. Results: Thirty-nine proteins are differentially abundant between HPV (+) and HPV (-) OSCC. Among them, COPS3, DYHC1, and S100A8 are unfavorable for tumor recurrence and survival in contrast to A2M and Serpine1, which low levels show association with better DFS. Remarkably, S100A8 is considered an independent prognostic factor for lower survival rate, and at high levels, it alters tumor-associated immune profiling, showing a lower proportion of M1 macrophages and dendritic cells. HPV (+) OSCC also displayed the pathogen-associated patterns receptor which, when activated, triggered S100A8 and NF?B inflammatory responses. Conclusion: HPV (+) OSCC has a peculiar microenvironment pattern, distinctively of HPV (-), involving expression of pathogen-associated pattern receptors, S100A8 overexpression, and NF?B activation and responses that had important consequences in prognosis and may guide therapeutic decisions.","fileCount":"51","fileSizeKB":"29747864","spectra":"1176237","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"New insights into the impact of human papillomavirus on oral cancer in young patients: proteomic approach reveals a novel role for s100a8;DatasetType:Proteomics","pi":[{"name":"Adriana Franco Paes Leme","email":"adriana.paesleme@lnbio.cnpem.br","institution":"Head of Mass Spectrometry Laboratory, Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD041856","task":"ea1b3646893042a388a322bfa6b69ed1","id":"280"}, {"dataset":"MSV000099404","datasetNum":"99404","title":"Label-based comparative proteomics to understand progression of precancerous lesions to oral squamous cell carcinoma","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759788548000","created":"Oct. 6, 2025, 3:09 PM","description":"Oral squamous cell carcinomas typically arise from precancerous lesions such as leukoplakia and erythroplakia. These lesions exhibit a range of histological changes from hyperplasia to dysplasia and carcinoma in situ, during their transformation to malignancy. The molecular mechanisms driving this multistage transition remain incompletely understood. To bridge this knowledge gap, our current study utilizes label based comparative proteomics to compare protein expression profiles across different histopathological grades of leukoplakia, erythroplakia, and OSCC samples, aiming to elucidate the molecular changes underlying lesion evolution.","fileCount":"68","fileSizeKB":"67443802","spectra":"1144739","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Erythroplakia;Oral squamous cell carcinoma;Label-based proteomics;Leukoplakia;DatasetType:Proteomics","pi":[{"name":"Hariprasad Gururao","email":"dr.hariprasadg@gmail.com","institution":"Professor, Deptt of Biophysics, All India Institute of Medical Sciences, New Delhi, India","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054190","task":"166940966c3a4b6d9f42cea7533a0336","id":"281"}, {"dataset":"MSV000099403","datasetNum":"99403","title":"GC-MS metabolomics of Brunfelsia grandiflora","user":"LPN_IKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759779654000","created":"Oct. 6, 2025, 12:40 PM","description":"Metabolomic study about differents morphological structures (leaves, roots and stem bark) of Brunfelsia grandiflora","fileCount":"247","fileSizeKB":"8693165","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brunfelsia grandiflora (NCBITaxon:1035550)","instrument":"GCMS-QP2020NX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Leaves;roots;stem bark;Mass spectrometry;gas chromatography;DatasetType:Metabolomics","pi":[{"name":"Leysmar Abigail Parra Guzman","email":"leysmar.parra@est.ikiam.edu.ec","institution":"Universidad Regional Amazonica IKIAM","country":"Ecuador"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0d08c3b1c9b94c10ab70412385943c97","id":"282"}, {"dataset":"MSV000099402","datasetNum":"99402","title":"The CTLH Ubiquitin Ligase Substrates ZMYND19 and MKLN1 Negatively Regulate mTORC1 at the Lysosomal Membrane","user":"tangh","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759772339000","created":"Oct. 6, 2025, 10:38 AM","description":"TMTpro 12plex of 4 groups (sgCtrl ALP, sgCtrl DMSO, sgMAEA ALP, and sgMAEA DMSO) in triplicate","fileCount":"29","fileSizeKB":"45177780","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"TMTpro;EBVaGC;MAEA;DatasetType:Proteomics","pi":[{"name":"Benjamin E. Gewurz","email":"bgewurz@bwh.harvard.edu","institution":"Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD069168","task":"457dd2d0547d44b5bcea09c51d1d7537","id":"283"}, {"dataset":"MSV000099401","datasetNum":"99401","title":"Early-stage gradient optimization for large-scale culture extract purification","user":"redghoti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759772000000","created":"Oct. 6, 2025, 10:33 AM","description":"This experiment simply includes a sample run on a few new gradients to assess best approaches for purification of extract from a large-scale culture.","fileCount":"11","fileSizeKB":"1184572","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Methylobacterium aquaticum (NCBITaxon:270351)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metallophore;lanthanophore;gram-negative;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2f680276cd42461bbffe18f8ead79041","id":"284"}, {"dataset":"MSV000099400","datasetNum":"99400","title":"Amyloid beta induced upregulation of BAG3 modulates neuronal proteostasis","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759765858000","created":"Oct. 6, 2025, 8:50 AM","description":"Our findings identify BAG3 as a potential key modulator of proteostasis in human neurons. Its regulation across genetic backgrounds and pathological stimuli suggests a central role in\nmaintaining degradation capacity in a disease setting like Alzheimers disease.","fileCount":"711","fileSizeKB":"416241312","spectra":"0","psms":"1696522","peptides":"70514","variants":"150579","proteins":"25105","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"NA","keywords":"BAG3, autophagy, ubiquitin proteasome system, neurons,;DatasetType:Proteomics","pi":[{"name":"Tracy Young Pearse","email":"tpearse@bwh.harvard.edu","institution":"Brigham and Womens Hospital and Harvard Medical School","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD069166","task":"bbf8f582a0374b7cb8e40545bae11553","id":"285"}, {"dataset":"MSV000099399","datasetNum":"99399","title":"Analysis data of 13CGly3P in liver and plasma in ALMS1 WT and ALMS1 KO mice treated or not with a preventive approach of anti-ACBP antibodies","user":"chemabsp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759763662000","created":"Oct. 6, 2025, 8:14 AM","description":"Raw metabolomic data from Mus musculus liver and plasma used in the article - Identification of ACBP as a potential target in ciliopathic obesity using multi-omic network analysis. It includes ALMS1 WT and ALMS1 KO groups, with and without preventive anti-ACBP antibodies. Samples were collected 2 hours after 13C-glucose administration. These data support the analyses reported in the cited manuscript.","fileCount":"189","fileSizeKB":"305370","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (house mouse)","instrument":"Agilent 1290 UHPLC + QQQ 6470;Agilent 7890A GC + QQQ 7000C;Dionex U3000 + Orbitrap Q-Exactive","modification":"Not applicable","keywords":"ACBP;ALMS1;METABOLOME;CILIA;OBESITY;DatasetType:Metabolomics","pi":[{"name":"Jose Manuel Bravo San Pedro","email":"josemabr@ucm.es","institution":"University Complutense of Madrid","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f2d09d8055674509b0540fcbe49fb4a9","id":"286"}, {"dataset":"MSV000099398","datasetNum":"99398","title":"Analysis data of 13Cpalmitate in ALMS1 WT and ALMS1 KO mice treated or not with a preventive approach of anti-ACBP antibodies","user":"chemabsp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759761932000","created":"Oct. 6, 2025, 7:45 AM","description":"Raw metabolomic data from Mus musculus liver used in the article - Identification of ACBP as a potential target in ciliopathic obesity using multi-omic network analysis. 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These data support the analyses reported in the cited manuscript.","fileCount":"110","fileSizeKB":"871","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (house mouse)","instrument":"Acquity I-Class UPLC (Waters) + Xevo TQ-S micro (triple cuadrupolo, Waters)","modification":"not applicable","keywords":"ACBP;ALMS1;METABOLOME;CILIA;OBESITY;DatasetType:Metabolomics","pi":[{"name":"Jose Manuel Bravo San Pedro","email":"josemabr@ucm.es","institution":"University Complutense of Madrid","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9774571888aa476ca551ee9162eac328","id":"287"}, {"dataset":"MSV000099396","datasetNum":"99396","title":"Metabolomic data of ALMS1 WT and ALMS1 KO mice before and after symptoms of Alstrom syndrome","user":"chemabsp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759759919000","created":"Oct. 6, 2025, 7:11 AM","description":"RAW metabolomics data from Mus musculus liver, plasma and WAT used in - Identification of ACBP as a potential target in ciliopathic obesity through multi-omics network analysis. 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Samples spanned the nervous (hippocampus, cerebrospinal fluid), connective (brown, subcutaneous, and visceral\/abdominal fat), digestive (stomach, duodenum, jejunum, ileum, cecum, colon, liver, gallbladder), immune (spleen, thymus), reproductive (testes, uterus), excretory (kidney, bladder), endocrine (pancreas), cardiovascular (heart), muscular (quadriceps), and respiratory (lung) systems, plus biofluids (plasma, urine) and digestive products (feces). Lipidomics was performed by LC-MS\/MS on a Thermo Scientific Orbitrap Exploris 240 coupled to a Vanquish UHPLC in both positive and negative ion modes. Analytes were separated on a Waters ACQUITY Premier BEH C18 column (50 x 2.1 mm, 1.7 um) prior to high-resolution MS acquisition.","fileCount":"1887","fileSizeKB":"62323936","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolome Atlas;Aging Mice;Lipidomics;DatasetType:Metabolomics","pi":[{"name":"Oliver Fiehn","email":"ofiehn@ucdavis.edu","institution":"University of California, Davis","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5ddc4bdaeec44e09acd806b2b6731d48","id":"290"}, {"dataset":"MSV000099387","datasetNum":"99387","title":"The Organ_resolved Metabolome Atlas of the Aging Mice_HILIC_POS and NEG","user":"milliu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759690298000","created":"Oct. 5, 2025, 11:51 AM","description":"We profiled polar metabolites across multiple organs and fluids from C57BL\/6NCrl (B6NCrl-MVP) wild-type mice at two ages (16 and 92 weeks), including both sexes. Samples spanned the nervous (hippocampus, cerebrospinal fluid), connective (brown, subcutaneous, and visceral\/abdominal fat), digestive (stomach, duodenum, jejunum, ileum, cecum, colon, liver, gallbladder), immune (spleen, thymus), reproductive (testes, uterus), excretory (kidney, bladder), endocrine (pancreas), cardiovascular (heart), muscular (quadriceps), and respiratory (lung) systems, plus biofluids (plasma, urine) and digestive products (feces). Polar metabolomics was performed by LC-MS\/MS on a Thermo Scientific Q Exactive HF-X Quadrupole-Orbitrap coupled to a Vanquish UHPLC in positive mode. Metabolites were separated on a Waters ACQUITY Premier BEH Amide column (50 x 2.1 mm, 1.7 um) prior to high-resolution MS acquisition.","fileCount":"1887","fileSizeKB":"32510853","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolome Atlas;Aging Mice;DatasetType:Metabolomics","pi":[{"name":"Oliver Fiehn","email":"ofiehn@ucdavis.edu","institution":"University of California, Davis","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d88064578c8949099b212cc026187d78","id":"291"}, {"dataset":"MSV000099384","datasetNum":"99384","title":"Reconnecting Vagus Nerve to the Heart through Nerve Conduit Preserves Cardiac Function in a Minipig Model of Right Cardiac Vagotomy","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759671330000","created":"Oct. 5, 2025, 6:35 AM","description":"The right vagus nerve (RVN) plays a crucial role in maintaining cardiac homeostasis, and its intrathoracic resection leads to postoperative cardiac complications. Developing effective method to repair the RVN after surgical transection at the heart level is a critical unmet clinical need. Here we show that early reconnection of the RVN to the heart promoted by implantable Chitosan\/Poly-e-caprolactone cuff-like nerve guidance conduit (ChiPCL. C-NGC) significantly preserves cardiac mechanical function in minipigs subjected to right cardiac vagotomy (RVT). Animals that were randomly treated with ChiPCL. C-NGC showed improved global circumferential, longitudinal, and radial strain, along with reduced diastolic dyssynchrony. Histopathology revealed 20% viable vagal fascicles, normalized levels of myocardial parasympathetic fibers, oxidative stress- and aging-related markers, and prevented interstitial myocardial fibrosis in treated group. Our findings suggest that preserving a limited number of RVN fascicles and their neurofilaments prevents early cardiac remodeling by lowering oxidative stress-mediated premature senescence of cardiac cells. Reconnecting the RVN to the heart via ChiPCL C-NGC presents a potential therapeutic strategy to prevent RVT-induced heart failure following thoracic surgery or heart and lung transplantation","fileCount":"33","fileSizeKB":"50834703","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sus scrofa (NCBITaxon:9823)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Vagus Nerve, Vagotomy, Implatation, Aging markers, Minipigs;DatasetType:Proteomics","pi":[{"name":"Alessandro Cellerino","email":"Alessandro.Cellerino@leibniz-fli.de","institution":"Leibniz Institute on Aging, Beutenbergstr. 11, 07745 Jena","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD069137","task":"e53390eebaa4477da18a270cdaa0b593","id":"292"}, {"dataset":"MSV000099383","datasetNum":"99383","title":"RNase L regulates the antiviral proteome by accelerating mRNA decay, inhibiting nuclear mRNA export, and repressing RNAPII-mediated transcription ","user":"camerondouglas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759613040000","created":"Oct. 4, 2025, 2:24 PM","description":"Ribonuclease L (RNase L) is an antiviral endoribonuclease that triggers widespread degradation of cellular mRNAs. Here, we show that the degradation of cellular mRNA by RNase L is a conserved response to flaviviruses, including Zika virus (ZIKV), dengue virus serotype 2 (DENV-2), and West Nile virus (WNV). Quantitative mass spectrometry in response to dsRNA or ZIKV infection shows that RNase L broadly downregulates the cellular proteome, reducing proteins with short half-lives involved in cell cycle progression, cellular metabolism, and protein synthesis. The mRNAs encoded by interferon-stimulated genes (ISGs) evade mRNA decay by RNase L, allowing for protein synthesis of ISG-encoding mRNAs. However, RNase L dampens ISG protein synthesis by triggering a block in nuclear mRNA export and repressing RNAPII-mediated transcription at later times during the antiviral response. These findings implicate reprograming of the cellular proteome as primary means by which RNase L combats viral infection, tumorigenesis, and immune dysregulation. ","fileCount":"84","fileSizeKB":"190416577","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"RNaseL;Virus;Innate Immunity;mRNA;dsRNA;DatasetType:Proteomics","pi":[{"name":"Ciaran Seath","email":"cseath@ufl.edu","institution":"University of Florida","country":"USA"},{"name":"James M. Burke","email":"james.burke@ufl.edu","institution":"The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"cc30b97371304904a294dab9ac87112d","id":"293"}, {"dataset":"MSV000099381","datasetNum":"99381","title":"Marine Roseobacter sulfur amino lipids (SALs) extraction","user":"LuisePal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759600482000","created":"Oct. 4, 2025, 10:54 AM","description":"The Roseobacter Clade Bacteria (RCB) play a crucial role in marine ecosystems, particularly Ruegeria pomeroyi, which utilize organosulfur compounds such as 2,3-dihydroxypropanesulfonate (DHPS) and dimethylsulfoniopropionoate (DMSP). Recently, a new class of sulfonolipids, sulfur amino lipids (SALs), was identified in these bacteria, with possible structures proposed by Smith et al. (ISME Journal, 2021, 15, 2440-2453). This study aims to confirm or revise the proposed structures for SAL-656 and SAL-672. Two candidates for SAL-656 and SAL-672 were synthesized, namely 3-acyloxyacylamides of homotaurine and cysteinolic acid, respectively. Tandem mass spectrometry (MS\/MS) analysis of synthetic and natural SALs revealed significant discrepancies, leading to the exclusion of proposed structures. Further exploration of lipid extracts from R. pomeroyi identified related lipoforms of SAL-656 and SAL-672, which form two distinct families based on LC-MS\/MS and molecular network analysis. While the mass spectrometric data allow exclusion of previously proposed structures and provide insights into acyl groups and headgroups, the complete structures of SAL-656 and SAL-672 remain elusive. Nonetheless, the data are consistent with revised structures based on cysteinolic acid or 3-amino-2-hydroxypropanesulfonic acid wherein both hydroxyl and amino groups are acylated. Our findings reveal the SALs as a group of sulfonolipids that are distinct from more studied classes of sulfonolipids, with implications for understanding their biosynthesis and ecological roles in marine environments.","fileCount":"5","fileSizeKB":"603002","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruegeria pomeroyi DSS-3 (NCBITaxon:246200)","instrument":"Vanquish UHPLC linked to an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA)","modification":"no","keywords":"sulfur cycle;organosulfur;enzymes;sulfonates;roseobacter;DatasetType:Other (Lipidomics)","pi":[{"name":"Professor Spencer J Williams","email":"sjwill@unimelb.edu.au","institution":"Bio21 Institute Parkville, The University of Melbourne","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"914192b12c3b4ea086a04da15db95f9d","id":"294"}, {"dataset":"MSV000099376","datasetNum":"99376","title":"CMMC_multiplex_synthesis_Ibuprofen_quantification","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759522549000","created":"Oct. 3, 2025, 1:15 PM","description":"MS\/MS fragmentation data of Reaction mixture and biological samples acquired on Q Exactive - 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with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"199","fileSizeKB":"28624628","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CMMC;drugs;multiplex synthesis;bile acid;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"766a84c26010414b86224569beaccdd2","id":"296"}, {"dataset":"MSV000099374","datasetNum":"99374","title":"CMMC_synthesis_compounds_and_biological_samples_used_for_RT_matching","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759522187000","created":"Oct. 3, 2025, 1:09 PM","description":"MS\/MS fragmentation data of reaction mix and bilogical samples acquired on Q Exactive - 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Data dependent experiments of tomato juices are included. Blood plasma pools are labeled with \"QC\" and juice samples are labeled with \"Juice.\"","fileCount":"49","fileSizeKB":"7228662","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6546 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;blood plasma;nutrition;tomato juice;clinical trial;carotenoids;DatasetType:Metabolomics","pi":[{"name":"Jessica Cooperstone","email":"cooperstone.1@osu.edu","institution":"The Ohio State University","country":"United States"},{"name":"Maria Sholola","email":"sholola.1@osu.edu","institution":"Ohio State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"66c3cb696d174227adbb2c89efc5c334","id":"298"}, {"dataset":"MSV000099371","datasetNum":"99371","title":" Itaconate transport across the plasma membrane and Salmonella-containing vacuole via MCT1\/4 modulates macrophage antibacterial activity","user":"biomeng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1759507046000","created":"Oct. 3, 2025, 8:57 AM","description":"Non-targeted metabolomics in AZD3965-treated Mct4-\/- and WT BMDM.","fileCount":"41","fileSizeKB":"4583906","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap mass spectrometer, Exploris 480, Thermo Scientific","modification":"MS:1002864 - 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Substantial lipid changes have been observed previously in lupus patients, and hence we carried out the most comprehensive lipidomics study in lupus to date using LipidMatch Flow. In this study, we investigated various sub-categories of lupus including lupus nephritis, active versus non-active lupus, as well as comparisons to non-lupus controls. A total of 1,105 unique lipids spanning 36 lipid classes (or sub-classes) were annotated in blood plasma samples; of these, 111 lipids changed significantly between controls and active lupus. We determined for the first-time specific oxidized lipid markers, with oxidized triacylglycerols being the most significantly increased lipid sub-class in active lupus as compared to controls. Other indicators of oxidative stress included decreased lipids containing ether linkages and\/or polyunsaturated fatty acids. Increased ceramide (d18:1\/16:0) and decreased 20-22 carbons containing species (especially 20:4) indicated an inflammatory response in patients with active lupus. Furthermore, we determined significant downregulation of phosphatidylserines, which are known inflammation suppressors, in patients with lupus and a decrease in Coenzyme Q9 and Q10 with supplementation of lupus patients with these compounds shown to be protective. Several unique lipids with unknown biology are also shown to significantly change in active lupus. Many of these trends were also observed in non-active lupus, suggesting lipidomics related changes may occur early in disease development. In conclusion, this comprehensive lipidomics study expands our knowledge of the lipid alterations associated with lupus, providing insights into disease pathogenesis and depleted lipids which could serve as therapeutic targets. 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Despite this progress, the maternal-fetal interface, particularly in the context of fetal aneuploidy, remains underexplored. This study addressed this gap by performing an exploratory, label-free mass spectrometry-based proteomic analysis of maternal urine from 15 pregnancies with normal karyo-type and 9 with fetal aneuploidy.","fileCount":"633","fileSizeKB":"198450376","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fetal aneuploidy;urine proteomics;label-free proteomics;DatasetType:Proteomics","pi":[{"name":"Iuga Cristina-Adela","email":"iugac@umfluj.ro","institution":"MEDFUTURE Research Center for Advanced Medicine","country":"Romania"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD068958","task":"64dc4d7125fb427eaf01bf57caafbe2f","id":"323"}, {"dataset":"MSV000099284","datasetNum":"99284","title":"Blank Tomato Sample spiked with Pesticide Mixture at different spike levels without inclusion list","user":"joaldi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1758897238000","created":"Sep. 26, 2025, 7:33 AM","description":"This dataset was used as a case study nontarget screening with spectral alerts. Spectral alerts were mined with MS2LDA 2.0. It includes six samples: blank tomato sample, a tomato sample spiked at 200 ppb and 10 ppb, a blank orange sample, an orange sample spiked at 200 ppb and 10 ppb. The spiking was conducted with a pesticide mixture containing 211 compounds. No inclusion list was used for DDA acquisition in positive mode.","fileCount":"25","fileSizeKB":"1086056","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Solanum lycopersicum (NCBITaxon:4081)","instrument":"Orbitrap IQ-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pesticides, NTS, DDA, Food Safety, HRMS;DatasetType:Other (Xenobiotics)","pi":[{"name":"Jonas Dietrich","email":"jonas.dietrich@wur.nl","institution":"Wageningen University and Research","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f66d9319f2854dcb94dd4509c9c3d5f1","id":"324"}, {"dataset":"MSV000099283","datasetNum":"99283","title":"GNPS - one dataset one sample one human","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1758866231000","created":"Sep. 25, 2025, 10:57 PM","description":"Feces from a human run on a Vanquish coupled to an Orbitrap Exploris 240. 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Proteins were digested in-gel by trypsin. Peptides were measured on a Q Exactive Plus Orbitrap mass spectrometer.\n\nRaw data files were processed by MaxQuant software package (version 2.1.3.0) using its integrated Andromeda search engine. Spectral data were searched against a target-decoy database consisting of the forward and reverse sequences of the UniProt C. briggsae (release 2023_02; 21,756 entries) and E. coli (release 2023_01; 5,064 entries) reference proteomes and a list of common contaminants. False discovery rate (FDR) was set to 1% at both peptide and protein levels. MaxLFQ quantification algorithm was employed.\n","fileCount":"10","fileSizeKB":"6201455","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis briggsae (NCBITaxon:6238)","instrument":"Q Exactive Plus","modification":"MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\"","keywords":"Protein-protein interactions, C. briggsae, PID-3;DatasetType:Proteomics","pi":[{"name":"Rene Ketting","email":"R.Ketting@imb-mainz.de","institution":"Institute of Molecular Biology, Mainz","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD068824","task":"294232600cda4be6a328e99b2b8d8981","id":"327"}, {"dataset":"MSV000099271","datasetNum":"99271","title":"Diatom_Dissolved_Lipidomes_Si_Limitation_Growth_phase","user":"imanolulloa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1758748916000","created":"Sep. 24, 2025, 2:21 PM","description":"Dissolved lipid samples from three diatom species and two diatom isolates. Diatoms were grown with or without silicon and sampled during both logarithmic and stationary growth. 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As a result, HDR MS1 showed improved dynamic range and sensitivity compared to conventional full range scans, resulting in higher number of peptides and protein identifications under identical MS2 parameters, less redundant precursor ion sampling, and higher rate of quantified precursor ions. 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These files provide a resource for metabolite profiling, natural product discovery, and comparative studies in cosmetic and plant metabolomics research.","fileCount":"4","fileSizeKB":"308779","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cucumis sativus (NCBITaxon:3659)","instrument":"liquid chromatography mass spectroscopy","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cucumber extract, Japanese cucumber;DatasetType:Other (Untargeted metabolomics)","pi":[{"name":"AIDA YUSRINA BINTI SALEH","email":"aida.yusrina161@gmail.com","institution":"UPM","country":"Malaysia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"06a5ee8d65184968ac878e339f8d98f5","id":"388"}, {"dataset":"MSV000099097","datasetNum":"99097","title":"GNPS Local Cucumber (Cucumis Sativus L.)","user":"214807","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757428708000","created":"Sep. 9, 2025, 7:38 AM","description":"This dataset contains LCMS\/MS data from Cucumis sativus (cucumber) extracts prepared for potential skincare applications. Local cucumber samples were subjected to water extraction, followed by concentration. The extracts were analyzed by liquid chromatography mass spectrometry (LCMS\/MS) to profile metabolites of interest. The dataset includes raw LCMS\/MS files. These data may be useful for researchers working on plant metabolomics, natural product discovery, and cosmetic ingredient development.","fileCount":"4","fileSizeKB":"303049","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cucumis sativus (NCBITaxon:3659)","instrument":"liquid chromatography mass spectroscopy","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cucumber extract;DatasetType:Other (Untargeted metabolomics)","pi":[{"name":"AIDA YUSRINA BINTI SALEH","email":"aida.yusrina161@gmail.com","institution":"UPM","country":"Malaysia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6ac5700b60474e66a25be928dba4a399","id":"389"}, {"dataset":"MSV000099095","datasetNum":"99095","title":"PHF19 drives the formation of PRC2 clusters to enhance motility in TNBC cells","user":"syncell","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757398171000","created":"Sep. 8, 2025, 11:09 PM","description":"Polycomb Repressive Complex 2 (PRC2) is a key regulator of transcriptional repression and chromatin organization, essential in development and disease. While its enzymatic activity is well characterized, the factors governing PRC2 subnuclear organization, particularly in cancer cells, are largely unknown. Here, we integrate in situ subcellular proteomics, high-resolution imaging, and functional genomics to investigate PRC2 compartmentalization in triple-negative breast cancer (TNBC) cells. We identify PHF19, a sub-stoichiometric PRC2 accessory subunit as upregulated in TNBC, and central to the formation of endogenous, micron-scale nuclear PRC2 clusters. These structures act as spatial hubs that stabilize local PRC2 occupancy and reinforce H3K27me3 macro-domain organization. Mechanistically, an intrinsically disordered region (IDR) in PHF19 is required for clustering and for promoting TNBC cell motility. Our findings uncover a non-enzymatic layer of PRC2 regulation, where local PRC2 compartmentalization through accessory subunits, directly influences cellular behavior, with implications for disease and development.","fileCount":"18","fileSizeKB":"15981473","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Polycomb;EZH2;PCL3;Chromatin organization;H3K27me3;Biomolecular condensates;IDR;Triple-negative Breast Cancer;Cell migration;Optoproteomics;DatasetType:Proteomics","pi":[{"name":"Cristiana Lungu","email":"cristiana.lungu@izi.uni-stuttgart.de","institution":"Institute of Cell Biology and Immunology, University of Stuttgart; Stuttgart Research Center Systems Biology, University of Stuttgart","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD068214","task":"bc0dd0b43b3e487690fe5eeec19f34f4","id":"390"}, {"dataset":"MSV000099090","datasetNum":"99090","title":"GNPS - CMMC_Multiplex_synthesis_small_molecules","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757372513000","created":"Sep. 8, 2025, 4:01 PM","description":"MS\/MS fragmentation data of the compounds acquired on Q Exactive - with\r\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"19","fileSizeKB":"1030294","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sythesis;CMMC;bile acid;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7db8c41a68974906b8dc1017bf550db7","id":"391"}, {"dataset":"MSV000099086","datasetNum":"99086","title":"Identification of VIPP1-interacting proteins in Arabidopsis via1 mutant. 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Cell-cell interactions, which are largely mediated by cell-surface proteins, control many critical aspects of development and physiology; as such, dysregulation of glial cell-surface proteins in particular is hypothesized to play an important role in age-related neurodegeneration. However, it remains technically difficult to profile glial cell-surface proteins in intact brains. Here, we applied a cell-surface proteomic profiling method to glial cells from intact brains in Drosophila. Importantly, this enabled us to fully profile cell-surface proteomes in-situ, preserving native cell-cell interactions that would be omitted using more traditional proteomics methods. Applying this platform to young and old flies, we investigated how glial cell-surface proteomes change during aging. We identified candidate genes predicted to be involved in normal brain aging, including several associated with neural development and synapse wiring molecules not previously thought to be particularly active in glia. Through a functional genetic screen, we identified one surface protein, DIP-B, which is down-regulated in old flies and can increase fly lifespan when overexpressed in adult glial cells. We further performed whole-head single-nucleus RNA-seq, and revealed that DIP-B overexpression mainly impacts glial and fat cells. We also found that glial DIP-B overexpression was associated with improved cell-cell communication, which may contribute to the observed lifespan extension. Our study is the first to apply in-situ cell-surface proteomics to glial cells in Drosophila, and to identify DIP-B as a potential glial regulator of brain aging.\n","fileCount":"8","fileSizeKB":"5870729","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila (NCBITaxon:7215)","instrument":"Q Exactive HF-X","modification":"TMT10-Full-Lys, C-carbamidomethylation, M-oxidation, N-term acetylation","keywords":"glial cell;cell surface;proximity labeling;DatasetType:Proteomics","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"87ac3fe22ea04005891f977a1829840b","id":"395"}, {"dataset":"MSV000099077","datasetNum":"99077","title":"Untargeted HRLC-HRMS\/MS metabolomics data (ESI+) of fungal strains from the order Hypocreales ","user":"YNPlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757332053000","created":"Sep. 8, 2025, 4:47 AM","description":"Untargeted LC-MS\/MS metabolomics data (ESI+) from a collection of 82 fungal strains belonging to the order Hypocreales, with 5 Xylariales strains included as outgroup","fileCount":"2553","fileSizeKB":"136504708","spectra":"4029209","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Akanthomyces_Attenuatus_MUCL_8126;Akanthomyces_G78;Akanthomyces_lecani_DSM_111009;Akanthomyces_lecani_MUCL8115;Akanthomyces_lecani_YNP1;Akanthomyces_lecanii_MUCL_8115;Akanthomyces_muscarius_MUCL9713;Beauveria_bassiana_DSM_1344;Beauveria_bassiana_DSM_62075;Beauveria_bassiana_DSM_875;Beauveria_bassiana_IHEM_3558;Beauveria_bassiana_MB199430;Beauveria_brongniartii_DSM_6651;Beauveria_brongniartii_MB309469;Beauveria_caledonica;Beauveria_felina_DSM_4678;Beauveria_felina_MB116173;Claviceps_fusiformis_DSM_2942;Claviceps_paspali_DSM_883;Claviceps_paspali_DSM_885;Claviceps_purpurea_3488;Claviceps_purpurea_DSM_714;Claviceps_purpurea_DSM_715;Claviceps_purpurea_DSM_716;Claviceps_viridis_DSM_882;Cordyceps_amoene-rosea_IHEM_18564;Cordyceps_fumosorosea_MB_820980;Cordyceps_javanica_MB_820982;Cordyceps_militaris_DSM_1153;Cordyceps_militaris_DSM_23612;Cordyceps_militaris_IHEM_5792;Cordyceps_ophioglossoides_DSM_1208;Cordyceps_ophioglossoides_IHEM_5799;Cordyceps_sp_D1;Epichloe_coenophiala_MB805488;Epichole_typhina_MB165057;Fusarium_acaciae_mearnsii_CBS_110255;Fusarium_boothi_CBS_110251;Fusarium_G73;Fusarium_G74;Isaria_farinosa_MB156563;Lecanicillium_aphanocladii_MUCL_58163;Lecanicillium_coprophilum_MUCL_594;Lecanicillium_fungicola_MUCL_9781;Lecanicillium_psalliote_MUCL_9800;Lecanicillium_saksenae_MUCL_18310;Metapochonia_bulbilosa MUCL_34289;Metapochonia_bulbilosa_MUCL_8257;Metarhizium_anisopliae_DSM_21704;Metarhizium_anisopliae_MB_429455;Metarhizium_anisopliae_MUCL_9815;Metarhizium_brunneum_MUCL9645;Metarhizium_bulbilosa_MUCL_34289;Metarhizium_flavoviride_DSM_11336;Metarhizium_flavoviride_DSM_11337;Metarhizium_flavoviride_IHEM_3994;Metarhizium_MUCL_4166;Neonectria_wollenw_MB3469;Ophiocordyceps_aphodi_MB504221;Ophiocordyceps_gracilis_MB504277;Ophiocordyceps_pseudogibbellulae_MB814746;Pochonia_chlamydosporia_9880;Pochonia_chlamydosporia_MUCL_4182;Pochonia_chlamydosporia_MUCL_8330;Purpureocillium_lilacinum_DSM_846;Sarocladium_G77;Sarocladium_G79;Simplicilium_lanosoniveum_56234;Simplicilium_lanosoniveum_56315;Simplicilium_lanosoniveum_56330;Simplicilium_lanosoniveum_56433;Simplicilium_subtropicum_MUCL_8672;Simplicillium_lamellicola_56290;Simplicillium_lamellicola_DSM_3347;Simplicillium_lamellicola_DSM_56442;Simplicillium_lamellicola_MUCL_44211;Simplicillium_lamellicola_MUCL_9740;Tolypocladium_cylindrosporum_MB324638;Tolypocladium_inflatum_DSM_63544;Tolypocladium_inflatum_IHEM_4517;Torrubiella_piperis_MB_500023;Trichoderma_atroviride_CBS_122147;Xylaria_digitata_DSM914;Xylaria_hipoxylon_DSM106648;Xylaria_longipes_DSM_107022;Xylaria_polymorpha_MB_246876;Xylaria_sp_P1","instrument":"IDX-Orbitrap Mass Spectrometer (Thermo Fisher Scientific)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hypocreales;fungi;DatasetType:Metabolomics","pi":[{"name":"Pablo Cruz-Morales","email":"pcruzm@biosustain.dtu.dk","institution":"Danmarks Tekniske Universitet","country":"Denmark"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"102bab5c4eb4402ab26551f4329bea83","id":"396"}, {"dataset":"MSV000099076","datasetNum":"99076","title":"GNPS - bacterial monocultures with bile acids and drugs mix 2","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757302606000","created":"Sep. 7, 2025, 8:36 PM","description":"Monocultures of the drug screening associating with the MassiVE MSV000096589 mixture 6 72 h. Samples were run on Kinetex (phenomenex) polar C18 100 mm x 2.1 mm 2.6 um particle size. ","fileCount":"471","fileSizeKB":"28565766","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Monocultures, bile acid, drug, drug mix 2, 72 h;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"10add175630348a79bcea5254367d4c4","id":"397"}, {"dataset":"MSV000099071","datasetNum":"99071","title":"In-situ glial cell-surface proteomics identifies pro-longevity factors in Drosophila","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757268958000","created":"Sep. 7, 2025, 11:15 AM","description":"Much focus has shifted towards understanding how glial dysfunction contributes to age-related neurodegeneration due to the crucial roles glial cells play in maintaining healthy brain function. Cell-cell interactions, which are largely mediated by cell-surface proteins, control many critical aspects of development and physiology; as such, dysregulation of glial cell-surface proteins in particular is hypothesized to play an important role in age-related neurodegeneration. However, it remains technically difficult to profile glial cell-surface proteins in intact brains. Here, we applied a cell-surface proteomic profiling method to glial cells from intact brains in Drosophila. Importantly, this enabled us to fully profile cell-surface proteomes in-situ, preserving native cell-cell interactions that would be omitted using more traditional proteomics methods. Applying this platform to young and old flies, we investigated how glial cell-surface proteomes change during aging. We identified candidate genes predicted to be involved in normal brain aging, including several associated with neural development and synapse wiring molecules not previously thought to be particularly active in glia. Through a functional genetic screen, we identified one surface protein, DIP-B, which is down-regulated in old flies and can increase fly lifespan when overexpressed in adult glial cells. We further performed whole-head single-nucleus RNA-seq, and revealed that DIP-B overexpression mainly impacts glial and fat cells. We also found that glial DIP-B overexpression was associated with improved cell-cell communication, which may contribute to the observed lifespan extension. Our study is the first to apply in-situ cell-surface proteomics to glial cells in Drosophila, and to identify DIP-B as a potential glial regulator of brain aging.","fileCount":"8","fileSizeKB":"5870729","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila (NCBITaxon:7215)","instrument":"Q Exactive HF-X","modification":"TMT10-Full-Lys, C-carbamidomethylation, M-oxidation, N-term acetylation","keywords":"glial cell;cell surface;proximity labeling;DatasetType:Proteomics","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a6271d898bfa4182908c677328b2b5cd","id":"398"}, {"dataset":"MSV000099062","datasetNum":"99062","title":"GNPS-Untargeted metabolomics on samples from a genetic mouse model of Primary Sclerosing Cholangitis (PSC).","user":"cbez","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757118153000","created":"Sep. 5, 2025, 5:22 PM","description":"Liver, ileum, cecum, colon, serum, feces, and bile juice samples were collected from the 36 mice. MS\/MS data acquisition was carried out on a Thermo Q Exactive mass spectrometer in positive ionization mode, with chromatographic separation achieved using a Phenomenex Polar C18 column.","fileCount":"617","fileSizeKB":"35045964","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Liver, ileum, cecum, colon, serum, feces, bile juice, mice, PSC, cholangitis;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b676baab927446d19d80fccd726c811d","id":"399"}, {"dataset":"MSV000099057","datasetNum":"99057","title":"NTA Offshore Oil Platform Seawater LCHRMS neg","user":"montmasis","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757095206000","created":"Sep. 5, 2025, 11:00 AM","description":"Nontarget LC-HMRS dataset associated with publication: \nMoller et al. Persistence-Directed Testing of Chemicals Discharged from Offshore Oil Platforms Combined with Non-Targeted Analysis (2025)\nEnvironmental Science & Technology \nPI: Philipp Mayer, Technical University of Denmark, Dept. of Environmental & Resource Engineering\nData produced at: National Facility for Exposomics | SciLifeLab (Stockholm University, Sweden)\n","fileCount":"291","fileSizeKB":"32956658","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"offshore produced seawater","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"biodegradation;OECD 309;LC-HRMS;Orbitrap;whole effluent testing;produced water;DatasetType:Metabolomics;DatasetType:Other (Exposomics)","pi":[{"name":"Philipp Mayer","email":"philm@dtu.dk","institution":"DTU","country":"Denmark"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6180478aec2140a68890105662447b01","id":"400"}, {"dataset":"MSV000099055","datasetNum":"99055","title":"GNPS - Samples for: Cloud Based Storage, Analysis and Analysis Pipelines of Mass Spectrometric Data in the OCI Cloud Computing Environment","user":"Kruttika","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757092965000","created":"Sep. 5, 2025, 10:22 AM","description":"Hilic Column, Negative mode data, containing #MSK-QC2-1 mix of standards listed here: A mix of Caffeine (13C3, 99%) D-Glucose (13C6, 99%) Sodium benzoate (13C6, 99%) Sodium citrate (13C3, 99%) Sodium octanoate (13C8, 99%) Sodium propionate (13C3, 99%) Stearic acid, sodium salt (13C18, 98%) Succinic acid, disodium salt (13C4, 99%) 4 2 D-Sucrose (13C6, 98%). 2 ul injection volume with 10 fold dilution","fileCount":"127","fileSizeKB":"465662","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cloud computing, Virtual computers, Mass Spectrometry, OCI, Oracle, Systems management, Nextflow, Docker, Skyline;DatasetType:Metabolomics","pi":[{"name":"Jonathan E. Katz","email":"jonathan@proteowizard.org","institution":"Ellison Medical Institute","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"6fc56c4c5f6a41ba8c8186b5d14d4870","id":"401"}, {"dataset":"MSV000099053","datasetNum":"99053","title":"ZAP triggers mRNA decay during the regulation of aberrant protein production","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757092058000","created":"Sep. 5, 2025, 10:07 AM","description":"The endoplasmic reticulum (ER) is essential for the proper folding and processing of secretory and membrane proteins. These proteins are guided to the ER by signal peptides recognized by the signal recognition particle (SRP). When this process is impaired, cells rely on quality control mechanisms to prevent the accumulation of misfolded or mislocalized proteins. One such mechanism, known as regulation of aberrant protein production (RAPP), targets mRNAs encoding mutated signal peptides for degradation and also eliminates the corresponding aberrant proteins. Using a functional genetic screen, we identify the zinc finger antiviral protein (ZAP) as a key component of the RAPP pathway. Using proteomics and enhanced UV crosslinking and immunoprecipitation (eCLIP) experiments, we show that ZAP-S isoform associates with SRP components and facilitates degradation of aberrant mRNAs and proteins. ZAP exerts its role by recognizing faulty proteins early in their biogenesis and targeting them, along with their encoding mRNAs, for degradation. Loss of ZAP activates ER stress and the integrated stress response, highlighting its central role in safeguarding protein targeting and maintaining cellular homeostasis.","fileCount":"3","fileSizeKB":"2264714","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Signal recognition particle (SRP), Regulation of aberrant protein production (RAPP), Zinc finger antiviral protein (ZAP), mRNA degradation, ER stress;DatasetType:Proteomics","pi":[{"name":"Colin Wu","email":"colin.wu2@nih.gov","institution":"NCI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"485d81850ac842a98e14b7348b6627b0","id":"402"}, {"dataset":"MSV000099052","datasetNum":"99052","title":"NTA Offshore Oil Platform Seawater LCHRMS pos","user":"montmasis","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757091775000","created":"Sep. 5, 2025, 10:02 AM","description":"Nontarget LC-HMRS dataset associated with publication: \nMoller et al. Persistence-Directed Testing of Chemicals Discharged from Offshore Oil Platforms Combined with Non-Targeted Analysis (2025)\nEnvironmental Science & Technology \nPI: Philipp Mayer, Technical University of Denmark, Dept. of Environmental & Resource Engineering\nData produced at: National Facility for Exposomics | SciLifeLab (Stockholm University, Sweden)\n","fileCount":"291","fileSizeKB":"43032999","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"offshore produced seawater","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"biodegradation;OECD 309;LC-HRMS;Orbitrap;whole effluent testing;produced water;DatasetType:Metabolomics;DatasetType:Other (Exposomics)","pi":[{"name":"Philipp Mayer","email":"philm@dtu.dk","institution":"DTU","country":"Denmark"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f015755683e548fc84b690f1e448e651","id":"403"}, {"dataset":"MSV000099051","datasetNum":"99051","title":"LAM Plasma Extracellular Vesicles Proteome Analysis","user":"mk57mk","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757087990000","created":"Sep. 5, 2025, 8:59 AM","description":"The plasma EV proteome was analyzed using nanoLC-MS\/MS. Data were analyzed using Maxquant (1.6.2.6). ","fileCount":"15","fileSizeKB":"11663056","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"nanoLC-MS\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"exosomes, extracellular vesicles, lymphangioleiomyomatosis, LAM;DatasetType:Proteomics","pi":[{"name":"Magdalena Karbowniczek","email":"magdalena.karbowniczek@ttuhsc.edu","institution":"Texas Tech University Health Sciences Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1f7322442da240d4ac3858fb7b9b8c03","id":"404"}, {"dataset":"MSV000099049","datasetNum":"99049","title":"Nutritional Potential of Xuta (Jatropha curcas L.) Protein","user":"Nils_2023","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757077328000","created":"Sep. 5, 2025, 6:02 AM","description":"Three Xuta varieties (JPNT1, JPNT2, and JPNT3) harvested in three consecutive years (2022, 2023, and 2024) were analysed. The harvested seeds were sun-dried for 2-3 days, de-hulled immediately, and the kernels dried further on plastic or fibre mats under direct sunlight until the moisture content was <6% was achieved. The kernels were then stored in jute sacks out of direct sunlight. All seeds were sourced from Jatropowers research farms in India, respectively JPNT1 and 2 from A.S. Kulam Village, Coimbatore district, Tamil Nadu, India, and JPNT3 from Illuppunagaram Village, Tiruppur District, Tamil Nadu, India. Afterwards a hydrothermal treatment was applied prior to the digestion by treating the kernels for 40 min at 100% humidity at 125 C in a combi steamer. After treatment, the kernels were left to air-dry at room temperature for 10 min and subsequently cooled at 4 degree C for another 10 min. All kernels (untreated and treated) were ground in a blender and stored at 4 degree C. \n\nThe samples were further digested according to Brodkorb et al. (2019) using the INFOGEST method:\n\nA sample amount corresponding to 0.2 g protein is weighed, based on a total volume of 40 mL. For the oral phase, the sample was mixed with 4 mL ultra-pure water using an Ultra-Turrax(R) at a maximum rotation speed for 30 sec.. The resulting paste-like sample was then diluted with 4 mL simulated salivary fluid (SSF) containing 1 mM CaCl2(H2O)2. Under constant agitation, the pH was adjusted to 7.0 with 1 M NaOH using an automatic titration device. The appropriate amount of human salivary amylase was then added to achieve an activity of 75 U\/mL. To achieve a 1x concentration of SSF, the mixture was filled up to 10 mL with water and was incubated for 2 min. at 37 C. A sample of 2 mL each was collected. Afterwards, 6.4 mL of pre-warmed simulated gastric fluid (SGF) was added, which contained a lipase activity of 60 U\/mL and a pepsin activity of 2000 U\/mL due to the rabbit gastric extract used, and 0.15 mM CaCl2(H2O)2 in the final digestion mixture. The pH value was adjusted to 3.0 using 1 M HCl solution, and the mixtures were filled up to 16 mL with ultra-pure water. The samples were again incubated at 37 C for 2 h with sufficient shaking. At this point, 2 mL samples were withdrawn. For the final intestinal phase, simulated intestinal fluid (SIF) was added to the mixture in a ratio of 1:1 (v\/v), which corresponds to a volume of 7.7 mL. After adjusting the pH to 7.0 using 1 M NaOH solution, a final concentration of 10 mM bile salts was added. The samples were then incubated for 30 min at 37 C with constant stirring. Subsequently, CaCl2(H2O)2 was then added to reach a concentration of 0.6 mM in SIF, followed by the corresponding volume of porcine pancreatin to give a final mixture with an activity of 100 U\/mL trypsin and 2,000 U\/mL lipase. The pH was then adjusted to 7.0 using 1 M NaOH, after which the mixture was filled up to a final volume of 28 mL, and incubated for 2 h at 37 C with constant shaking. Digestion was stopped by adding the 4-(2-aminoethyl) benzensulfonylfluoride (AEBSF) protease inhibitor, reaching a final concentration of 0.05 mM after 120 min of the intestinal phase. All the samples were then immediately snap frozen in liquid nitrogen. After defrosting, the samples were separated into soluble (S) and insoluble (P) fractions by centrifugation at 4500 rpm and 4 C for at least 30 min, with the supernatant being collected, frozen, and immediately freeze-dried.\n\nPeptides were separated an Evosep One LC system using a 40 samples per day (40 SPD) Whisper-zoom standardized gradient (32.5 min). Eluting peptides were analyzed using a timsTOF Pro ion mobility spectrometry (IMS) quadrupole time of flight mass spectrometer operated in data-dependent acquisition parallel accumulation with serial fragmentation (DDA-PASEF) mode. Ionization of peptides took place at a temperature of 180 C and a capillary voltage of 1600 V. A blank run was performed between all samples, during which the ion mobility was automatically recalibrated. MS and MS\/MS scan range was 100 to 1700 m\/z, the ion mobility ranges (expressed as 1\/K0) 0.85 to 1.3 Vs\/cm2. A polygon filtering was applied in the m\/z and ion mobility area to exclude the low m\/z of singly charged ions for PASEF precursor selection. Ramp and accumulation time was set to 100 ms. The number of PASEF ramps was set to 4 with a ramp rate of 9.42 Hz and charge minimum of 0 and a maximum of 5. The quadrupole isolation width was set to 2 for m\/z = 700 and 3 for m\/z = 800. Collision energy was 27 eV for ion mobility (1\/K0) 0.85 Vs\/cm2 and 45 eV for ion mobility (1\/K0) 1.3 V*s\/cm2 respectively. Active precursor exclusion was activated with a window of 0.40 minutes.\n\nBrodkorb, A., Egger, L., Alminger, M. et al. INFOGEST static in vitro simulation of gastrointestinal food digestion. 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One liter of seawater for the 55% light level and the deep chlorophyll max was filtered through a 0.2 micron Corning filter, spiked with internal standard, and extracted onto a solid phase extraction cartridge (Waters HLB 6cc). Dissolved metabolomes were eluted through the SPE cartridges using methanol, and the lipidome was analyzed using reverse-phase HPLC and Orbitrap mass spectrometry. ","fileCount":"14","fileSizeKB":"367435","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Natural surface ocean community ","instrument":"Q Exactive","modification":"none","keywords":"dissolved meta-lipidome;marine lipidome;dissolved organic matter;DOM;ocean;oxylipins;fatty acids;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Bethanie Edwards","email":"bethanie_edwards@berkeley.edu","institution":"UC-Berkeley","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"06829701e4904e3aa6853dec673801b9","id":"408"}, {"dataset":"MSV000099039","datasetNum":"99039","title":"Keratinocyte derived extracellular vesicles in painful diabetic neuropathy_James_CD_2025","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757025734000","created":"Sep. 4, 2025, 3:42 PM","description":"Abstract\nPainful diabetic neuropathy (PDN) is a challenging complication of diabetes with patients experiencing a painful and burning sensation in their extremities. Existing treatments provide limited relief without addressing the underlying mechanisms of the disease. PDN involves the gradual degeneration of nerve fibers in the skin. Keratinocytes, the most abundant epidermal cell type, are closely positioned to cutaneous nerve terminals, suggesting the possibility of bi-directional communication. Extracellular vesicles are lipid-bilayer encapsulated nanovesicles released from many cell types that mediate cell to cell communication. The role of keratinocyte-derived extracellular vesicles (KDEVs) in influencing signaling between the skin and cutaneous nerve terminals and their contribution to the genesis of PDN has not been explored. In this study, we characterized KDEVs in a well-established high-fat diet mouse model of PDN using primary adult mouse keratinocyte cultures. We obtained highly enriched KDEVs through size-exclusion chromatography and then analyzed their molecular cargo using proteomic analysis and small RNA sequencing. We found significant differences in the protein and microRNA content of high-fat diet KDEVs compared to KDEVs obtained from control mice on a regular diet, including pathways involved in axon guidance and synaptic transmission. Additionally, using an in vivo conditional extracellular vesicle reporter mouse model, we demonstrated that epidermal-originating GFP-tagged KDEVs are retrogradely trafficked into the dorsal root ganglion (DRG) neuron cell bodies. This study presents the first comprehensive isolation and molecular characterization of the KDEV protein and microRNA cargo in RD and HFD mice. Our findings suggest a potential novel communication pathway between keratinocytes and DRG neurons in the skin, which could have implications for PDN.","fileCount":"34","fileSizeKB":"9055746","spectra":"0","psms":"46509","peptides":"12403","variants":"12403","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Ascend","modification":"MS:1001460 - This term should be given if the modification was unknown.;UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Painful diabetic neuropathy;Extracellular vesicles;keratinocyte-derived extracellular vesicles;DatasetType:Proteomics","pi":[{"name":"jeffrey Savas","email":"jeffrey.savas@northwestern.edu","institution":"Northwestern University Feinberg","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD068095","task":"bbab21d121e6485cae3ba2f30be47322","id":"409"}, {"dataset":"MSV000099031","datasetNum":"99031","title":"Engineering unnatural cells with a 21st amino acid as a living epigenetic sensor","user":"yuhu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757006815000","created":"Sep. 4, 2025, 10:26 AM","description":"Living animals rely extensively on posttranslational modifications (PTMs) to regulate protein activity, stability, subcellular localization, and protein protein interactions. These modifications are tightly controlled by the balance of writer and eraser enzymes, which add or remove PTMs on proteins. Current strategies to measure writer and eraser activities in living animals largely depend on invasive methods such as single cell sequencing, quantitative mass spectrometry, or activity based probes, which often lack cell or tissue specificity. In this study, we report the development of autonomous cells, both prokaryotic and eukaryotic, with the ability to biosynthesize and genetically encode acetyllysine using genetic code expansion technology. These engineered living sensors with a site specific acetyllysine modification can be transplanted into living animals, enabling real time monitoring of PTM dynamics in living cells and their visualization within animal models. We further demonstrate the utility of these cells in tracking deacetylase activity and assessing the effects of deacetylase inhibitors on PTM dynamics in living animals.","fileCount":"5","fileSizeKB":"211739","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli","instrument":"Rice University","modification":"No","keywords":"ncAA AcK GCE biosynthesis sensor Sirtuins;DatasetType:Proteomics","pi":[{"name":"Han Xiao","email":"han.xiao@rice.edu","institution":"Rice University","country":"United states"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b9361ceb3a8149f9949e40d8fafff87c","id":"410"}, {"dataset":"MSV000099030","datasetNum":"99030","title":"Early cardiomyocyte dysfunction from anthracycline exposure is driven by conserved RNA protein co expression networks","user":"saypaul","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1757004423000","created":"Sep. 4, 2025, 9:47 AM","description":"This study uses human induced pluripotent stem cell-derived cardiomyocytes iPSC-CMs from six individuals treated with sublethal, clinically relevant doses of three ACs Doxorubicin, Epirubicin, Daunorubicin and a related TOP2B-inhibiting drug Mitoxantrone to model chemotherapeutic associated cardiotoxicity 3 and 24 hours post treatment. Peptide mixtures were analyzed by nanoflow liquid chromatography-tandem mass spectrometry using a nano LC chromatography system UltiMate 3000 RSLCnano, Dionex, coupled on-line to a Thermo Orbitrap Eclipse mass spectrometer through a nanospray ion source. Instrument performance was verified by analyzing a standard six protein mix digest before the sample set run, between each experimental block and at the end of the experiment. Protein batches were block randomized by individual, where batch contained sequentially randomized samples from each individual. One protein mix digest of the individual block was run before and after all randomized samples. A protein mix digest comprising all 60 experimental samples at the end of each run was also measured. The protein mix data files were analyzed to confirm that instrument performance remained consistent throughout the experiment. In total 60 experimental samples were treated with one drug at one timepoint per individual. 17 samples were pooled by batch. 9 pooled samples consisted of total pool samples. This lead to a total of 88 samples analyzed further in downstream analysis.","fileCount":"163","fileSizeKB":"196097939","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"No","keywords":"Anthracycline, Cardiomyocyte, Cardiotoxicity;DatasetType:Proteomics","pi":[{"name":"Michelle C. Ward","email":"miward@utmb.edu","institution":"University of Texas Medical Branch at Galveston","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD068081","task":"a8c11fad7a1a4e99864a62a0f2856384","id":"411"}, {"dataset":"MSV000099025","datasetNum":"99025","title":"4a016 P35 C18 CV vs GF vs oMM12 colonized mice gut-microbiota","user":"Tommaso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1756968912000","created":"Sep. 3, 2025, 11:55 PM","description":"hydroalcoholic extracts of fecal samples from mice with the following gut-microbiota colonization: conventional, germ-free and oMM12. chromatographic system: 0.1% formic acid and ACN. 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Samples analyzed using UHPLC-HRMS with ZICHILIC chromatography. 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It includes Blank samples and pooled QCs. Also, iterative DDA (Thermo's AqcuireX Deep Scan) was carried out in a pooled QC. Feature tables were obtained with mzmine 4.7.29 using the LC-MS DDA workflow. ","fileCount":"43","fileSizeKB":"2334883","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Household Dust","instrument":"Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Household dust;LC-HRMS\/MS;Exposomics;Metabolomics","pi":[{"name":"Angel Sanchez-Illana","email":"angel.illana@uv.es","institution":"University of Valencia","country":"Spain"},{"name":"Pablo Miralles","email":"pablo.miralles@fisabio.es","institution":"FISABIO-Public Health","country":"Spain"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"676161ce705a4e78a87c6547967fa312","id":"414"}, {"dataset":"MSV000099010","datasetNum":"99010","title":"Requirement of ClpX for CtsR dissociation from its operator elements upon heat stress in Bacillus subtilis - Conditional mutants","user":"buschl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1756891627000","created":"Sep. 3, 2025, 2:27 AM","description":"A sudden increase in temperature triggers Bacillus subtilis to activate expression of stress-specific heat shock proteins of the CtsR (class three stress repressor) regulon to withstand the adverse conditions. Key members of this regulon, such as ATPases, proteolytic subunits and their adaptors, which can assemble to the functional Clp protease system, perform crucial roles in maintaining cellular proteostasis, while their transcription is repressed by CtsR during vegetative growth. Upon heat shock, a conformational change in a thermosensing glycine-rich loop causes CtsR to detach from its DNA operators, enabling the transcriptional activation of the regulon. Novel data from a clpX-deficient strain demonstrated that in addition, the presence of the ATPase ClpX is essential for the CtsR dissociation from its DNA binding site. To further elucidate this role of ClpX, we constructed a conditional clpX strain, in which clpX induction is decoupled from its native transcriptional control. This conditional expression system mimicked a clpX-deficient phenotype under non-inducing conditions and restored the wild-type phenotype upon induction. Our results indicate that the full induction of the CtsR regulon, particularly clpE, requires both heat and the presence of ClpX, thereby extending the current model for the transcriptional activation of genes repressed by CtsR.\n\nThe proteomic data set of the conditional mutant strains is presented.","fileCount":"2841","fileSizeKB":"153443192","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis (NCBITaxon:1423)","instrument":"timsTOF HT","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Clp protease;ClpX;Heat;CtsR;B. subtilis;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Uwe Voelker","email":"voelker@uni-greifswald.de","institution":"University Medicine Greifswald","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD068018","task":"29e65172fd0d4057b0dcf3595fc7170c","id":"415"}, {"dataset":"MSV000099009","datasetNum":"99009","title":"Requirement of ClpX for CtsR dissociation from its operator elements upon heat stress in Bacillus subtilis - Deletion mutants","user":"buschl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1756891015000","created":"Sep. 3, 2025, 2:16 AM","description":"A sudden increase in temperature triggers Bacillus subtilis to activate expression of stress-specific heat shock proteins of the CtsR (class three stress repressor) regulon to withstand the adverse conditions. Key members of this regulon, such as ATPases, proteolytic subunits and their adaptors, which can assemble to the functional Clp protease system, perform crucial roles in maintaining cellular proteostasis, while their transcription is repressed by CtsR during vegetative growth. Upon heat shock, a conformational change in a thermosensing glycine-rich loop causes CtsR to detach from its DNA operators, enabling the transcriptional activation of the regulon. Novel data from a clpX-deficient strain demonstrated that in addition, the presence of the ATPase ClpX is essential for the CtsR dissociation from its DNA binding site. To further elucidate this role of ClpX, we constructed a conditional clpX strain, in which clpX induction is decoupled from its native transcriptional control. This conditional expression system mimicked a clpX-deficient phenotype under non-inducing conditions and restored the wild-type phenotype upon induction. Our results indicate that the full induction of the CtsR regulon, particularly clpE, requires both heat and the presence of ClpX, thereby extending the current model for the transcriptional activation of genes repressed by CtsR.\n\nThe data set of the deletion mutants is presented. ","fileCount":"90","fileSizeKB":"230939024","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis (NCBITaxon:1423)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Clp protease;ClpX;B. subtilis;Heat;CtsR;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Uwe Voelker","email":"voelker@uni-greifswald.de","institution":"University Medicine Greifswald","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD068017","task":"6f7246df5fd44a8c87e7f4f2bb96addf","id":"416"}, {"dataset":"MSV000099006","datasetNum":"99006","title":"GNPS - BIB5814-PVA42_GC-MS_SPECIES2_polar-nonpolar_metabolomics","user":"bbrandao","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1756838496000","created":"Sep. 2, 2025, 11:41 AM","description":"BIB5814-PVA42_GC-MS_SPECIES2_polar-nonpolar_metabolomics 2025","fileCount":"48","fileSizeKB":"351515","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Species2","instrument":"GC-MS","modification":"No","keywords":"GC-MS;DatasetType:Metabolomics","pi":[{"name":"Bruno Ruiz Brandao da Costa","email":"bruno.ruiz.costa@usp.br","institution":"University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7937f83b67e14ac795312d2483c85bc1","id":"417"}, {"dataset":"MSV000099005","datasetNum":"99005","title":"GNPS - An effective response to respiratory inhibition by a Pseudomonas aeruginosa excreted quinoline promotes Staphylococcus aureus fitness and survival in co-culture","user":"enchiles","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1756838349000","created":"Sep. 2, 2025, 11:39 AM","description":"Triplicate cultures of S. aureus USA300_LAC were cultured overnight in TSB before diluting to 0.1 (A600) in 5 mL of TSB in 25 mL culture tubes. 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The samples were frozen at -80C until transferred to the metabolomics core of the Rutgers Cancer Institute of New Jersey for analysis.","fileCount":"243","fileSizeKB":"2282771","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus aureus subsp. aureus USA300_LAC","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"SrrAB;Rex;respiration;HQNO;Pseudomonas aeruginosa;Staphylococcus aureus;DatasetType:Metabolomics","pi":[{"name":"Jeffrey M. 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Stratified bootstrap analysis confirmed linearity and accuracy across the dynamic range, with DIA achieving lower limits of quantification (0.6 ppm) versus DDA (1.6 ppm). While both workflows reliably quantified most high-risk HCPs, DIA provided expanded proteome coverage and enhanced fold-change precision. 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An essential feature of oocyte meiosis is the reduction of genomic content to half, which is achieved by two successive divisions without an intervening S-phase. A known regulator of this event is a kinase called Mos that is exclusively expressed in oocytes during meiosis and activates the MEK\/ERK\/MAPK pathway. However, the downstream targets of the Mos-MAPK pathway and their significance in oocyte meiosis remains largely understudied. In this project, using phosphoproteomics on starfish (Patiria miniata) oocytes, we identify two predominant subsets of proteins that are targeted by Mos-MAPK at the critical time point - metaphase of meiosis I. These include proteins involved in CPE-mediated polyadenylation and cytoskeleton regulators. To complement this experiment, we performed DIA proteomics on Mos inhibited (20 micromolar U0126) and control oocytes at subsequent stages of meiosis (at 36 mins, 60 minutes and 90 minutes post hormone addition in U0126 inhibited oocytes and at metaphase I, meiosis I to meiosis II transition, metaphase II, 2 pronuclei and finally at the first mitotic division of the zygote for control oocytes). In this experiment, we identified 7,480 protein groups of which 5,103 protein groups could be quantified. We did not find significant changes in protein abundance across these time points and conditions, indicating that the proteome of starfish oocytes remains largely stable during meiosis.","fileCount":"62","fileSizeKB":"258208850","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Patiria miniata","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"meiosis, cytoskeleton, translational regulation, oocytes, Patiria miniata;DatasetType:Proteomics","pi":[{"name":"Henning Urlaub","email":"henning.urlaub@mpinat.mpg.de","institution":"Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences; Bioanalytics, Department of Clinical Chemistry, University Medical Center Goettingen","country":"Germany"},{"name":"Juliane Liepe","email":"juliane.liepe@mpinat.mpg.de","institution":"Research Group Quantitative and Systems Biology, Max Planck Institute for Multidisciplinary Sciences","country":"Germany"},{"name":"Peter Lenart","email":"peter.lenart@mpinat.mpg.de","institution":"Research Group Cytoskeletal Dynamics in Oocytes, Max Planck Institute for Multidisciplinary Sciences","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD067579","task":"e06c19b7c97840d68aa7c838684e32cf","id":"452"}, {"dataset":"MSV000098899","datasetNum":"98899","title":"Untargeted metabolomic analysis of 14 yellow dye plants","user":"LindsayMN","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755767047000","created":"Aug. 21, 2025, 2:04 AM","description":"14 yellow dye plants were extracted in triplicate in a mixture of MeOH\/H2O 1:1 (v\/v). LC-HRMS\/MS analysis was performed with a Waters SYNAPT G2-Si mass spectrometer. 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Chromatographic separation was performed on a Kinetex 2.1 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA)","fileCount":"360","fileSizeKB":"17583923","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9a2481e54bff49dcb909e14c71245558","id":"454"}, {"dataset":"MSV000098891","datasetNum":"98891","title":"GNPS - U19 Express Plasma dataset","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755716266000","created":"Aug. 20, 2025, 11:57 AM","description":"n = ~40 samples for U19 Express plasma dataset. Vanquish UHPLC system coupled to a Exploris 240-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.1 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"175","fileSizeKB":"8084530","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;U19;plasma;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b44fdd48d14e4670b5c4cec87aa57f7b","id":"455"}, {"dataset":"MSV000098890","datasetNum":"98890","title":"Set1 NEG Protein identification in Ph. vulgaris","user":"Taniahigueras","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755716250000","created":"Aug. 20, 2025, 11:57 AM","description":"Analysis of peptides generated by enzymatic digestion with alcalase in Chilean bean proteins\n","fileCount":"79","fileSizeKB":"90923","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phaseolus vulgaris (NCBITaxon:3885)","instrument":"compact","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"alcalase;Phaseolus vulgaris;Phaseolin;DatasetType:Proteomics","pi":[{"name":"Tania Higueras","email":"taniahigueras@udec.cl","institution":"Universidad de Concepcion","country":"Chile"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c98dde554484d9aabdf5ec1ab0a49d1","id":"456"}, {"dataset":"MSV000098886","datasetNum":"98886","title":"GNPS - Trichoderma reesei peptaibols : Raw analysis and database for molecular network","user":"elouarilias","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755677801000","created":"Aug. 20, 2025, 1:16 AM","description":"This dataset includes the raw LC MS\/MS data acquired on a Bruker timsTOF instrument, provided as complete .d directories, covering fungal extracts and the reference standard used in the study. In addition, mass spectrometry peak list files (MGF) and corresponding CSV tables of peptaibols are supplied for tSNE based database generation in MetGem.","fileCount":"86","fileSizeKB":"1547050","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichoderma reesei (NCBITaxon:51453)","instrument":"timsTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Peptaibols;HRMS\/MS;Database;Molecular networking;Fungi;DatasetType:Metabolomics","pi":[{"name":"Ilias El Ouar","email":"elouar.ilias@gmail.com","institution":"IFP Energies Nouvelles ","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a84e60bb6f8b4d1b8c65ba317840c937","id":"457"}, {"dataset":"MSV000098883","datasetNum":"98883","title":"GNPS - Targeting FSP1 triggers ferroptosis in lung cancer","user":"seonminkim","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755668498000","created":"Aug. 19, 2025, 10:41 PM","description":"Raw mass spectrometry data were acquired via LC-MS to quantify oxidized lipids and Coenzyme Q9 (CoQ9) in mouse lung tumor and cell line samples. A Parallel Reaction Monitoring (PRM) strategy was employed for oxidized lipids, while a Data-Dependent Acquisition (DDA) method was used for CoQ9.","fileCount":"279","fileSizeKB":"30064020","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"Oxidized lipids","keywords":"Oxidized lipids;Oxidized phospholipids;Coenzyme Q9;FSP1;Ferroptosis;Lung cancer;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Yun Pyo Kang","email":"yunpyo.kang@snu.ac.kr","institution":"Seoul National University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ef456b371c3a4b9491e48e9137188603","id":"458"}, {"dataset":"MSV000098881","datasetNum":"98881","title":"GNPS - Mouse Feces APOE KO FXR KO IHC Haddad","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755650406000","created":"Aug. 19, 2025, 5:40 PM","description":"Mouse fecal samples from APOE KO and APOE KO FXR KO animals under high fat and high cholesterol (HFHC) diet exposed to intermittent hypoxia and hypercapnia (IHC). 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Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA)","fileCount":"555","fileSizeKB":"10800235","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"APOE;IHC;hypoxia;hypercapnia;FXR;High Fat Diet;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"915b919d472b4b5fa2bf6e8c62b6770a","id":"459"}, {"dataset":"MSV000098879","datasetNum":"98879","title":"Single cell proteomics of hepatocytes derived from patients with liver disfunction","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1755639957000","created":"Aug. 19, 2025, 2:45 PM","description":"Single human hepatocytes were derived from patients with normal liver function and deleterious mutations that often lead to liver cancer. 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Penicillic acid quantification was performed using LC-MS peak intensity data from bacterial and fungal extracts and their co-cultures, compared against a calibration curve prepared from the pure standard at 0.1, 0.25, 0.5, 1, 2.5, 5, 10, and 25 uM.","fileCount":"55","fileSizeKB":"62689779","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus westerdijkiae (NCBITaxon:357447);Brachybacterium alimentarium (NCBITaxon:47845);Staphylococcus equorum (NCBITaxon:246432)","instrument":"timsTOF fleX MALDI-2","modification":"no","keywords":"cheese rinds;fungal bacterial interactions;penicillic acid;mycotoxins;DatasetType:Other (Quantification)","pi":[{"name":"Laura M. 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Here we provide evidence that for a well-established benefit of NAD+ precursors in mice, faster liver regeneration, nearly the entire effect can be attributed to the concentration of NAD+ in hepatocyte mitochondria. We find that mitochondrial NAD+ concentration in hepatocytes of male mice is determined by the expression of the transporter SLC25A51 (MCART1), as has previously been shown in cultured cells. Heterozygous loss of SLC25A51 modestly decreases mitochondrial NAD+ content in multiple tissues and impairs liver regeneration, while hepatocyte-specific overexpression is sufficient to enhance regeneration comparably to the effect of systemic supplements, despite increasing NAD+ only in mitochondria. Thus, the hepatocyte mitochondrial NAD+ pool is a key determinant of the rate of liver regeneration.","fileCount":"215","fileSizeKB":"4867418","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hepatocyte;NAD+;mitochondria;liver regeneration;DatasetType:Metabolomics","pi":[{"name":"Joseph A. 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The fission yeast Schizosaccharomyces pombe is petite-negative, but some nuclear mutations enable the loss of its mitochondrial genome.\nResults: Here, we characterize the classical petite-positive mutation ptp1-1 as a loss of function allele of the proteasome 19S regulatory subunit component mts4\/rpn1, involved in the ubiquitin-dependent degradation pathway. By comparison with another petite-enabling mutation in the g-subunit of the F1-ATPase, we show that ptp1-1 does not rescue mitochondrial membrane potential. Instead, the mutation results in increased levels of mitochondrial and cytoplasmic chaperones and an altered oxidative stress response.\nConclusions: ptp1-1 is a partial loss of function mutation of the proteasome that enables growth of cells devoid of mitochondrial DNA through a mechanism that is independent of mitochondrial membrane potential rescue and associated with proteasome dependent regulation of mitochondrial protein import precursors and the oxidative stress response.","fileCount":"211","fileSizeKB":"19344002","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Schizosaccharomycetaceae (NCBITaxon:4894)","instrument":"Orbitrap Eclipse;timsTOF HT","modification":"No","keywords":"Mitochondria;petite;mtDNA;proteasome;yeast;DatasetType:Proteomics","pi":[{"name":"Mikel Zaratiegui","email":"zaratiegui@dls.rutgers.edu","institution":"Department of Molecular Biology and Biochemistry, Division of Life Sciences, School of Arts and Science. 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Mice were injected with AAV9s encoding troponin T promoter-driven BioID2 fusion proteins (myc-BioID2-Venus-CAAX as control, myc-BioID2-Rac1-WT, and myc-BioID2-Rac1-C178S) at postnatal day 6. At 2 months of age, mice were fed ad libitum with high biotin chow (Teklad, Cat #TD.02458). Forty-eight hours post diet change, mice were sacrificed and hearts excised, rinsed in ice-cold PBS, and flash frozen in liquid nitrogen. Left ventricular tissue was homogenized in modified RIPA buffer (50 mM Tris, 150 mM NaCl, 0.1% SDS, 0.5% sodium deoxycholate, 1% Triton X-100, pH 7.5) in a beadmill homogenizer (Next Advance) and sonicated. Lysates were cleared by centrifugation at 12,000 rpm for 10 minutes at 4C. Lysates (4.5 mg) were incubated with streptavidin-coated magnetic beads (Fisher Scientific, Cat #88817) with end-over-end rotation at 4C for 18-20 hours then washed twice in modified RIPA buffer, once in 1 M KCl, 0.1 M Na2CO3, 2% SDS in Tris pH 7.5, and then in 2 M urea in 10 mM Tris pH 8.0 followed by two more washes in modified RIPA buffer. Lastly, beads were washed in ice-cold 1X PBS and flash frozen in liquid nitrogen prior to proteomics analysis. On-bead digestion and subsequent liquid chromatography with tandem mass spectrometry (LC-MS\/MS) analyses were performed exactly as described previously at the University of Michigan Proteomics Resource Facility (84). Briefly, samples were reduced, alkylated, trypsin digested, and reconstituted samples were labeled with TMT 16-plex reagents (Thermo Scientific, Cat #A44521) and subjected to LC-MS\/MS. Sequenced peptides were mapped to the mouse proteome and abundance normalized to total sequenced peptides. 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This study investigated whether immune, inflammatory, and endothelial dysfunction at 2 months post-discharge are associated with LPDM in children recovering from CSM. We conducted a case-control study nested within a randomized placebo-controlled trial of daily co-trimoxazole in HIV-negative children aged 2 to 59 months with CSM in four Kenyan hospitals. Cases were children who died between 2 and 6 months post-discharge; controls were survivors frequency-matched by sex, site, and trial arm. 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This stress response leads to activation of a variety of regulatory and metabolic pathways required for production of secondary metabolites including activation of conserved metabolic pathways for energy and substrate supply and species-specific secondary metabolites biosynthetic gene clusters. Furthermore, several promoter sequences contributing to upregulation of secondary metabolism induced by salinity stress were identified. 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Specifically, anaplerotic carbon recycling through pyruvate carboxylase promotes tricarboxylic acid cycle fluxes to generate 50-60% NADPH yield and 60-80% NADH yield, resulting in up to 6-fold greater ATP surplus than with succinate metabolism; the glyoxylate shunt sustains cataplerotic flux through malic enzyme for the remaining NADPH yield. This quantitative blueprint affords cofactor imbalance predictions in proposed engineering of key metabolic nodes in lignin valorization pathways.\n\nThe cells were digested for proteomics analysis following the E4 protocol published recently. E4 filters (CDS Analytical, Oxford, PA) were used. For LCMS, Ultimate 3000 nanoLC coupled to Orbitrap Eclipse and FAIMS PRO interface were used. 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It also contains a timecourse of lambda phosphatase treatment of a phosphoproteome-derived peptide library derived from pervanadate-treated HEK293T cells. 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In summary, each simulator unit consists of four connected glass vessels that are fed semi-continuously every third hour. The four vessels in the simulator (V1toV4) model different compartments of the human colon from the proximal (V1) to the distal part (V4), each having a different controlled pH (pH 5.5 to 7) and flow rate.","fileCount":"63","fileSizeKB":"14812672","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human ","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Microbiome;Gut;Metabolomics;Lipids;Bile acids;DatasetType:Metabolomics","pi":[{"name":"Santosh Lamichhane","email":"santosh.lamichhane@utu.fi","institution":"University of Turku","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8aebb28e37cd4890b76d0b4fdb8b18dd","id":"501"}, {"dataset":"MSV000098778","datasetNum":"98778","title":"Single cell analysis for oocytes and early embryos","user":"Baiyi_Quan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754886947000","created":"Aug. 10, 2025, 9:35 PM","description":"While non-mammalian embryos often rely on spatial pre-patterning, for decades it was\nbelieved that blastomeres of mouse and human embryos were developmentally\nequivalent. However, emerging evidence suggests early mouse and human\nblastomeres differ in developmental potential. Here, using multiplexed and label-free\nsingle-cell proteomics, we identify over three hundred asymmetrically abundant proteins\n- many involved in protein degradation and transport - that divide mouse 2-cell stage\nblastomeres into two distinct clusters, which we term alpha and beta. These\nasymmetries intensify at the 4-cell stage and are detectable as early as the zygote.\nFertilisation acts as a trigger for this breaking of symmetry and sperm entry point\ncorrelates with the gradient of proteome asymmetry. Perturbation of beta-enriched\nproteins (Gps1, Nedd8) alters lineage segregation. Embryos derived from beta\nblastomeres have more epiblast cells, while alpha blastomeres are associated with a\nlower developmental potential. Human 2-cell embryos show similar clustering and\nenrichment patterns, supporting conservation of this early asymmetry. Our findings\nreveal a previously unrecognized proteomic pre-patterning triggered by fertilisation in\nmammalian embryos, with implications for understanding totipotency and early lineage\nbias.","fileCount":"109","fileSizeKB":"90985998","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Single cell proteomics, embryo, oocyte, zygote;DatasetType:Proteomics","pi":[{"name":"Tsui-Fen Chou","email":"tfchou@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"739ffc72a3294fea9969d02562e65074","id":"502"}, {"dataset":"MSV000098776","datasetNum":"98776","title":"Pat2 Mass Spec Results Y154A - Haloferax volcanii","user":"jomamill","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754859424000","created":"Aug. 10, 2025, 1:57 PM","description":"Mass spectrometry analysis of Pat2Y154A compared to control strain","fileCount":"9","fileSizeKB":"422785","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Haloferax volcanii DS2 (NCBITaxon:309800)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"haloferax volcanii;acetylation;Pat2;Mass Spectrometry;DatasetType:Proteomics","pi":[{"name":"Julie A. 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","fileCount":"725","fileSizeKB":"27053947","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"vaginal fluid;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Tal Korem","email":"tal.korem@columbia.edu","institution":"Columbia University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"10c2907d8a824dd7897cd42eb18b0487","id":"506"}, {"dataset":"MSV000098762","datasetNum":"98762","title":"Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells","user":"indranil_ohsu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754601134000","created":"Aug. 7, 2025, 2:12 PM","description":"The local microenvironment plays a critical role in determining cellular phenotype. While responses to many individual ligands have been well characterized, the integration of multiple extracellular signals into a cohesive molecular and phenotypic response remains largely unexplored. Here, we systematically investigate the combinatorial effects of Oncostatin M, Transforming Growth Factor Beta 1, and Epidermal Growth Factor on MCF10A mammary epithelial cells. Live-cell imaging revealed that ligand combinations produce emergent phenotypic responses distinct from single-ligand treatments, suggesting induction of new molecular programs. RNA sequencing showed synergistic upregulation of genes involved in migration and chemotaxis, including CXCL3 and CXCL5. Partial least squares regression identified transcriptional signatures associated with cellular phenotypes quantified from image data, which we validated in independent datasets. Finally, functional analysis revealed that synergistic upregulation of CXCR2 signaling, mediated by CREB activation, contributes to increased cell motility. This study provides a framework for understanding how complex ligand interactions shape phenotypic and molecular landscapes.","fileCount":"34","fileSizeKB":"25685399","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cell Signaling, Microenvironment, Cell Migration, Pathway Integration, Cytokine;DatasetType:Proteomics","pi":[{"name":"Laura M. 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Upon activation, macrophages increase glycolysis producing the antibacterial aldehyde methylglyoxal. To test if bacterial methylglyoxal resistance is required for robust infections, we sought to identify Mycobacterium tuberculosis defense mechanisms against methylglyoxal. We identified phoP mutants were among the most highly sensitive strains to methylglyoxal in vitro. phoP mutants are attenuated in mice but were even more attenuated in mice that accumulate methylglyoxal. We further found phoP bacilli exhibited increased membrane permeability and were more permeable to methylglyoxal. Suppressor mutations in the fatty acid Beta-oxidation genes fadE25 or fixB restored impermeability and resistance to methylglyoxal to a phoP mutant. Together, our data show that a major virulence role for PhoP is to provide Mycobacterium tuberculosis resistance to methylglyoxal toxicity in vivo by regulating cell envelope integrity. The mass spectrometry files supporting this hypothesis are deposited here.","fileCount":"701","fileSizeKB":"106153077","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium tuberculosis H37Rv (NCBITaxon:83332)","instrument":"timsTOF HT","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"Mycobacterium tuberculosis;methylglyoxal;aldehyde;pathogenesis;fatty acid oxidation;DatasetType:Proteomics","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyumc.org","institution":"NYU School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc7e3479d4364dee951b60a2d5632f16","id":"509"}, {"dataset":"MSV000098758","datasetNum":"98758","title":"The secretion of Pseudomonas unconventional peroxidase facilitates extracellular carbon acquisition from heterogeneous lignin","user":"lcy7528","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754565968000","created":"Aug. 7, 2025, 4:26 AM","description":"To investigate the potential interactions of DypB3152 with additional T6SS0137 components, co-immunoprecipitation mass spectrometry (coIP-MS) was performed in P. putida A514, carrying the FLAG-tagged DypB3152 vector, while A514 with the FLAG-tagged vector acted as the control ","fileCount":"7","fileSizeKB":"2004905","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas putida","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"co-IPMS;DatasetType:Metabolomics","pi":[{"name":"Liang Congying","email":"cyliang0819@163.com","institution":"Shandong University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4b621dc80f5c40f7bdc059e72d3e03ec","id":"510"}, {"dataset":"MSV000098757","datasetNum":"98757","title":"Targeted isolation of prenylated flavonoids from Paulownia tomentosa fruit extracts via AI-guided workflow integrating LC-UV-HRMS\/MS","user":"christophb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754554637000","created":"Aug. 7, 2025, 1:17 AM","description":"The raw data supporting manuscript entitled Targeted isolation of prenylated flavonoids from Paulownia tomentosa fruit extracts via AI-guided workflow integrating LC-UV-HRMS\/MS. Data contain LC-UV-HRMS\/MS analysis of pre-fractionated chloroform portion of ethanolic extract from immature fruits of P. tomentosa using custom AcquireX workflow with 4 iterations to acquire fragmentation data in negative polarity mode with HCD 20, 30, 40 eV. Moreover LC-HRMS polarity switching data for confirmation of isolated compounds is provided.","fileCount":"86","fileSizeKB":"9945167","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Paulownia tomentosa (Thunb.) Steud. 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Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA)","fileCount":"175","fileSizeKB":"4131215","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mouse;fecal;BSH;DatasetType:Metabolomics","pi":[{"name":"Amir Zarrinpar","email":"azarrinpar@ucsd.edu","institution":"University of California San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b649cc213f234b49bd1871bec7a78014","id":"513"}, {"dataset":"MSV000098743","datasetNum":"98743","title":"Shotgun proteomics of cell lysates and absolute quantification of E. coli, Z. mobilis, C. thermocellum glycolytic proteins","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754492251000","created":"Aug. 6, 2025, 7:57 AM","description":"For E. coli, C. thermocellum, Z. mobilis: shotgun proteomics analyses of tryptic digests of cell lysates; direct infusion of cell lysates spiked with isotopically labelled peptides to perform absolute quantification of specific proteins of interest, primarily related to glycolysis ","fileCount":"74","fileSizeKB":"41955817","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Zymomonas mobilis (NCBITaxon:542);Clostridium thermocellum","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"proteomics;absolute quantification;DatasetType:Proteomics","pi":[{"name":"Daniel Amador-Noguez","email":"amadornoguez@wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"},{"name":"Joshua Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fe8160b5de1c402fb221cb0beaa06d9b","id":"514"}, {"dataset":"MSV000098740","datasetNum":"98740","title":"Proteomic analysis of a murine model of extreme aging (DDA) ","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754484277000","created":"Aug. 6, 2025, 5:44 AM","description":"This is a second repository for a multi-organ investigation of a murine model of extreme aging. This repository features data that was acquired in DDA (pasef) mode using a 60SPD method on a TIMSTOF Flex mass spectrometer coupled to an EvoSep One system. DDA files were used to investigate high abundance protein post-translational modifications which were difficult to examine in the diaPASEF studies. ","fileCount":"2958","fileSizeKB":"277912640","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Aging;Extreme aging;Multi-organ aging;DatasetType:Proteomics","pi":[{"name":"Ben Orsburn","email":"orsburn@pitt.edu","institution":"University of Pittsburgh","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"84dbafc2b8f746b99ea44c738c9b2eae","id":"515"}, {"dataset":"MSV000098739","datasetNum":"98739","title":"Trajectories of microbiome derived bile acids in early life insights into the progression to islet autoimmunity ","user":"Lamichhane2025","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754459498000","created":"Aug. 5, 2025, 10:51 PM","description":"Here, we analyzed early life MCBA patterns and their link to islet autoimmunity. We quantified 110 MCBAs in 303 stool samples collected longitudinally (3 to36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody negative. ","fileCount":"305","fileSizeKB":"55383926","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acid;Microbiome;Gut;Diabetes;Type 1 Diabetes;DatasetType:Metabolomics","pi":[{"name":"Santosh Lamichhane","email":"santosh.lamichhane@utu.fi","institution":"University of Turkuy","country":"Finland"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"91f6ba939ef642779869c0709eee8d10","id":"516"}, {"dataset":"MSV000098734","datasetNum":"98734","title":"Raw Data for Anthocyanin identification from mixed flavonoid populations in flowers by positive and negative mode LCMSMS","user":"kscampos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754428749000","created":"Aug. 5, 2025, 2:19 PM","description":"Anthocyanin identification from mixed flavonoid populations in flowers by positive and negative mode LC-MS\/MS. This data set includes the raw files for methanolic extracts of Clitoria ternatea and Viola sororia run in LC-MS\/MS which we obtained for the purpose of qualitatively identifying anthocyanin and flavonol molecules present in such flowering plants. Extracted pigment samples were analyzed using a Waters (Milford, Massachusetts) Xevo TQ Absolute UPLC-MS\/MS system with ACQUITY (Milford, Massachusetts) UPLC Premier. Compound separation was performed using an ACQUITY PREMIER CSH Phenyl-Hexyl column (1.7 uM VanGuard Fl 2.1 x 50 mm Column) with a column temperature set to 50 C. Mobile phase A was composed of 0.1% formic acid from Macron (Radnor, Pennsylvania) and mobile phase B was 100% acetonitrile, LC\/MS grade from Fisher Scientific (Fair Lawn, New Jersey). The flow rate was set to 0.4 mL\/min and the gradient was non linear with composition as follows: 0-2 min, 0-10% B; 3-23 min, 10-40% B; 23-26 min, 40-100% B; 28-30 min, 100-0% B. Electrospray ionization was employed in both positive and negative modes. Time of- flight mass spectra in the m\/z range 100- 1200 and MS\/MS scans in the m\/z range 50- 2000 were obtained with fast data-dependent acquisition in centroid mode. Other mass spectrometry conditions were all as follows: nitrogen gas temperature, 350 C; drying gas flow rate, 800 L\/hr; cone gas, 50 L\/hr; cone voltage, 75 V; capillary voltage, 3 kV (positive mode) and 2 kV (negative mode); and collision energy, 10- 100 V. The mass axis was calibrated using a solution of sodium formate clusters ranging from 50-2000 Da. The instrument was calibrated real time with internal calibrant (LockSpray Leucine-Enkephalin Single Point MS) every 10 seconds.","fileCount":"266","fileSizeKB":"5388363","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"viola sororia;Clitoria ternatea (NCBITaxon:43366)","instrument":"Xevo TQ MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"anthocyanins;Viola sororia;Clitoria ternatea;cyanidin;delphinidin;myricetin;pigments;DatasetType:Metabolomics","pi":[{"name":"Rachel W. Martin","email":"rwmartin@uci.edu","institution":"University of California Irvine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"42d659d908fe4279b283cbad9fafb5a1","id":"517"}, {"dataset":"MSV000098732","datasetNum":"98732","title":"Zebrafish exposed to N-ethyl pentedrone - Neurotoxicity based on toxicometabolomics ","user":"AleGodoi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754426195000","created":"Aug. 5, 2025, 1:36 PM","description":"Zebrafish were exposed to a synthetic cathinone, called N-ethyl pentedrone. Their brains were dissected and the metabolites were extracted with ice-cold methanol added to IS (MDMA-d5).","fileCount":"26","fileSizeKB":"7439973","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"LCMS-9030","modification":"NA","keywords":"N-ethyl pentedrone;Zebrafish;Metabolomics;Brain;New psychoactive substances;DatasetType:Metabolomics","pi":[{"name":"Alexandre Barcia de Godoi","email":"a165201@dac.unicamp.br","institution":"UNICAMP","country":"Brasil"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"694a5b55a35c4d3e935f99ef1df505cf","id":"518"}, {"dataset":"MSV000098730","datasetNum":"98730","title":"Enabling spatial metabolomics and spatial proteomics from the same tissue section","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754414513000","created":"Aug. 5, 2025, 10:21 AM","description":"We developed a workflow for comprehensive multi-omics profiling from a single tissue section (STS) using different mass spectrometry (MS)-modalities. We addressed key challenges associated with the need for serial sections and substrate incompatibilities between the modalities. We enhanced the functionality of an insulative substrate by employing metal-assisted approach, enabling its integration into dual applications for metabolite and proteomics imaging from STS using complementary MS-techniques. This allows for metabolite imaging using matrix-assisted laser desorption\/ionization-MS imaging (MALDI-MSI) while preserving its compatibility for subsequent proteome profiling with laser capture microdissection (LCM)-based MS technology. Peptides were identified using DIA-NN.","fileCount":"114","fileSizeKB":"104546176","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Populus trichocarpa (NCBITaxon:3694)","instrument":"Orbitrap Astral","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"spatial multi-omics;single tissue section;DatasetType:Proteomics","pi":[{"name":"Dusan Velickovic","email":"dusan.velickovic@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"f3e94ed8e1134f21bf796409be01d529","id":"519"}, {"dataset":"MSV000098728","datasetNum":"98728","title":"Overexpression of the signaling-coordinator GAB2 can play an important role in Acute Myeloid Leukemia progression","user":"saimukund","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754411803000","created":"Aug. 5, 2025, 9:36 AM","description":"Label free quantification (LFQ) proteomics experimental data from a study of murine acute myeloid leukemia (AML) that spontaneously develops in mice with Dnmt3aR878H\/+ x Npm1cA\/+ bone marrow. These mice spontaneously develop myelomonocytic AML in 6-15 months. We characterized pre-leukemic bone marrow samples, and 11 independent spontaneous AMLs that developed in these doubly-mutant mice (\"mAML1-11\").10 of 11 AMLs contained an amplification of murine chromosome 7 (chr7), usually as the only structural variant. Furthermore, we identified two non-leukemic mice where whole genome sequencing revealed amplification of chromosome 7 (+7) and no other cooperating mutations in identifiable driver genes (pre-tumor, +7 only). One of these clonal expansions was tested twice in secondary transplant assays, and did not commonly yield fatal disease when transplanted into recipients, suggesting that +7 is an intermediate step in AML progression. Further experiments identified Gab2 as an important gene on chromosome 7 for AML pathogenesis in this model. Retroviral overexpression of Gab2 in Dnmt3aR878H\/+ x Npm1cA\/+ bone marrow led to expansion of bone marrow cells both in vitro and in vivo in transplanted, recipient mice, as well as to accelerated development of AML; the resulting AML samples are called GAB2 mAML in this dataset. Measurements were performed from bulk bone marrow of mice. Data can be explored further at mAML.leylab.org. Note that data uploaded here were analyzed using the publicly available FragPipe software, with full workflow details available for download. In the JCI publication in press and on the mAML.leylab.org website, data were analyzed as described in the methods section, with expected slight variation in the protein quantification results. The conclusions presented in the publication are supported by both analyses. ","fileCount":"372","fileSizeKB":"1747927682","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Pro","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:26 - \\\"S-carbamoylmethylcysteine cyclization (N-terminus).\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"acute myeloid leukemia;AML;DatasetType:Proteomics","pi":[{"name":"Timothy J. Ley","email":"timley@wustl.edu","institution":"Washington University in St. Louis","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e077cdd60abc4d4a8c6e3cb283fa754c","id":"520"}, {"dataset":"MSV000098727","datasetNum":"98727","title":"Zebrafish larvae proteome after exposure to tramadol and o-desmethyltramadol: raw data","user":"PedroR","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754410924000","created":"Aug. 5, 2025, 9:22 AM","description":"The presence of pharmaceuticals in natural habitats is an increasing concern. In particular, the antidepressant tramadol (TRA) and its metabolite o-desmethyltramadol (OTRA). However, investigation of their impact on fish, particularly on their proteome, still needs attention. \r\nZebrafish larvae were exposed to 0.1 or 100 ug\/L of TRA or OTRA until reaching 168 hpf. The larvae proteome was then investigated through shotgun proteomics, employing the filter-aided sample preparation method (FASP) followed by high-throughput LC-MS\/MS analysis. The work was partially supported by SIGNAL (COMPETE2030-FEDER-00877500, funded by Programa Inovação e Transição Digital (COMPETE 2030), Portugal 2030 and the Foundation for the Science and Technology (FCT), and by UIDB\/04423\/2020 and UIDP\/04423\/2020 programmes. Pedro Rodrigues was supported through FCT (2023.09236.CEECIND\/CP2848\/CT0003,https:\/\/doi.org\/10.54499\/2023.09236.CEECIND\/CP2848\/CT0003). Alexandre Campos and Mário Jorge Araújo also acknowledge the funding by for the Scientific Employment Stimulus Program (CEECIND\/03767\/2018 and CEECIND\/CP2848\/CT0005, https:\/\/doi.org\/10.54499\/2023.06491.CEECIND\/CP2848\/CT0005, respectively).","fileCount":"2","fileSizeKB":"14656974","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Danio rerio;Shotgun proteomics;Tramadol;O-desmethyltramadol;DatasetType:Proteomics","pi":[{"name":"Alexandre Campos","email":"acampos@ciimar.up.pt","institution":"CIIMAR","country":"Portugal"},{"name":"Antonio Paulo Carvalho","email":"apcarval@fc.up.pt","institution":"Faculty of Sciences Porto University","country":"Portugal"},{"name":"Luis Oliva Teles","email":"loteles@fc.up.pt","institution":"Faculty of Sciences Porto University","country":"Portugal"},{"name":"Maria V Turkina","email":"maria.turkina@liu.se","institution":"Linkopings University","country":"Sweden"},{"name":"Mario Jorge Araujo","email":"mario.araujo@ciimar.up.pt","institution":"CIIMAR","country":"Portugal"},{"name":"Pedro Rodrigues","email":"prodrigues@ciimar.up.pt","institution":"CIIMAR","country":"Portugal"},{"name":"laura Guimaraes","email":"guimlid@gmail.com","institution":"CIIMAR","country":"Portugal"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"904f0015403147f28c861d827bb2d68f","id":"521"}, {"dataset":"MSV000098726","datasetNum":"98726","title":"Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex","user":"mazurkiewicz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754407179000","created":"Aug. 5, 2025, 8:19 AM","description":"LC-MS\/MS data associated with: \"Yeonji Chung, Chewon Yim, Gilberto P. Pereira, Sungjoon Son, Lisbeth R. Kjoelbye, Lauren E. Mazurkiewicz, Amy M. Weeks, Friedrich Foerster, Gunnar von Heijne, Paulo C.T. Souza, Hyun Kim; Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex. 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We report that KIF13B regulates ciliary protein composition and EV shedding in cultured kidney epithelial cells, with effects that vary over time. In early stages of ciliation, Kif13b-\/- cells aberrantly accumulate PC2, FLOT1, and HGS within cilia. These cells also produce fewer small EVs through the GW4869-sensitive, nSMase2 pathway, and release large EVs enriched with CCDC198 and the centriole distal appendage protein CCDC92, which also localizes to the ciliary tip. Upon cilia maturation, Kif13b-\/- cells accelerate large EV release of numerous ciliary proteins, including PC2, BBSome components, and IFT proteins, which correlates with gradual depletion of CCDC92 and PC2 from the ciliary tip and shaft, respectively. Furthermore, over time, Kif13b-\/- cells show an upregulation in the release of small EVs, which differ in composition from wild-type small EVs. Specifically, the mutant small EVs lack several proteins that are enriched in small EVs from BBSome-deficient cells, such as the palmitoyl transferase ZDHHC5, which localizes to cilia, accumulates within cilia of BBSome-deficient cells, and regulates ciliary length and PC2 levels. Collectively, our work suggests that KIF13B acts at the level of centriole distal appendages to limit ciliary protein entrance and promote endocytic retrieval downstream of the BBSome. Furthermore, this study is the first to show that CCDC198 and ZDHHC5 localize to primary cilia, suggesting they are potential novel candidates for ciliopathies.","fileCount":"1765","fileSizeKB":"103306894","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Ultra 2","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\"","keywords":"DIA;Proteomics;Cilia;Extracellular Vesicle;KIF13B;DatasetType:Proteomics","pi":[{"name":"Karsten Boldt","email":"karsten.boldt@uni-tuebingen.de","institution":"Eberhard-Karls Universitaet Tuebingen","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066965","task":"63a217b8b4a04d43a964a1e6691836fc","id":"523"}, {"dataset":"MSV000098721","datasetNum":"98721","title":"GNPS-Guizhou university-soil Metabonomics","user":"wsw090215","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754366257000","created":"Aug. 4, 2025, 8:57 PM","description":"Soil samples were extracted with 2 mL of pre-cooled 50% methanol solution extraction solvent containing 0.1% formic acid,freeze-dry,separated by ACQUITY UPLC HSS T3 column and analyzed by positive and negative mode mass spectrometry","fileCount":"112","fileSizeKB":"11669298","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"unkown;environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"soil metabonomics;DatasetType:Metabolomics","pi":[{"name":"ShuWei Wu","email":"1543975837@qq.com","institution":"Guizhou university","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fe493ffb118c4ddaa03d3a6587dcfb9e","id":"524"}, {"dataset":"MSV000098719","datasetNum":"98719","title":"Overexpression of the signaling-coordinator GAB2 can play an important role in Acute Myeloid Leukemia progression","user":"saimukund","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754342872000","created":"Aug. 4, 2025, 2:27 PM","description":"Tandem-mass-tag (TMT) proteomics experimental data from a study of murine acute myeloid leukemia (AML) that spontaneously develops in mice with Dnmt3aR878H\/+ x Npm1cA\/+ bone marrow. These mice spontaneously develop myelomonocytic AML in 6-15 months. We characterized pre-leukemic bone marrow samples, and 11 independent spontaneous AMLs that developed in these doubly-mutant mice (\"mAML1-11\").10 of 11 AMLs contained an amplification of murine chromosome 7 (chr7), usually as the only structural variant. Furthermore, we identified two non-leukemic mice where whole genome sequencing revealed amplification of chromosome 7 (+7) and no other cooperating mutations in identifiable driver genes (pre-tumor, +7 only). One of these clonal expansions was tested twice in secondary transplant assays, and did not commonly yield fatal disease when transplanted into recipients, suggesting that +7 is an intermediate step in AML progression. Further experiments identified Gab2 as an important gene on chromosome 7 for AML pathogenesis in this model. Retroviral overexpression of Gab2 in Dnmt3aR878H\/+ x Npm1cA\/+ bone marrow led to expansion of bone marrow cells both in vitro and in vivo in transplanted, recipient mice, as well as to accelerated development of AML; the resulting AML samples are called GAB2 mAML in this dataset. Measurements were performed from bulk bone marrow of mice. Data can be explored further at mAML.leylab.org. Note that data uploaded here were analyzed using the publicly available FragPipe software, with full workflow details available for download. In the JCI publication and on the mAML.leylab.org website, data were analyzed as described in the methods section, with expected slight variation in the protein quantification results. The conclusions presented in the publication are supported by both analyses.\r\n","fileCount":"519","fileSizeKB":"97343609","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:26 - \\\"S-carbamoylmethylcysteine cyclization (N-terminus).\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"AML;acute myeloid leukemia;DatasetType:Proteomics","pi":[{"name":"Timothy J. Ley","email":"timley@wustl.edu","institution":"Washington University in St. Louis","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066949","task":"fd06a7462c554038b5a1e932c3221fdb","id":"525"}, {"dataset":"MSV000098717","datasetNum":"98717","title":"LC-MS\/MS Kynurenine pathway data miR-132KO","user":"HebertSH","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754320655000","created":"Aug. 4, 2025, 8:17 AM","description":"Raw data from LC-MS\/MS analysis of kynurenine pathway metabolites in miR-132KO and WT mice treated or not with LPS for 24h.","fileCount":"4","fileSizeKB":"43","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Acquity TQ-XS, Waters, Milford, MA","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"miR-132;QUIN;KMO;DatasetType:Metabolomics","pi":[{"name":"Sebastien hebert","email":"Sebastien.Hebert@crchudequebec.ulaval.ca","institution":"CHUL Quebec","country":"Canada"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD066936","task":"edca5b9f59c6462398e3ea66a497797f","id":"526"}, {"dataset":"MSV000098714","datasetNum":"98714","title":"Targeted LC-MS\/MS with non-annotated m\/z-features in MetE CRISPRi strain","user":"JRapp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754296147000","created":"Aug. 4, 2025, 1:29 AM","description":"A FI-MS screen identified accumulating m\/z-features in E. coli metE CRISPRi strain which cannot be annotated as iML1515 metabolites. These m\/z-features were measured via targeted LC-MS\/MS and strcuture elucidation was performed via SIRIUS.","fileCount":"55","fileSizeKB":"356479","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"6546 Q-TOF LC\\\/MS (Agilent instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Non-canonical E. coli metabolites;CRISPRi;DatasetType:Metabolomics","pi":[{"name":"Prof. Hannes Link","email":"hannes.link@uni-tuebingen.de","institution":"University Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"96973cdc0a814ac3ba608cf7a3f56578","id":"527"}, {"dataset":"MSV000098713","datasetNum":"98713","title":"Proteomic Profiling of Conventional and Cultured Chicken Meat","user":"helen259","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754295836000","created":"Aug. 4, 2025, 1:23 AM","description":"This project aimed to compare the proteomic profiles between conventional chicken meat and cultured chicken meat produced through cell culture techniques. Proteins were extracted, separated using SDS-PAGE and two-dimensional gel electrophoresis (2-DE), and identified through mass spectrometry. KEGG pathway enrichment and STRING-based protein-protein interaction network analyses were performed to evaluate metabolic characteristics and structural differences between the groups. Conventional meat exhibited a high abundance of glycolytic and muscle contraction-associated proteins, while cultured meat showed elevated expression of proteins involved in stress response and redox regulation. These datasets provide fundamental insights for improving the quality and ensuring the safety of cultured meat products.","fileCount":"211","fileSizeKB":"3151735","spectra":"60486","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gallus gallus (NCBITaxon:9031)","instrument":"nanoACQUITY UPLC;LTQ Orbitrap XL","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Cultured meat, Conventional meat, Proteomics, 2-DE analysis, Mass spectrometry, Protein identification;DatasetType:Proteomics","pi":[{"name":"IHyeon Cho","email":"mukuro259@gmail.com","institution":"SangMyung University","country":"South Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066918","task":"380de88b859a4269b7d4065573509291","id":"528"}, {"dataset":"MSV000098712","datasetNum":"98712","title":"FI-MS analysis of E. coli CRISPRi library","user":"JRapp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754287095000","created":"Aug. 3, 2025, 10:58 PM","description":"In this study, we measured the metabolome response of 1,515 CRISPR interference (CRISPRi) E. coli strains targeting all genes in the iML1515 metabolic model with flow-injection mass spectrometry.","fileCount":"6056","fileSizeKB":"3905351238","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"6546 Q-TOF LC\\\/MS (Agilent instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CRISPRi;FI-MS;E. coli;DatasetType:Metabolomics","pi":[{"name":"Prof. Hannes Link","email":"hannes.link@uni-tuebingen.de","institution":"University Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"fbef5a72b6d543d7a903af9f8a7c49b0","id":"529"}, {"dataset":"MSV000098710","datasetNum":"98710","title":"Liver tissue proteomics with TMT-based quantification","user":"bangree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754225197000","created":"Aug. 3, 2025, 5:46 AM","description":"Liver tissue proteomics with TMT-based quantification","fileCount":"61","fileSizeKB":"39731083","spectra":"622047","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral Zoom","modification":"UNIMOD:35 - 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This includes collection of iterative DDA LC-QTOF MS\/MS data and DIA LC-IMS-MS\/MS data from Agilent 6560 drift tube IMS platform, and DDA LC-MS\/MS data from Orbitrap Lumos platform. Samples include lipid extracts from a set of Comparative Reference (CompRef) materials of protemomics and metabolomics studies by by the Clinical Proteomic Tumor Analysis Consortium, which were patient-derived xenograft (PDX) tumor samples from established basal and luminal breast cancer intrinsic subtypes that were grown in mice. NIST SRM 1950 plasma was also included as a QC sample for test and method optimization.","fileCount":"1941","fileSizeKB":"98075695","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"6560 Q-TOF LC\\\/MS;Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics;mass spectrometry;ion mobility spectrometry;Data-dependent acquisition;Data-independent acquisition;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Xueyun Zheng","email":"xueyun.zheng@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"eef7361fa490451e8def7612c94a58cf","id":"532"}, {"dataset":"MSV000098701","datasetNum":"98701","title":"GNPS Maloney lab LCMS Data 073125","user":"malonekn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1754014468000","created":"Jul. 31, 2025, 7:14 PM","description":"Citrus and soil bacterial extracts and fractions, plus media controls from Summer 2025 [doi:10.25345\/C5FB4X02N] [dataset li","fileCount":"1715","fileSizeKB":"21949203","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not applicable","instrument":"6538 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Citrus bacteria;DatasetType:Metabolomics","pi":[{"name":"Katherine Maloney","email":"kmaloney@pointloma.edu","institution":"Point Loma Nazarene University - San Diego, CA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9795b3ea6f464dcc84ae85a810883191","id":"533"}, {"dataset":"MSV000098695","datasetNum":"98695","title":"Data files for Theta nanoESI emitters with solution additives","user":"ebaezbol","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753926194000","created":"Jul. 30, 2025, 6:43 PM","description":"The files contain the data used for the manuscript with the title: Improved Mass Analysis of Proteins and Protein Complexes Present in Common Biological Buffers and Physiological Concentrations of NaCl Using Solution Additives Delivered by Theta Emitters. A description about the integration time is also attached. Note: the 5600 used in this work was modified for ion\/ion reactions.","fileCount":"88","fileSizeKB":"5550523","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"TripleTOF 5600","modification":"not applicable","keywords":"Native ESI-MS, non-volatile salts, theta emitter, biological buffers, protein analysis, solution additives;DatasetType:Proteomics","pi":[{"name":"Scott McLuckey","email":"mcluckey@purdue.edu","institution":"Purdue University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f5477c1fe0fa43968b3a822b21b1e3ea","id":"534"}, {"dataset":"MSV000098694","datasetNum":"98694","title":"Microscaled Cell Surface Proteomics for Cryo-preserved Cells and Tissue Samples","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753912540000","created":"Jul. 30, 2025, 2:55 PM","description":"Cell surface proteins (CSPs) regulate key cellular functions and represent valuable targets for diagnostics and therapeutics. Despite advances in proteomic workflows, CSP analysis from cryopreserved or low-input clinical samples remains limited by technical constraints, including reduced membrane integrity, inefficient labeling, and high background. To address these challenges, we optimized and benchmarked two complementary surface enrichment strategies compatible with low-input applications (fewer than 1 million cells) and real-world sample types, including fresh, viably cryopreserved, and dissociated solid tissues.\nWe systematically compared oxidation-based N-glycoprotein capture and WGA-HRP-mediated proximity labeling across a range of input amounts using both solid tumor (A549) and \nhematologic cancer (KMS-12-BM) cell lines. The N-glycopeptide method yielded superior specificity in low-input contexts, while WGA-HRP captured complementary CSP subsets. Together, the methods identified more than 700 CSPs, with approximately 175 unique identifications per protocol. Both workflows detected dynamic EGFR internalization following EGF stimulation and maintained high reproducibility (Pearson correlation greater than 0.9) between fresh and cryopreserved preparations.\nTo extend these findings to tissue-derived samples, we optimized dissociation protocols for healthy endometrium and applied the N-glycopeptide method to cryopreserved dissociated endometrium from three healthy donors. Enzymatic dissociation enabled accurate CSP profiling from fewer than 1 to 2 million cells.\nThis study provides a systematic comparison of two leading surface proteomics approaches, validates their performance on cryopreserved and low-input specimens, and demonstrates applicability to clinically relevant tissues. 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Plasma and Urine samples were extracted using cold methanol (9:1, v\/v), and urine samples were pretreated with urease prior to extraction.","fileCount":"587","fileSizeKB":"15446245","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"GC-MS;LC-qTOF-MS","modification":"no","keywords":"Metabolomics, Cardiopulmonary Bypass, Hypothermia, Plasma, Urine, Biomarkers;DatasetType:Metabolomics","pi":[{"name":"Oguzhan Durmaz","email":"durmazogz@gmail.com","institution":"Ankara University ","country":"Turkey"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b8b3dfbb67bb4e279982862d0acb13c1","id":"538"}, {"dataset":"MSV000098690","datasetNum":"98690","title":"Top-Down Individual Ion Mass Spectrometry Reveals 85-110 kDa Catenin Phospho-Proteoforms Regulated by Actomyosin Contractility","user":"jfhorner","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753904864000","created":"Jul. 30, 2025, 12:47 PM","description":"Data associated with the manuscript \"Top-Down Individual Ion Mass Spectrometry Reveals 85-110 kDa Catenin Phospho-Proteoforms Regulated by Actomyosin Contractility\"","fileCount":"33","fileSizeKB":"35732769","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Orbitrap Eclipse;Orbitrap Ascend","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Catenins;Top-Down Proteomics;Individual Ion Mass Spectrometry;Proteoforms;DatasetType:Proteomics","pi":[{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2a94f6861d074acf89c6ed6e54a4ffb0","id":"539"}, {"dataset":"MSV000098688","datasetNum":"98688","title":"Exhaled breath from conventional and conventionalized mice","user":"AmaliaBerna","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753896232000","created":"Jul. 30, 2025, 10:23 AM","description":"This is GCxGC MS data from exhaled breath from conventional and conventionalized mice as well as germ-free controls. 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However, hmC can co-exist with C and mC in different combinations in the two strands of CpG dyads, such as hmC\/C, hmC\/mC, or hmC\/hmC, and it is poorly understood, how these combinatorial marks differ in their protein interactomes and regulatory functions.\nTo systematically identify nuclear proteins that bind to distinct hmC-containing CpG dyads, we conducted DNA pulldown experiments using promoter probes harboring defined dyad modifications. In this study, we used nuclear extracts from mouse brain tissue and a DNA probe based on part of the Sp1 promoter sequence. For each dyad configuration, C\/C, mC\/mC, hmC\/mC, hmC\/C, and hmC\/hmC, five technical replicates were performed.","fileCount":"43","fileSizeKB":"84191585","spectra":"918348","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cytosine modifications, nuclear binding proteins, interaction proteomics, bottom-up proteomics;DatasetType:Proteomics","pi":[{"name":"Petra Janning","email":"petra.janning@mpi-dortmund.mpg.de","institution":"MPI of Molecular Physiology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066764","task":"10de2db29b6648d78defa1bcbc9b782a","id":"543"}, {"dataset":"MSV000098679","datasetNum":"98679","title":"S. elongatus PCC 7942 Limited Proteolysis Structural Proteomics (JM-PB-DP3), TPP-MS-TMT10","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753844553000","created":"Jul. 29, 2025, 8:02 PM","description":"The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus PCC 7942 cell lysates treated across 10 temperatures (37 to 82 deg C in 5 deg C increments, prepared using thermal proteome profiling by mass spectrometry (TPP-MS), and fractionated for TMT10 proteomic analysis. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline, followed by Tandem Mass Tag 10-Plex (TMT10) quantitation using PlexedPiper.","fileCount":"404","fileSizeKB":"137879280","spectra":"0","psms":"4058599","peptides":"740763","variants":"936261","proteins":"5738","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"Cyanobacteria;Light Fluctuation;Structural Proteomics;Redox Proteomics;Thermal Proteome Profiling;Thiol Oxidation;DatasetType:Proteomics","pi":[{"name":"John T. 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Sample data was obtained from S. elongatus PCC 7942 cell lysates treated with pronase (1:200 enzyme:substrate ratio) and prepared using limited proteolysis by mass spectrometry (LiP-MS) for Label-free quantification (LFQ) proteomic analysis. Peptides were identified using FragPipe.","fileCount":"735","fileSizeKB":"126530132","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Cyanobacteria;Light Fluctuation;Structural Proteomics;Redox Proteomics;Limited Proteolysis;Thiol Oxidation;DatasetType:Proteomics","pi":[{"name":"John T. 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Sample data was obtained from S. elongatus PCC 7942 cell lysates treated with different non-specific proteases (1:200 or 1:500 enzyme:substrate ratio) and prepared using limited proteolysis by mass spectrometry (LiP-MS) for global proteomic analysis. Tested proteases include: Proteinase K, Ficin, Thermolysin, Pronase, and\/or Trypsin only. Peptides were identified using MaxQuant.","fileCount":"95","fileSizeKB":"37362702","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Cyanobacteria;Light Fluctuation;Structural Proteomics;Redox Proteomics;Limited Proteolysis;Thiol Oxidation;DatasetType:Proteomics","pi":[{"name":"John T. 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To facilitate comparative lipidomic research across brain-diseases we established a data commons named the Neurolipid Atlas, that we have pre-populated with novel human, mouse and isogenic induced pluripotent stem cell (iPSC)-derived lipidomics data for different brain diseases. We show that iPSC-derived neurons, microglia and astrocytes display distinct lipid profiles that recapitulate in vivo lipotypes. Leveraging multiple datasets, we show that the AD risk gene ApoE4 drives cholesterol ester (CE) accumulation in human astrocytes recapitulating CE accumulation measured in the human AD brain. Multi-omic interrogation of iPSC-derived astrocytes revealed that cholesterol plays a major role in astrocyte interferon-dependent pathways such as the immunoproteasome and major histocompatibility complex (MHC) class I antigen presentation. We show that through enhanced cholesterol esterification ApoE4 suppresses immune activation of astrocytes. Our novel data commons, available at neurolipidatlas.com, provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.","fileCount":"21","fileSizeKB":"91798557","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Alzheimers Disease (AD), Parkinsons disease and Amyotrophic Lateral Sclerosis;iPSCs;ApoE4;Multiomics;DatasetType:Proteomics","pi":[{"name":"Rik van der Kant","email":"r.h.n.vander.kant@vu.nl","institution":"Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam,","country":"The Netherlands"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD066725","task":"c9982b124a224f3f80d16b8c8d0d1ead","id":"547"}, {"dataset":"MSV000098667","datasetNum":"98667","title":"Fibrotic remodeling drives chronic kidney disease in organic acidurias, role of TGFbeta mediated extracellular matrix deposition","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753779008000","created":"Jul. 29, 2025, 1:50 AM","description":"Propionic aciduria (PA uria) and methylmalonic aciduria (MMA uria) are rare inborn errors of metabolism caused by defects in the propionate catabolic pathway. While chronic kidney disease (CKD) is a well-established complication in MMA-uria, renal involvement in PA uria has only come into focus more recently, and the underlying mechanisms remain poorly understood.\nWe investigated human renal epithelial cells from patients with PA uria, MMA uria, and healthy controls under metabolic stress, induced by methylmalonic acid, methylcitric acid, high protein, or isoleucine\/valine enriched media. Proteomic profiling revealed significant enrichment of extracellular matrix (ECM) related pathways in PA uria cells. Both PA uria and MMA uria cells exhibited increased deposition of fibronectin and collagen fibers, which was further amplified under metabolic stress conditions.\nTransforming growth factor beta (TGFbeta) signaling was identified as a key profibrotic pathway. Pharmacological inhibition of the TGFbeta receptor signaling normalized fibronectin and collagen deposition in both PA uria and MMA uria cells. Treatment with losartan, an angiotensin II type 1 receptor blocker known to modulate TGFbeta signaling, also reversed the enhanced ECM deposition.\nThis is the first study to mechanistically link ECM remodeling and TGFbeta signaling to CKD pathogenesis in both PA uria and MMA uria. Our findings highlight fibrotic remodeling as a shared pathogenic feature and suggest that losartan, a widely available and well-tolerated drug, could be repurposed to mitigate renal fibrosis in these disorders.\n","fileCount":"455","fileSizeKB":"130941977","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"propionic acuduria, methylmalonic aciduria, chronic kidney disease, fibrosis, extracellular matrixc, TGF-beta signaling, renal epithelial cells;DatasetType:Proteomics","pi":[{"name":"Dr. Dr. Anke Schumann","email":"anke.schumann@uniklinik-freiburg.de","institution":"Faculty of Medicine, Freiburg University Hospital","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066707","task":"44590705603e4c1fa981a7429ace4131","id":"548"}, {"dataset":"MSV000098666","datasetNum":"98666","title":"The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753774222000","created":"Jul. 29, 2025, 12:30 AM","description":"Lipid changes in the brain have been implicated in many neurodegenerative diseases including Alzheimers Disease (AD), Parkinsons disease and Amyotrophic Lateral Sclerosis. 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To facilitate comparative lipidomic research across brain-diseases we established a data commons named the Neurolipid Atlas, that we have pre-populated with novel human, mouse and isogenic induced pluripotent stem cell (iPSC)-derived lipidomics data for different brain diseases. We show that iPSC-derived neurons, microglia and astrocytes display distinct lipid profiles that recapitulate in vivo lipotypes. Leveraging multiple datasets, we show that the AD risk gene ApoE4 drives cholesterol ester (CE) accumulation in human astrocytes recapitulating CE accumulation measured in the human AD brain. Multi-omic interrogation of iPSC-derived astrocytes revealed that cholesterol plays a major role in astrocyte interferon-dependent pathways such as the immunoproteasome and major histocompatibility complex (MHC) class I antigen presentation. We show that through enhanced cholesterol esterification ApoE4 suppresses immune activation of astrocytes. Our novel data commons, available at neurolipidatlas.com, provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.","fileCount":"25","fileSizeKB":"206253620","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"ApoE4, neurolipids, Alzheimer Disease (AD), Parkinson disease, Amyotrophic Lateral Sclerosis;DatasetType:Proteomics","pi":[{"name":"Rik van der Kant","email":"r.h.n.vander.kant@vu.nl","institution":"Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam,","country":"The Netherlands"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD066703","task":"09239539258a42378fb77e3d90eafbb1","id":"550"}, {"dataset":"MSV000098661","datasetNum":"98661","title":"Neurons Sequester the Cholesterol-Inhibiting TFEB in Oligodendrocyte Cytoplasm to Safeguard Myelination and Neural Function","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753731151000","created":"Jul. 28, 2025, 12:32 PM","description":"Samples ECL1_1260429_F1-F8 are TMT6plex samples fractionated into 8 fractions using the Pierce High pH Reversed-Phase Peptide Fractionation Kit. Samples are optic nerves protein lysates. Channels 126, 127, 128 are control samples (TFEBdPM-Halo) and channels 129, 130, 131 are mutant samples (Mog-Cre; TFEBdPM-Halo).\n\nSamples 1251765_F1-F8 are TMT6plex samples fractionated into 8 fractions using the Pierce High pH Reversed-Phase Peptide Fractionation Kit. Samples are day 14 in vitro differentiated oligodendrocytes protein lysates. Channels 126, 127, 128 are control samples (TFEBdPM-Halo) and channels 129, 130, 131 are mutant samples (Mog-Cre; TFEBdPM-Halo).","fileCount":"49","fileSizeKB":"75499652","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"Myelination;neuron-oligodendrocyte interaction;transcription factor EB;neural circuit function;transcriptional regulation;cholesterol biosynthesis;DatasetType:Proteomics","pi":[{"name":"Lu Sun","email":"lu.sun@utsouthwestern.edu","institution":"UT Southwestern","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a06ea3e2d81f472ebaa4da885be95382","id":"551"}, {"dataset":"MSV000098659","datasetNum":"98659","title":"GNPS - Pisolithus arhizus fruiting bodies dichloromethane methanol extract","user":"mbeniddir","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753726641000","created":"Jul. 28, 2025, 11:17 AM","description":"dichloromethane-Methanol (1:1) extract and fractions obtained from fruiting bodies of Pisolithus arhizus ","fileCount":"6","fileSizeKB":"111751","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pisolithus arhizus","instrument":"Agilent 6546 Qtof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pisolithus arhizus;Macromycete;Pulvinic acid dimers;DatasetType:Metabolomics","pi":[{"name":"Mehdi Beniddir","email":"mehdi.beniddir@universite-paris-saclay.fr","institution":"Universite Paris-Saclay","country":"France"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"e654cba91213444180b7adaf05c739ce","id":"552"}, {"dataset":"MSV000098657","datasetNum":"98657","title":"Spotted hyena lymph node, liver, and lung proteomes","user":"dtabb73","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753703763000","created":"Jul. 28, 2025, 4:56 AM","description":"Proteomics using Draft Genomes: a Case Study in Spotted Hyena\n\nCrocuta crocuta, or spotted hyena, are one of four remaining hyena species, notable for its preference for hunting rather than scavenging. Until 2020, no annotated genome had been published for the species; by 2023, three had been published. These bottom-up proteomes, measured in 2020, were used to evaluate the quality of these three genomes for C. crocuta, establishing that the genome annotation featured by UniProt and NCBI lags behind the alternatives in identification sensitivity.\n\nSample handling and mass spectrometry are detailed in 1330MASS_ANALYTICALREPORT.pdf. Notably, these data were produced with Cys alkylated by MMTS rather than iodoacetamide. The search results come from FragPipe 23, using the \"Shao.faa\" fasta plus contaminants and decoys.\n\nThese shotgun proteomes were collected in roughly three sets. The three \"Test\" experiments (March and July 2020) established the amount of peptides loaded on column and asked how peptide diverse the samples were. The 13 RPLC experiments (August 2020) represented peripheral, head, abdominal, or thoracic lymph nodes (PL, HL, AL, or TL) from three different animals (571, 572, and 575) plus a few liver and lung samples. The 12 \"Fraction\" RAWs (September 2020) represent ten bRPLC fractions of a head lymph node pool. See the QuaMeter.tsv table for more details.\n\nThese animals are the same as were used for RNA-Seq in NCBI PRJNA658551.","fileCount":"164","fileSizeKB":"44594180","spectra":"0","psms":"386256","peptides":"143941","variants":"166520","proteins":"32994","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crocuta crocuta (NCBITaxon:9678)","instrument":"Q Exactive","modification":"MOD:00110 - \\\"A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"DDA;shotgun;DatasetType:Proteomics","pi":[{"name":"David L. Tabb","email":"dtabb@sun.ac.za","institution":"Stellenbosch University","country":"South Africa"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD066654","task":"65b1434dd1fc4d67831814362ad0539e","id":"553"}, {"dataset":"MSV000098653","datasetNum":"98653","title":"Siderophores_Pseudomonas chlororaphis S15","user":"Iriska","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753697748000","created":"Jul. 28, 2025, 3:15 AM","description":"A comprehensive metabolomic profiling of P. chlororaphis S15 under iron-deficient conditions. Untargeted LC-MS\/MS analysis (TripleTOF 5600+ System mass spectrometer (AB Sciex Pte. Ltd., Singapore)). 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Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"afaf24e62cec407189c44bf2003d2bc8","id":"555"}, {"dataset":"MSV000098649","datasetNum":"98649","title":"MAX a label-free proteomics study of the rat dentate gyrus and serum in exercise and middle age","user":"SebastianDH","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753616631000","created":"Jul. 27, 2025, 4:43 AM","description":"Label-free proteomics study of middle age and 8 weeks of voluntary wheel-running exercise in two cohorts of male Sprague-Dawley rats. \n\nThe 2021_11_18 dataset contains n=80 dentate gyrus samples from n=40 rats (n=10 per group; four experimental groups). Each rat produced one dorsal and one ventral dentate section. Pooled QC samples are also included. Samples were analyzed on a Bruker timsTOF Pro in DDA mode connected to an EvoSep One running an 88-minute gradient with the 15 SPD method. Samples were sonicated in 8M Urea + 1M TEAB, reduced with DTT and alkylated with IAA, digested with Promega Seq-grade Porcine Trypsin, and desalted with ZipTips.\n\nThe 2023_02_07 dataset contains serum n=40 samples from the same rats as in 2021_11_18. Pooled QC samples are also included and were used for DDA-based spectral library generation. Sera were depleted of serum albumin, transferrin, and immunoglobulin G (IgG) with a 4.6x100 mm Mouse-3 Multi Affinity Removal Column (Agilent) for high-performance liquid chromatography (HPLC). The column was connected to an Akta Purifier (GE Healthcare\/Amersham Biosciences) HPLC system, running with Unicorn software (version 5.31). Sera were analyzed on a Bruker timsTOF Pro in DIA mode connected to an EvoSep One running a 44-minute gradient with the 30 SPD method. Depleted samples were solubilized in 0.5% Rapigest, reduced with DTT and alkylated with IAA, digested with Promega Seq-grade Porcine Trypsin, and desalted with ZipTips.\n\nThe 2023_05_17 dataset contains n=42 dentate gyrus samples from a second cohort of rats (3 experimental groups). Each rat produced one whole dentate gyrus sample. Pooled QC samples are also included and were used for DDA-based spectral library generation. Samples were analyzed on a Bruker timsTOF Pro in DIA mode connected to an EvoSep One running an 88-minute gradient with the 15 SPD method. Samples were sonicated in 8M Urea + 1M TEAB, reduced with DTT and alkylated with IAA, digested with Promega Seq-grade Porcine Trypsin, and desalted with ZipTips.","fileCount":"84590","fileSizeKB":"1724179360","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"timsTOF Pro","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"aging;exercise;hippocampus;dentate gyrus;serum;LFQ;rodent;middle age;DatasetType:Proteomics","pi":[{"name":"Yvonne Nolan","email":"y.nolan@ucc.ie","institution":"University College Cork","country":"Ireland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066617","task":"1c3f87690d7749dc9173e7259ccd47f9","id":"556"}, {"dataset":"MSV000098647","datasetNum":"98647","title":"GNPS - Metabolomics of E. scolopes hemocytes exposed to magnetonanoparticles","user":"balunaslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753475267000","created":"Jul. 25, 2025, 1:27 PM","description":"Raw data and Metabolomics of hemocytes from the Hawaiian bobtail squid E. scolopes exposed to Vibrio fischeri and magnetic nanoparticles ","fileCount":"143","fileSizeKB":"2970568","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Euprymna scolopes (NCBITaxon:6613)","instrument":"SYNAPT G2-Si","modification":"NA","keywords":"hawaiian bobtail squid, vibrio fischeri, magnetic nanoparticles;DatasetType:Metabolomics","pi":[{"name":"Marcy J. 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We use uMap proximity labeling, distributed throughout chromatin to study how HDAC inhibition alters interactions. We then apply this approach to de-orphan a high throughput screening hit SR1815. We show that SR1815 is a kinase inhibitor that hits CLK proteins and alters RNA splicing. 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Samples consisted of 3-week-old rosette tissue, and were taken across the daily cycle (12L\/12D), specifically at time points ZT0, ZT6, ZT12, and ZT18. This investigation revealed JAZ4 mediated metabolism. 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Samples consisted of 3-week-old rosette tissue and were taken across the daily cycle (12L\/12D), specifically at time points ZT0, ZT6, ZT12, and ZT18. This investigation revealed JAZ4 mediated regulatory pathways. 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MG-132 was applied overnight before sample harvesting. After 48 hours of transfection, the cells were collected, and flag tagged GluA3 along with its interacting proteins were enriched through immunoprecipitation using a rabbit anti flag antibody, and then subjected to mass spectrometric analyses. ","fileCount":"8","fileSizeKB":"23797720","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus (NCBITaxon:10114);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"GluA3;DatasetType:Proteomics","pi":[{"name":"Hui-Lin Pan","email":"huilinpan@mdanderson.org","institution":"MD Anderson Cancer Center","country":"USA"},{"name":"Jiusheng Yan","email":"jyan1@mdanderson.org","institution":"MD Anderson Cancer Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3544d97b3de348468224f992034727d1","id":"568"}, {"dataset":"MSV000098624","datasetNum":"98624","title":"Large-scale multi-omic analysis identifies noncoding somatic driver mutations and nominates ZFP36L2 as a driver gene for pancreatic ductal adenocarcinoma","user":"laufey_a","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753295698000","created":"Jul. 23, 2025, 11:34 AM","description":"Background The identification and characterization of somatic cancer driver mutations in the noncoding genome remains challenging. \r\nObjective To broadly characterize noncoding driver mutations for pancreatic ductal adenocarcinoma (PDAC). \r\nDesign Using mutation calls from whole-genome sequence (WGS) data in PDACs and genome-scale maps of accessible gene regulatory regions in normal- and tumor-derived pancreatic samples, we analyzed enrichment of noncoding mutations in gene regulatory regions relevant to normal- and tumor-derived pancreatic contexts. Functional follow up of potential driver mutations was performed using chromatin interaction analyses, massively parallel reporter assays (MPRA) and targeted analysis of selected noncoding somatic mutations.\r\nResults We first created genome-scale maps of accessible chromatin regions (ACRs) and histone modification marks (HMMs) in pancreatic cell lines and purified pancreatic acinar and duct cells. Integration with whole-genome mutation calls from 506 PDACs revealed 314 ACRs\/HMMs significantly enriched with 3,614 noncoding somatic mutations (NCSMs). Chromatin interaction analysis identified 416 potential target genes and MPRA revealed 178 NCSMs impacting reporter activity (19.45% of those tested). Targeted luciferase validation confirmed negative effects on gene regulatory activity for NCSMs near ZFP36L2 and CDKN2A. For the former, CRISPR interference (CRISPRi) identified ZFP36L2 as a target gene (16.0 - 24.0% reduced expression, P = 0.023-0.0047), and growth inhibition after overexpression of ZFP36L2 (4.1 - 14.1-fold reduction, P = 6.0x10-4 - 3.2x10-3) implicates a possible tumor suppressor function.\r\nConclusion Our integrative approach provides a catalog of potential noncoding driver mutations and nominates ZFP36L2 as a novel PDAC driver gene with a likely tumor suppressor function.\r\n","fileCount":"25","fileSizeKB":"27118430","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Mutations, Pancreatic Cancer, Gene Regulation, Chromatin, Epigenetics.;DatasetType:Proteomics","pi":[{"name":"Laufey Amundadottir","email":"amundadottirl@mail.nih.gov","institution":"NCI\/NIH","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a84cd0e2d7934637bd15cf450dfedee7","id":"569"}, {"dataset":"MSV000098622","datasetNum":"98622","title":"Accounting for longitudinal peak quality metrics with MSstats+ enhances differential analysis in proteomic experiments with data-independent acquisition","user":"karayelozge","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753294607000","created":"Jul. 23, 2025, 11:16 AM","description":"Mass spectrometry-based proteomics with data-independent acquisition benefits\nfrom advanced instrumentation and computational analysis. Despite continued im-\nprovements, the quality of quantification may be poor for some measurements. As\nthe scale of proteomic experiments increases, these poor-quality measurements are\nchallenging to characterize by hand, yet they undermine the detection of differentially\nabundant proteins and the downstream biological conclusions. We introduce MSstats+,\na computational workflow that takes as input not only peak intensities reported by data\nprocessing tools such as Spectronaut, but also quality metrics such as peak shape and\nretention time, as well as longitudinal run order profiles of these metrics. MSstats+\ntranslates these metrics into a single measure of quality, and downweights poor quality\nmeasurements when detecting differentially abundant proteins. The method offers a\nnatural treatment of missing value imputation, weighting the imputed values according\nto the quality metrics in the run. We demonstrate the accuracy of the resulting differ-\nential analysis, as compared to the standard implementations, in four experiments: two\ncustom benchmarking studies with intentionally induced anomalies, a controlled mix-\nture of proteomes, and a large-scale clinical investigation. MSstats+ is implemented in\nthe family of open-source R\/Bioconductor packages MSstats, making it accessible for\nroutine and modular use.","fileCount":"84","fileSizeKB":"453278966","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Astral, DIA, MSstats, clinical proteomics, CSF, K562;DatasetType:Proteomics","pi":[{"name":"Ozge Karayel","email":"karayelo@gene.com","institution":"Genentech","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD066486","task":"fdf984642108451cbdece7303e47f2d2","id":"570"}, {"dataset":"MSV000098618","datasetNum":"98618","title":"Circadian tryptophan metabolism contributes to systemic aryl hydrocarbon activity","user":"ewmorgan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753289629000","created":"Jul. 23, 2025, 9:53 AM","description":"This dataset contains .mzml files used to support our manuscript. It contains LC-MS\/MS analysis of serum, liver, kidney, and heart metabolite extractions. Samples were collected from C57BL6 mice every four hours for 24 hours. Mice were feed restricted to ZT12-ZT24 and fed a semi-purified diet, AIN-93G.","fileCount":"162","fileSizeKB":"113652523","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"ZenoTOF 7600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Tryptophan;AHR;Circadian rhythm;DatasetType:Metabolomics","pi":[{"name":"Gary Perdew","email":"ghp2@psu.edu","institution":"Pennsylvania State University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"86cdc54691d648fc9f563f1116e0f106","id":"571"}, {"dataset":"MSV000098614","datasetNum":"98614","title":"Characterization of a GpsB-associated regulator of PBP1a reveals the organization of the cell wall remodeling complex of Streptococcus pneumoniae","user":"fdelolme","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753275754000","created":"Jul. 23, 2025, 6:02 AM","description":"Class A PBPs (aPBPs) play a key role in the biosynthesis and remodeling of peptidoglycan, the main component of the bacterial cell wall. The human bacterial pathogen Streptococcus pneumoniae produces three aPBPs, which are regulated to maintain the ovoid shape of the bacterium. Although their exact functions remain unclear, evidence suggests that PBP1a and PBP2a activities are closely coordinated. In this study, we elucidated the function of an unknown function protein named GarP (GpsB-associated regulator of PBP1a), in the regulation of PBP1a activity. We showed that GarP localizes to the division septum and its absence leads to morphological defects. We further identified a GpsB-binding motif in GarP as well as in PBP2a, the PG deacetylase PgdA and the muramidase MpgA. Our analysis of genetic and protein interactions, combined with cell imaging, supports a model of a molecular complex that coordinates PG remodeling during S. pneumoniae cell division.","fileCount":"7","fileSizeKB":"629657","spectra":"0","psms":"3062","peptides":"1234","variants":"1445","proteins":"230","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptococcus pneumoniae (NCBITaxon:1313)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"peptidoglycan, cell wall, Streptococcus pneumoniae, cell division and morphogenesis, penicillin-binding proteins;DatasetType:Proteomics","pi":[{"name":"Christophe GRANGEASSE","email":"christophe.grangeasse@cnrs.fr","institution":"MMSB-UMR5086-CNRS","country":"France"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD066468","task":"4821144117e5420b89e91ad83b84a005","id":"572"}, {"dataset":"MSV000098609","datasetNum":"98609","title":"Proteostatic Stress Response is a Mechanistic Driver of T Cell Exhaustion and a New Therapeutic Opportunity for Cancer Immunotherapy ","user":"searleb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753236395000","created":"Jul. 22, 2025, 7:06 PM","description":"Chronic infections and cancer cause T cell dysfunction known as exhaustion due to persistent antigen exposure, suboptimal co-stimulation and a plethora of hostile factors, which dampens protective immunity and limits the efficacy of immunotherapies1-4. The mechanisms behind T cell exhaustion remain poorly understood. Herein, we dissected the proteome of CD8+ exhausted T cells (Tex) across multiple states of exhaustion in the context of both chronic viral infections and cancer. We found that there was a non-stochastic pathway-specific discordance between mRNA and protein dynamics in T effector (Teff) versus Tex cells. We identified a unique proteostatic stress response (PSR) in Tex cells which we termed TexPSR. Contrary to canonical stress responses with reduced protein synthesis5,6, the TexPSR involves increased global translation activity and an upregulation of specialized chaperones, characterized further by the accumulation of protein aggregates, stress granules and autophagy-dominant protein catabolism. We established that disruption of proteostasis alone can convert Teff to Tex cells, and linked TexPSR mechanistically to persistent Akt signaling. Finally, we found that disruption of TexPSR-associated chaperones in CD8+ T cells improved cancer immunotherapy preclinically and demonstrated that high TexPSR feature in T cells in cancer patients confers poor response to immunotherapy clinically. Our findings collectively highlight TexPSR as a hallmark and a mechanistic driver of T cell exhaustion, raising the possibility of targeting proteostasis as a potential novel approach for cancer immunotherapy. ","fileCount":"248","fileSizeKB":"316606809","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"data independent acquisition;T Cell Exhaustion;cancer;proteostasis;DatasetType:Proteomics","pi":[{"name":"Brian C Searle","email":"searle.brian@mayo.edu","institution":"Mayo Clinic","country":"United States"},{"name":"Zihai Li","email":"Zihai.Li@osumc.edu","institution":"The Ohio State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066433","task":"f7b1b7e14b7948fda6a015faedb9f5db","id":"573"}, {"dataset":"MSV000098598","datasetNum":"98598","title":"CSF proteome mapping: Human cerebrospinal fluid LC-MS\/MS, Part 4","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753202089000","created":"Jul. 22, 2025, 9:34 AM","description":"1.6 mL CSF from a pool of 21 neurologically healthy donors was separated into a bound and a depleted fraction using a MARS Hu-14 column. This experiment represents the depleted fraction. Sample was in-solution trypsin digested and resulting peptides were fractionated into 66 fractions by mixed-mode reversed phase anion exchange (MM(RP-AX) using a Promix MP column. Each fraction was analyzed separately by LC-MS\/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to the CSF-PR.","fileCount":"136","fileSizeKB":"75523689","spectra":"1023385","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap;MS:1000031","modification":"MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:01090 - \\\"A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:01047 - \\\"A protein modification that effectively converts an L-lysine residue to a monohydroxylated lysine.\\\"","keywords":"Homo sapiens;Cerebrospinal fluid;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Astrid Guldbrandsen","email":"astrid.guldbrandsen@biomed.uib.no","institution":"PROBE","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000654","task":"258c4117c6314379a24db45bf3d1ba57","id":"574"}, {"dataset":"MSV000098597","datasetNum":"98597","title":"CSF proteome mapping: Human cerebrospinal fluid LC-MS\/MS, Part 2","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753201688000","created":"Jul. 22, 2025, 9:28 AM","description":"3 mL CSF from a pool of 21 neurologically healthy donors was separated into a bound and a depleted fraction using a MARS Hu-14 column. This experiment represents the depleted fraction. Gel separation on a gradient gel (SDS-PAGE) followed and the gel lane was cut into 46 fractions. Each fraction was in-gel trypsin digested and analyzed separately by LC-MS\/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to the CSF-PR.","fileCount":"98","fileSizeKB":"60059292","spectra":"770341","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap;MS:1000031","modification":"MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:01090 - \\\"A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\"","keywords":"Homo sapiens;Cerebrospinal fluid;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Astrid Guldbrandsen","email":"astrid.guldbrandsen@biomed.uib.no","institution":"PROBE","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000652","task":"5580dec958dc4255ab1be71d9dffff7a","id":"575"}, {"dataset":"MSV000098596","datasetNum":"98596","title":"Proteomics of human naive pluripotent and trophoblastic stem cells","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753200884000","created":"Jul. 22, 2025, 9:14 AM","description":"This project aims at identifying missing proteins in naive pluripotent and trophoblastic stem cells in the framework of the human proteome project (HPP). To date, as much as 1343 missing proteins remain to be credibly identified essentially, but not entirely, by mass spectrometry. The present results also constitute a first step towards the identification of potential biological markers for assessing stem cells and early embryo development.","fileCount":"23","fileSizeKB":"13446599","spectra":"0","psms":"249434","peptides":"52886","variants":"67977","proteins":"7302","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Human proteome project;missing proteins;human naive pluripotent and trophoblastic stem cells;DatasetType:Proteomics","pi":[{"name":"Charles Pineau","email":"proteome@univ-rennes1.fr","institution":"Protim Core facility - Irset Inserm U1085 - UAR Biosit CNRS 380 Inserm 018","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD035768","task":"f8777ceb74cf481f9ef56b7fedc2d55a","id":"576"}, {"dataset":"MSV000098595","datasetNum":"98595","title":"GNPS - Metabolites from methylobacterium aquaticum","user":"redghoti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753200103000","created":"Jul. 22, 2025, 9:01 AM","description":"This dataset contains mass spectrometry data from a metabolomics experiment focused on metabolites from a lanthanide-utilizing bacteria known as methylobacterium aquaticum. Lanthanides are used in alcohol dehydrogenation for this species. This run infused metals just prior to ionization to ideally more easily observe potential adducts. From the 2025\/07\/15 run. 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Using ultrasound-assisted extraction, liquid-liquid partitioning, and UHPLC-HRMS\/MS, we created a library of 72 samples screened against Mycobacterium tuberculosis H37Ra. The most active fractions were the non-polar extracts from Indigofera suffruticosa, Tetradenia riparia, and Zingiber zerumbet.\nThrough bioactivity-guided molecular networking, we integrated metabolomic and bioassays data to prioritize and annotate active metabolites, primarily flavonoids. Computational tools (GNPS, SIRIUS, TIMA-R) further enhanced structural prediction and dereplication. This approach offers an efficient strategy to identify known and novel bioactive compounds without requiring exhaustive isolation.","fileCount":"599","fileSizeKB":"156414424","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Indigofera suffruticosa (NCBITaxon:100149);Tetradenia riparia (NCBITaxon:992795);Zingiber zerumbet (NCBITaxon:311405);Davilla nitida (NCBITaxon:640651);Dipteryx punctata (NCBITaxon:1079074);Curatella americana (NCBITaxon:178812);Quassia amara (NCBITaxon:43725)","instrument":"impact II","modification":"mzmine","keywords":"mycobacterium tuberculosis;metabolomics;flavonoids;ethnopharmacology;mass spectrometry;mycobacteria;DatasetType:Metabolomics","pi":[{"name":"Elnur Garayev","email":"elnur.garayev@univ-amu.fr","institution":"Aix-Marseille University","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ff79acf220d04cd897800821ff6077a3","id":"578"}, {"dataset":"MSV000098584","datasetNum":"98584","title":"GNPS - 20250721_Bigelow_dataset_3_samples_245_to_322","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753136014000","created":"Jul. 21, 2025, 3:13 PM","description":"This metabolomics dataset was generated on an Exploris 480, and contains Pellet and Supernatant sample fractions of various Algae samples from the Bigelow Marine Labs. 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Lysate-based cell-free expression (CFE) is an emerging platform for accelerating the discovery and engineering of these natural products. While Escherichia coli cell extracts are widely used for CFE, Streptomyces extracts are believed to offer a more biochemically compatible environment for natural product synthesis. However, current Streptomyces-based CFE systems remain underdeveloped, with protocols that are either strain-specific or not readily scalable. To address these limitations and enable broader access to cell-free natural product biosynthesis, we present a generalizable and simple set of reaction conditions that support high-yield protein expression (180\u2013230?µg\/mL) in lysates derived from Streptomyces venezuelae NRRL B-65422 and Streptomyces lividans TK24. Like Escherichia coli-based systems, these extracts enable iterative and pathway-level biosynthesis, as demonstrated by the production of the polyketide flaviolin and the cyclic dipeptide albonoursin. Notably, the S. lividans lysate outperforms E. coli systems by also supporting the expression and catalytic activity of a (~250?kDa) type I polyketide synthase (T1PKS), producing its corresponding ethyl ketone product, 2-methyl-3-pentanone, without the need for precursor or post-translational modification supplements. To our knowledge, this represents the first demonstration coupling both expression and catalysis of a megasynthase in a Streptomyces-based system, and of a T1PKS in any bacterial extract. By addressing key challenges in the generalizability and scalability of prior Streptomyces CFE, we establish a protocol that enables parallelized evaluation of diverse lysate systems and provide a foundation for high-throughput T1PKS engineering in vitro.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008760) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"9","fileSizeKB":"471660","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces venezuelae NRRL B-65422, Streptomyces lividans TK24","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cell-free expression;natural products;biosynthesis;DatasetType:Metabolomics","pi":[{"name":"Hiroshi Otani","email":"HOtani@lbl.gov","institution":"LBL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"38cdc54c33ae41c3b5175d12974c13c1","id":"580"}, {"dataset":"MSV000098580","datasetNum":"98580","title":"GNPS - Xylaria sp. 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Though the addition of immune checkpoint blockade to carboplatin and etoposide treatment has improved outcome in SCLC patients, SCLC cells finally acquire the ability to evade immunosurveillance and resistance against immune checkpoint blockade. To elaborate molecular mechanisms that mediate SCLC immune evasion, we performed high dimensional profiling of human and murine SCLC specimens. We herein comprehensively analyzed matched human samples of primary and metastatic SCLC and found a loss of MHC-I in SCLC metastases indicating that MHC-I loss mediates SCLC immune evasion. Silencing MHC-I in SCLC cells drastically diminished immune cell infiltration and facilitated the formation of metastasis in mice by circumventing immune surveillance. Using mass spectrometry and phospho-tyrosine kinase analysis, we discovered that ERBB2 signaling suppresses MHC-I expression in SCLC cells and stimulates immune modulating transcripts. Mechanistically, genetic and\/or pharmacologic blockade of the ERBB2 signaling axis was sufficient to induce MHC-I expression and to prevent immune evasion in autochthonous murine SCLC in a STING-dependent manner. Finally, we demonstrate that the ERBB2 signaling axis regulates MHC-I expression on SCLC cells and is critical in maintaining immune evasion in SCLC. Most strikingly, we here uncover synergistic treatment efficacy by combining ERBB2 inhibition with PD-1 blockade eliciting profound responses in preclinical SCLC models and circumventing MHC-I loss under immunotherapy, suggesting this combination for future clinical trials in patients with SCLC.","fileCount":"111","fileSizeKB":"1155684055","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"MOD:00046 - \\\"A protein modification that effectively converts an L-serine residue to O-phospho-L-serine.\\\";MOD:00047 - \\\"A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine.\\\";MOD:00048 - \\\"A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine.\\\"","keywords":"ERBB2;DatasetType:Proteomics","pi":[{"name":"Roland Ullrich","email":"roland.ullrich@uk-koeln.de","institution":"University cologne","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066359","task":"5a606593ce4d487d939daba7aa712771","id":"582"}, {"dataset":"MSV000098577","datasetNum":"98577","title":"GNPS - Feeding experiments of Xylaria sp. 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M56 (NCBITaxon:1495638)","instrument":"Orbitrap Exploris 120","modification":"None","keywords":"Streptomyces;Cytochalasans;Bacterial modifications;DatasetType:Metabolomics","pi":[{"name":"Christine Beemelmanns","email":"christine.beemelmanns@helmholtz-hips.de","institution":"Helmholtz Institute for Pharmaceutical Research Saarland","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1feba891159e4e07a39b79de92297efa","id":"586"}, {"dataset":"MSV000098573","datasetNum":"98573","title":"GNPS - Co-culture Xylaria XSP14 - Streptomyces M56","user":"mariedayras2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753086891000","created":"Jul. 21, 2025, 1:34 AM","description":"Feature-based processing with MZmine2.53 of co-culture extract of Xylaria sp. XSP14 and Streptomyces sp. 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Network created with the .mgf file obtained by the ''batch annotation\" workflow in GNPS.\n","fileCount":"4","fileSizeKB":"2621","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"reference standards","instrument":"Orbitrap IQ-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Food Safety;Food Toxicants;WFSR spectral library;DatasetType:Metabolomics;DatasetType:Other (exposomics)","pi":[{"name":"Federico Padilla Gonzalez","email":"federico.padillagonzalez@wur.nl","institution":"Wageningen University & Research","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"68019c4e4f344c738d9fa3dc80f5732d","id":"588"}, {"dataset":"MSV000098567","datasetNum":"98567","title":"Mass Spectrometry-Based Mapping of Conformational Epitopes on SARS-CoV-2 Antigens Targeted by Monoclonal Antibodies","user":"ppianpaktr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1753067289000","created":"Jul. 20, 2025, 8:08 PM","description":"This study utilized diethylpyrocarbonate covalent labeling mass spectrometry (DEPC CL-MS) to map epitopes on the SARS-CoV-2 spike glycoprotein, focusing on the receptor-binding domain (RBD) of beta (B.1.351) and omicron (B.1.1.529) variants, as well as the original-variant S1 subunit. DEPC labeling with LC-MS\/MS identified antibody-binding sites and conformational shifts, revealing significant RBD flexibility and more consistent S1 labeling.","fileCount":"19","fileSizeKB":"11884066","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QExactive LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Covalent Labeling, Diethylpyrocarbonate, Epitope Mapping, Mass Spectrometry, Monoclonal Antibodies, SARS-CoV-2 Spike Glycoprotein;DatasetType:Proteomics","pi":[{"name":"Patanachai Limpikirati","email":"patanachai.l@pharm.chula.ac.th","institution":"Faculty of Pharmaceutical Sciences, Chulalongkorn University","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8f2b2030980547698d73974a1abb76a8","id":"589"}, {"dataset":"MSV000098566","datasetNum":"98566","title":"INLP discovery from M. fortuitum culture extracts","user":"kaiminj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752986684000","created":"Jul. 19, 2025, 9:44 PM","description":"The dataset contains untargeted metabolomic data from Mycobacterium fortuitum wild-type culture extracts and INLP biosynthetic gene cluster (BGC) knockout strains, enabling comparative metabolomic analysis and precursor neutral-loss chromatography (pNLC) based annotation. MS\/MS spectra for compound 3 (fortcupinile A) and compound 4 (fortlipoamide A) are also included.","fileCount":"163","fileSizeKB":"3643084","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium fortuitum","instrument":"6545 Q-TOF LC\\\/MS","modification":"No PTMs are included in the dataset","keywords":"isonitrile lipopeptide, Mycobacterium fortuitum, fortcupinile A, fortlipoamide A, INLP 3, hydrolyzed LP 4;DatasetType:Metabolomics","pi":[{"name":"Wenjun Zhang","email":"wjzhang@berkeley.edu","institution":"University of California, Berkeley","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2f407c9f045241869832dc3768c35693","id":"590"}, {"dataset":"MSV000098563","datasetNum":"98563","title":"Porcine Sertoli Cell-Derived Exosomes Drive Spermatogonial Stem Cell differentiation through PSMD11-p38 MAPK-Mediated Redox Signaling","user":"ziqian","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752922188000","created":"Jul. 19, 2025, 3:49 AM","description":"Spermatogonial stem cell fate decisions-self-renewal versus differentiation-are orchestrated by complex intercellular communication within the testicular niche. While paracrine signaling has been extensively characterized, the role of extracellular vesicles, especially in livestock, remains poorly understood. Here we demonstrate that primary porcine Sertoli cell-derived exosomes constitute a previously unrecognized regulatory mechanism controlling SSC differentiation through redox homeostasis. Using an ex vivo porcine testicular culture system that recapitulates the native SSC microenvironment, we show that porcine Sertoli cell exosomes promote SSC differentiation, evidenced by decreased expression of stemness markers (GFRA1, UCHL1) and increased differentiation markers (KIT, STRA8). Proteomic profiling revealed enrichment of antioxidant enzymes (SOD1, SOD2, CAT etc.,) within these exosomes. Mechanistically, PSMD11 was identified as a novel regulatory protein within the exosome to modulate SSC redox balance via the p38 MAPK pathway. The differentiation of porcine SSCs was impaired by PSMD11 knockdown, while was recovered by exogenous PSMD11, confirming its functional significance. These findings establish exosome-mediated redox regulation as a fundamental mechanism governing SSC fate decisions, with implications for understanding male fertility, developing therapeutic strategies for azoospermia, and improving reproductive efficiency in agricultural species.","fileCount":"9","fileSizeKB":"6256763","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sus scrofa (NCBITaxon:9823)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Cell fate determination;Exosomes;Redox signaling;Sertoli cells;Spermatogonial stem cells;DatasetType:Proteomics","pi":[{"name":"Kang Zou","email":"kangzou@njau.edu.cn","institution":"Nanjing Agricultural University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066323","task":"eb3f329e525f4a3f917afff3a3ff039a","id":"591"}, {"dataset":"MSV000098561","datasetNum":"98561","title":"Gut-associated lymph and plasma proteomics and lipidomics in pigs","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752871667000","created":"Jul. 18, 2025, 1:47 PM","description":"Raw files and database of processed results for publication of proteomics and lipiomics analysis of pig lymph and plasma from gut-associated depots. 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Overmyer","email":"kovermyer@morgridge.org","institution":"University of Wisconsin - Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"534987bb97ca423f933a3873abe54687","id":"592"}, {"dataset":"MSV000098559","datasetNum":"98559","title":"Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis","user":"KanshinED1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752862587000","created":"Jul. 18, 2025, 11:16 AM","description":"Nuclear RNA homeostasis depends on the balance of transcription, RNA processing, degradation, and transport between the nucleus and cytoplasm. RNA degradation directed by the Integrator, nuclear exosome targeting (NEXT), and nuclear exosome complexes controls the accumulation of aberrant nuclear RNA. Here, we report that Drosophila oogenesis requires the Integrator, NEXT, and nuclear exosome complexes. Depletion of Integrator, NEXT, or nuclear exosome components in Drosophila female germ cells causes infertility and accumulation of 3 extended snRNAs, promoter upstream transcripts (PROMPTs), and cryptic transcripts. Our data highlight the essential role of nuclear RNA degradation and processing in Drosophila oogenesis and provide a catalog of RNAs whose nuclear levels are regulated by these three complexes. We propose that Integrator, NEXT, and the nuclear exosome support oogenesis by ensuring that inappropriate transcription does not overwhelm the limited supply of proteins that bind, process, and traffic RNA.","fileCount":"38","fileSizeKB":"28719450","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila (NCBITaxon:7215)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"NEXT;Ars2;exosome;Integrator;DatasetType:Proteomics","pi":[{"name":"Beatrix M Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"NYU Langone Grossman School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"e809d48462504fc9a05b26be6f165a3b","id":"593"}, {"dataset":"MSV000098556","datasetNum":"98556","title":"GNPS - Tatsi 2025 Microbiome Core Fecal Samples ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752856364000","created":"Jul. 18, 2025, 9:32 AM","description":" Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"121","fileSizeKB":"2931337","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fecal;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"44c63512c3c742ec968aadec74a7a9be","id":"594"}, {"dataset":"MSV000098555","datasetNum":"98555","title":"Exposure to a persistent organic pollutant mixture and sex-specific steatotic liver disease","user":"mmerchant","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752847153000","created":"Jul. 18, 2025, 6:59 AM","description":"A 2DLC-(TMTPro)-MS workflow was used to examine hepatic exposure to persistent organic pollutants (POPs) with steatotic liver disease (SLD). The goal was to determine the sex-specific impact of POPs on SLD and identify underlying sex-specific mechanisms. Male and female C57BL\/6 mice were fed either a western (WD) or control diet (CD) and exposed to vehicle control or a POP mixture (PCB 126 and chlordane) over a 12-week period. A second group of intact female or ovariectomized (OVX) mice were exposed to the same POP mixture or vehicle control for 2 weeks. Compared to their diet- and sex-matched controls, WD-fed female mice exposed to the POP mixture exhibited steatosis and these observations were absent in males. Chemical exposure, irrespective of sex and diet, activated hepatic xenobiotic receptors, namely the AHR (Cyp1a1\/Cyp1a2 induction) and CAR (Cyp1b10 induction), more robust CAR activation was observed in CD-fed females. This group also showed decreased liver gene expression for estrogen sulfotransferase (Sult1e1), a key enzyme in estrogen metabolism. Female mice exposed to the POP mixture were more susceptible to toxicant-associated SLD. Our findings emphasized the significance of considering biological sex in assessing disease risk","fileCount":"82","fileSizeKB":"79792654","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"liver;organic pollutant exposure;TMTPro;DatasetType:Proteomics","pi":[{"name":"Michael L. Merchant, PhD","email":"mlmerc02@louisville.edu","institution":"University of Louisville","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"59c6fb0b59ab412cbbfd20e656ab7b8e","id":"595"}, {"dataset":"MSV000098552","datasetNum":"98552","title":"GNPS - Collision-Induced Unfolding of High-m\/z Native-like Protein Ions within a Trapped Ion Mobility Spectrometer","user":"nborotto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752792027000","created":"Jul. 17, 2025, 3:40 PM","description":"Native mass spectrometry (nMS) is a powerful tool for the rapid characterization of protein ions and protein-ligand complexes. By coupling nMS with ion mobility spectrometry (IMS), and collisional activation, insights into protein con-formation and stability can be rapidly obtained. Originally incapable of this workflow, recent work enabled this collision-induced unfolding (CIU) process workflow on commercially available Bruker timsTOF instruments. This early work, however, faced challenges in transmitting larger proteins and only sought to unfold small proteins up to 29 kDa. In this study, we continue the development of this technique and optimized instrument settings, enabling the ionization and transmission of proteins up to 8,000 Th, and successfully unfolded proteins such as superoxide dis-mutase, beta-lactoglobulin, and ovalbumin on a timsTOF. When this TIMS activation technique is applied to large pro-tein ions, however, limited unfolding was observed for bovine serum albumin and no unfolding was observed for immunoglobulin G","fileCount":"41","fileSizeKB":"24626","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"assorted","instrument":"timsTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"collision induced unfolding;DatasetType:Other (Collision induced unfolding)","pi":[{"name":"Nicholas Borotto","email":"nborotto@unr.edu","institution":"University of Nevada","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"86116d4ecd224813b034c808c27244ef","id":"596"}, {"dataset":"MSV000098550","datasetNum":"98550","title":"Disruption of Leishmania major Vps36 gene using CRISPR\/Cas9 severely abrogates vesicle secretion and subsequent parasite infectivity and disease progression","user":"joseanegodinho","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752777105000","created":"Jul. 17, 2025, 11:31 AM","description":"Leishmania major promastigote samples were collected under two temperature conditions (25°C and 37°C). The Vps36 gene, a key component of the ESCRT-II complex involved in extracellular vesicle biogenesis in eukaryotic cells, was disrupted using CRISPR\/Cas9 technology. The resulting knockout strain (L. majorVps36null) was compared to the wild-type (L. majorWT) and the addback strain (L. majorVps36addback).","fileCount":"194","fileSizeKB":"3347125","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Leishmania major (NCBITaxon:5664)","instrument":"Thermo Scientific Orbitrap Exploris 240 ","modification":"N\\\/A","keywords":"Leishmania, CRISPR\/Cas9, Vesicle secretion, Leishmaniasis;DatasetType:Metabolomics","pi":[{"name":"Joseane Godinho and Laura-Isobel McCall","email":"jlpg.godinho@gmail.com","institution":"San Diego State University","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f6f431b36b0047e0badadd83060ae32e","id":"597"}, {"dataset":"MSV000098549","datasetNum":"98549","title":"GNPS - Nrf2 drives activation-driven expansion of CD4+ T-cells by modulating glucose and glutamine metabolism","user":"ryan_sheldon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752777055000","created":"Jul. 17, 2025, 11:30 AM","description":"Metabolomics data pertaining to \"Nrf2 drives activation-driven expansion of CD4+ T-cells by modulating glucose and glutamine metabolism\" manuscript","fileCount":"17","fileSizeKB":"3840527","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"CD4+ T-cells","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"T-cell activation;Antioxidation;adaptive immune cells;T-cell expansion;Immunometabolism;DatasetType:Metabolomics","pi":[{"name":"Kalyani Pyaram","email":"kpyaram@kumc.edu","institution":"University of Kansas Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"086da510cf5a47ad846a30c22c906dc2","id":"598"}, {"dataset":"MSV000098548","datasetNum":"98548","title":"Rare coding genetic variants confer high risk of ADHD, implicate neuronal biology, and impact socioeconomic outcomes","user":"klagelab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752776789000","created":"Jul. 17, 2025, 11:26 AM","description":"Attention deficit hyperactivity disorder (ADHD) is a childhood onset neurodevelopmental disorder with a large genetic risk component. It affects around 5% of children and 2.5% of adults and is associated with a range of severe outcomes. Here we identify three genes (MAP1A, ANO8, ANK2, P < 3.07e-6) implicated in ADHD by rare coding variants from exome sequencing of 8,895 individuals with ADHD and 53,780 controls. Rare deleterious variants in the three genes confer substantial risk for ADHD (odds ratios 5.55 - 15.13) and explain 5.2% of the overall rare variant heritability of ADHD, which was estimated to 2.5%. Protein-protein interaction networks of the three identified genes were enriched for rare variant risk of other neurodevelopmental disorders, and enrichment analyses pointed towards involvement of the networks in cytoskeleton organization, synapse function, and RNA processing. The top associated rare variant risk genes showed an increased mean expression across both pre- and postnatal brain developmental stages, with enrichment in several neuronal cell types including GABAergic and dopaminergic neurons, as well as among genes expressed in axons and in ion channel diseases. Rare protein-truncating variants were associated with lower socioeconomic status and lower education in individuals with ADHD, both before and after excluding individuals with co-occurring intellectual disability (ID). In line with this we identified a decrease in 2.25 intelligence quotient (IQ) points per rare deleterious variant in a German sample of adults with ADHD (N = 962). Individuals with both ADHD and ID showed increased load of rare variant risk overall, while individuals with other psychiatric comorbidities demonstrated increased load only for specific neurodevelopmental disorder gene sets. This suggests that psychiatric comorbidity (other than ID) in ADHD primarily is driven by rare variants in specific genes, rather than a general increased load across constrained genes.","fileCount":"74","fileSizeKB":"4966654","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos Pro;Orbitrap Exploris 480;Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"IP-MS;protein-protein interaction;human induced neurons;attention deficit hyperactivity disorder;DatasetType:Proteomics","pi":[{"name":"Kasper Lage","email":"klhansen@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066283","task":"fac6f395ba404b0f82fd52cf72c6022f","id":"599"}, {"dataset":"MSV000098544","datasetNum":"98544","title":"An early Miocene enamel proteome from an early diverging rhinocerotid","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752710659000","created":"Jul. 16, 2025, 5:04 PM","description":"The evolutionary history of Rhinocerotidae has been the subject of significant debate among palaeontologists, with several paradigm shifts within the last quarter century, typically centered around a speculated deep-basal split between Rhinocerotinae and Elasmotheriinae. Here, we recover an endogenous ancient enamel proteome from an Early Miocene (20+Ma) old rhinocerotid from the Haughton Formation of Canada\u2019s High Arctic. Ancient proteomes sufficient for phylogenetic analysis have not previously been recovered from beyond the Pliocene, making it difficult to reconstruct the evolutionary relationships and divergence times of fossil taxa that are beyond the reach of ancient DNA. Here, phylogenetic analysis of our proteomic data suggests the split between Elasmotheriinae and Rhinocerotinae occurred much later than previously speculated, in the late Eocene or Oligocene. The authenticity of ancient the ancient proteome is supported by a suite of post-translational modifications associated with advanced degradation, including a significant degree of arginine->ornithine conversion and high rates of advanced forms of tryptophan and histidine oxidation.","fileCount":"37","fileSizeKB":"15211125","spectra":"137360","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rhinocerotidae (NCBITaxon:9803)","instrument":"Q Exactive HF;Orbitrap Exploris 480","modification":"MOD:00428 - \\\"A protein modification that effectively replaces two hydrogen atoms with two hydroxyl groups.\\\";MOD:00696 - \\\"A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate').\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Rhinocerotidae;Enamel;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Enrico Cappellini","email":"enrico.cappellini@sund.ku.dk","institution":"Globe Institute, University of Copenhagen, Denmark","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052635","task":"850c0751596c447693f1b96a7477aed0","id":"600"}, {"dataset":"MSV000098537","datasetNum":"98537","title":"Next-Generation Protein Sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6","user":"kelleheroffice","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752689103000","created":"Jul. 16, 2025, 11:05 AM","description":"The vast complexity of the proteome currently overwhelms any single analytical technology in capturing the full spectrum of proteoform diversity. In this study, we evaluated the complementarity of two cutting-edge proteomic technologies, single-molecule protein sequencing and individual ion mass spectrometry, for analyzing recombinant human IL-6 (rhIL-6) at the amino acid, peptide, and intact proteoform levels. For single-molecule protein sequencing, we employed the recently released Platinum instrument. Next-Generation Protein Sequencing (NGPS) on Platinum utilizes cycles of N-terminal amino acid recognizer binding and aminopeptidase cleavage to enable parallelized sequencing of single peptide molecules. We found that NGPS produces single amino acid coverage of multiple key regions of IL-6, including two peptides within helices A and C, which harbor residues that reportedly impact IL-6 function. For top-down proteoform evaluation, we used individual ion mass spectrometry (I2MS), a highly parallelized Orbitrap-based charge detection MS platform. Single ion detection of gas-phase fragmentation products (I2MS2) gives significant sequence coverage in key regions of IL-6, including two regions within helices B and D that are involved in IL-6 signaling. Together, these complementary technologies delivered a combined 52% sequence coverage, offering a more complete view of IL-6 structural and functional diversity than either technology alone. This study highlights the complementarity of these protein detection methods to cover protein segments relevant to biological interactions more comprehensively. ","fileCount":"31","fileSizeKB":"2539334","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Platinum (Quantum-Si)","modification":"glycosylation","keywords":"proteoform;individual ion mass spectrometry;top-down mass spectrometry;cytokine;Platinum;Next-Generation Protein Sequencing;Single-molecule protein sequencing;DatasetType:Proteomics","pi":[{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f9e7c92d66364fe79af1a0f6eb8eb56f","id":"601"}, {"dataset":"MSV000098536","datasetNum":"98536","title":"SLFN11 counteracts the RFWD3-PRIMPOL DNA damage tolerance pathway to restrain gapped DNA synthesis in response to replication stress","user":"KanshinED1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752681929000","created":"Jul. 16, 2025, 9:05 AM","description":"Schlafen family member 11 (SLFN11) expression sensitizes cells to a spectrum of DNA-damaging chemotherapies. Previous studies have shown that SLFN11 is recruited to stalled replication forks in response to replication stress; however, the role of SLFN11 at stressed replication forks remains unclear. Using single-molecule DNA fiber analysis and super-resolution microscopy to interrogate the dynamics of individual replication forks, we show that SLFN11 acts upon stalled replication forks to suppress efficient fork restart. In the absence of SLFN11 expression, fork restart proceeds through a pathway involving the ubiquitin ligase RFWD3 and the DNA primase-polymerase PRIMPOL to facilitate gapped DNA synthesis. In the absence of SLFN11 expression, this pathway ensures that cells do not accumulate replication-associated DNA damage in response to stalled forks. Collectively, our results provide a mechanistic basis for how SLFN11 can counteract DNA damage tolerance by suppressing the RFWD3-PRIMPOL axis. \nThe deposit includes the mass spectrometry data files generated from this study.\n","fileCount":"580","fileSizeKB":"69521189","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF HT;Orbitrap Eclipse","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Schlafen-11, SLFN11, DNA synthesis, fork restart, PRIMPOL, RFWD3, fork-stalling, replication stress, hydroxyurea, DNA damage tolerance;DatasetType:Proteomics","pi":[{"name":"Beatrix M Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"NYU Langone Grossman School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD066219","task":"b54752a3f3bf4ea79c5a8b80a9c97bf5","id":"602"}, {"dataset":"MSV000098533","datasetNum":"98533","title":"GNPS - Metabolomics - black wattle bark - different solvents","user":"carolinafgomes","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752636187000","created":"Jul. 15, 2025, 8:23 PM","description":"MS\/MS data from a study which evaluated the effects of different extraction solvents to promote metabolite extraction from Black Wattle Bark, using untargeted metabolomics","fileCount":"886","fileSizeKB":"5249469","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Acacia mearnsii (NCBITaxon:139012)","instrument":"Bruker Impact II, QTOF MS","modification":"none","keywords":"metabolomics;proanthocyanidins;phenolic compounds;extraction solvents;extraction process;DatasetType:Metabolomics","pi":[{"name":"Carolina Feistauer Gomes","email":"carol.feistauer@gmail.com","institution":"Federal University of Rio Grande do Sul ","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6a7e54c14e8143ba8d5c73beb3f93806","id":"603"}, {"dataset":"MSV000098532","datasetNum":"98532","title":"SOD1 is a possible predictor of COVID-19 progression as revealed by plasma proteomics","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752631238000","created":"Jul. 15, 2025, 7:00 PM","description":"The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a worldwide health emergency. Patients infected with SARS-CoV-2 present with diverse symptoms relating to the severity of the disease. Determining the proteomic changes associated with these diverse symptoms and in different stages of infection is beneficial for clinical diagnosis and management. Here, we performed a Tandem Mass Tag (TMT)-labeling proteomic study on the plasma of healthy controls and COVID-19 patients, including those with asymptomatic infection (NS), mild syndrome (MS), and severe syndrome in the early phase (SSEP) and the later phase (SSLP). While the number of patients included in each group is low, our comparative proteomic analysis revealed that complement and coagulation cascades, cholesterol metabolism and glycolysis-related proteins were affected after infection with SARS-CoV-2. Compared to healthy controls, ELISA analysis confirmed that SOD1, PRDX2 and LDHA levels were increased in the patients with severe symptoms. Both gene set enrichment analysis and receiver operator characteristic analysis indicated that SOD1 could be a pivotal indicator for the severity of COVID-19. Our results indicated that plasma proteome changes differed based on symptoms and disease stages and SOD1 could be a predictor protein for indicating COVID-19 progression. These results may also provide new understanding for COVID-19 diagnosis and treatment.","fileCount":"186","fileSizeKB":"177978556","spectra":"3255057","psms":"449751","peptides":"7247","variants":"16499","proteins":"671","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:01720 - \\\"A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-126 reporter+balance group.\\\"","keywords":"Covid-19;Tmt;Plasma;Sod1;DatasetType:Proteomics","pi":[{"name":"Benhong Xu","email":"xubenhong@szcdc.net","institution":"Shenzhen Center for Disease Control and Prevention","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD024728","task":"4304efb39e2f4465992d06d83b882af3","id":"604"}, {"dataset":"MSV000098530","datasetNum":"98530","title":"Proteogenomic identification of Hepatitis B virus (HBV) genotype-specific HLA-I restricted peptides from HBV-positive patient liver tissues","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1752626424000","created":"Jul. 15, 2025, 5:40 PM","description":"The presentation of virus-derived peptides by HLA class I molecules on the surface of an infected cell and the recognition of these HLA-peptide complexes by, and subsequent activation of, CD8+ cytotoxic T cells provides an important mechanism for immune protection against viruses. Recent advances in proteogenomics have allowed researchers to discover a growing number of unique HLA-restricted viral peptides, resulting in a rapidly expanding repertoire of targets for immunotherapeutics (i.e. bispecific antibodies, engineered T-cell receptors (TCRs), chimeric antigen receptor T-cells (CAR-Ts)) to infected tissues. However, genomic variability between viral strains, such as Hepatitis-B virus (HBV), in combination with differences in patient HLA alleles, make it difficult to develop therapeutics against these targets. To address this challenge, we developed a novel proteogenomics approach for generating patient-specific databases that enable the identification of viral peptides based on the viral transcriptomes sequenced from individual patient liver samples. We also utilized DNA sequencing of patient samples to identify HLA genotypes and assist in target selection. Liver samples from 48 HBV infected patients, primarily from Asia, were examined to reconstruct patient-specific HBV genomes, identify regions within the human chromosomes targeted by HBV integrations and obtain a comprehensive view of HBV peptide epitopes using our HLA class-I (HLA-I) immunopeptidomics discovery platform. Two previously reported HLA associated HBV-derived peptides, HLA-A02 binder FLLTRILTI (S194-202) from the large surface antigen and HLA-A11 binder STLPETTVVRR (C141-151) from the capsid protein were validated by our discovery platform, but both were detected at a very low frequencies. In addition, we identified and validated, using heavy peptide analogues, novel strain-specific HBV-HLA associated peptides, such as GSLPQEHIVQK (P606-616) and variants. 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ZC3H4 is upregulated during differentiation, and its knockdown in differentiated HPV16- or HPV31-positive cells reduces late viral transcripts in an E2-BRD4-dependent manner. 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LC-MS\/MS was performed using an Orbitrap Fusion Tribid MS system (Thermo Fisher Scientific), and data was analyzed using Skyline (version 23.1.1.520; MacCoss Lab software) and FreeStyle? 1.8 SP2 (Thermo Fisher Scientific).","fileCount":"7","fileSizeKB":"1656934","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"DatasetType:Proteomics;PRM;NCLX","pi":[{"name":"Liang Feng","email":"liangf@stanford.edu","institution":"Stanford University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065767","task":"f926355682b347ce975965955ef3143b","id":"634"}, {"dataset":"MSV000098426","datasetNum":"98426","title":"Phosphorylation Toggles the SARS-CoV-2 Nucleocapsid Protein Between Two Membrane-Associated Condensate States","user":"haiyanzheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751560210000","created":"Jul. 3, 2025, 9:30 AM","description":"There is no abstract here, and we will describe later.","fileCount":"10","fileSizeKB":"793124","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"SARS coronavirus (NCBITaxon:227859)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"SARS-CoV-2;liquid-liquid phase separation (LLPS);phosphorylation;protein-RNA interactions;material properties;membrane interaction;DatasetType:Proteomics","pi":[{"name":"Benjamin S. 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We analyzed residual plasma samples from a previous SARS-CoV-2 challenge study of Mexican free-tailed bats (Tadarida brasiliensis) to identify candidate protein biomarkers of susceptibility and assessed the abundance of these same proteins in a wild population of this bat species in Texas. Using 2 uL plasma volumes, we generated proteomes from captive (n = 20; four resistant, five susceptible, 11 unchallenged) and wild (n = 15) bats using the S-Trap method and LC-MS\/MS, identifying 475 proteins using data-independent acquisition and a species-specific genome annotation generated by the Bat1K Project.","fileCount":"1196","fileSizeKB":"60142010","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Tadarida brasiliensis (NCBITaxon:9438)","instrument":"timsTOF HT","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Tadarida brasiliensis;plasma;bat;DatasetType:Proteomics","pi":[{"name":"Brett S. Phinney","email":"bsphinney@ucdavis.edu","institution":"University of California, Davis","country":"USA"},{"name":"Daniel J. 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The QUEST-MS method based on 96-well formatted sequential reversed phase chromatography allowing efficient enrichment of < 20 kDa proteins quickly and reproducibly. The LC\/MS\/MS data from 24 healthy controls, 19 benign prostate hypertrophy (BPH) patients, and 73 prostate cancer patients plasma were subjected to label-free quantification analysis on Expressionist proteome server. Data processing: Mascot Server 2.3.1 was used with the database SwissProt 2011_08 (531473 sequences,188463640 residues). Enzyme: semiTrypsin. Search parameters: Peptide Mass Tolerance : +- 3 ppm, Fragment Mass Tolerance:+-0.8 Da. Fixed modifications:Carbamidomethyl (C). Variable modifications:Oxidation (M),Deamidated (NQ). 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As viruses evolve by acquiring mutations, it is essential to identify a range of viral presented antigens. Utilizing HLA-peptidomics we Identified SARS-CoV-2-derived peptides presented by highly prevalent HLA Class-I (HLA-I) molecules using infected cells as well as overexpression of SARS-CoV-2 genes. We found 26 HLA-I peptides and 36 HLA class-II (HLA-II) peptides, which are estimated to be presented by at least one HLA allele in 99% of the world population. Among the identified peptides were recurrently presented HLA-I peptides, peptides derived from out-of-frame-ORFs and presentation-hotspots. Seven of these peptides were previously shown to be immunogenic, and we identified two novel immuno-reactive peptides using HLA-multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on viral-specific-presented antigens that span several of the viral genes.","fileCount":"306","fileSizeKB":"332155445","spectra":"8410079","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sars-cov-2;Immunopeptidomics;Hla-peptidomics;DatasetType:Proteomics","pi":[{"name":"Prof. Yardena Samuels","email":"yardena.samuels@weizmann.ac.il","institution":"Weizmann Institute of science","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD025499","task":"ddb85b6e41864eab89a39ad0350b06b3","id":"639"}, {"dataset":"MSV000098417","datasetNum":"98417","title":"Age-Dependent Changes in the Plasma Proteome of Healthy Adults","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751485824000","created":"Jul. 2, 2025, 12:50 PM","description":"Human blood plasma is a complex which communicates with most parts of the body and reflects changes in the state of the organism, therefore identifying age-related biomarkers can help to predict and monitor age-related physiological decline and diseases, as well as to find new treatments for diseases. In this study, TMT-LC-MS\/MS was utilized to screen for the differentially expressed plasma proteins in 118 healthy adults with different ages. Participants were divided into three groups: 21-30 (Young), 41-50 (Middle) and ?60 (Old), the number of differentially expressed proteins when Young vs Middle, Middle vs Old and Young vs Old were 82, 22 and 99, respectively. These proteins were found to be involved in numerous physiological processes such as \u201Cnegative regulation of smooth muscle cell proliferation\u201D and \u201Cblood coagulation\u201D. Meanwhile when Young vs Middle or Old, \u201CComplement and coagulation cascades\u201D was confirmed the top enriched pathway by KEGG pathway enrichment analysis. Functional phenotyping of the proteome demonstrated that the plasma proteomic profiles of Young adults were strikingly dissimilar to the Middle or Old adults. The results of this study mapped the variation in expression of plasma proteins, and provided information about possible biomarkers\/treatments for different kinds of age-related function disorders.","fileCount":"185","fileSizeKB":"123250877","spectra":"3195614","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Aging;healthy adults;plasma;proteomics;tmt-lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Xiaoyi Xiong","email":"xiongxy1989@hotmail.com","institution":"Department of Neurology, The Second Affiliated Hospital (Xinqiao Hospital), Army Medical University (Third Military Medical University), Chongqing 400037, China","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD016199","task":"9ef9be5c17e74f8590ba7a2650dc525a","id":"640"}, {"dataset":"MSV000098416","datasetNum":"98416","title":"Immunopeptidomics by use of a microfluidics chip.","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751485452000","created":"Jul. 2, 2025, 12:44 PM","description":"A microfluidics technology was implemented to the immunoaffinity purification process of MHC peptides in Ligandomics\/Immunopeptidomics. The thus purified HLA peptides were analysed by LCMS with the nanoElute LC and TimsTOF Pro Mass Spectrometer from Bruker. The aim of the microfluidics implementation was to improve the sensitivity and robustness while also reducing antibody and other material requirements in the immunoaffinity purification protocol.","fileCount":"32","fileSizeKB":"4835928","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\"","keywords":"Human;Bladder cancer;Ligandome;Patient derived organoid;Hla-i;Renal cell carcinoma;Microfluidics;Ovarian cancer;Immunopeptidome;Jy cell line;Chip;Mhc-i;Rcc;DatasetType:Proteomics","pi":[{"name":"Janne Lehtio","email":"janne.lehtio@ki.se","institution":"Dept. Oncology-Pathology, Scilifelab, Karolinska Institutet, Stockholm, Sweden","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD022194","task":"2142c982bde84263be6f9580993348a5","id":"641"}, {"dataset":"MSV000098414","datasetNum":"98414","title":"Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751483395000","created":"Jul. 2, 2025, 12:09 PM","description":"The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles both in the innate and adaptive immune system. Starting already during embryogenesis and continuing throughout our lives, these three Ags exert major functions in immune tolerance, defense against infections, and anticancer immune responses. Despite these important roles, identification and characterization of the peptides presented by these molecules has been lacking behind the more abundant HLA-A and HLA-B gene products. In this study, we elucidated the peptide specificities of these HLA molecules using a comprehensive analysis of naturally presented peptides.","fileCount":"256","fileSizeKB":"116305483","spectra":"1961280","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hla-e;Hla-g;Binding prediction;peptide motifs;Hla-c;Lc-msms;DatasetType:Proteomics","pi":[{"name":"Stefan Stevanovic","email":"stefan.stevanovic@uni-tuebingen.de","institution":"Department of Immunology, Interfaculty Institute for Cell Biology, T\uFFFDbingen, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD009531","task":"6d6bc8a2f46b410990bf4c0d1e8e6901","id":"642"}, {"dataset":"MSV000098413","datasetNum":"98413","title":"GNPS - Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry","user":"jymbcrc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751482816000","created":"Jul. 2, 2025, 12:00 PM","description":"Combined multi-omics analysis of proteomics, metabolomics, and lipidomics requires separate liquid chromatography mass spectrometry (LC-MS), which limit throughput and increase costs, hindering the application of mass spectrometry-based multi-omics to large-scale analyses. Here, we present simultaneous multi-omics analysis by direct infusion (SMAD), an integrated platform leveraging ion mobility mass spectrometry and self-developed software tools to enable single injection multi-omics analysis without liquid chromatography. SMAD allows quantification of over 9,000 metabolite m\/z features and over 1,300 proteins from the same sample in less than five minutes. We validated the efficiency and reliability of SMAD with three case studies. (1) mouse macrophages after M1\/M2 polarization and senescence, (2) a pilot drug screen in human cells, and (3) large-scale high-throughput drug screening of mammalian cells in 96-well plates. Finally, relationships between proteomic and metabolomic data are discovered by machine learning and validated. 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This experiment represents the bound fraction. Sample was in-solution trypsin digested and peptides were fractionated into 10 fractions by mixed-mode reversed phase anion exchange (MM(RP-AX) using a Promix MP column. Each fraction was analyzed separately by LC-MS\/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to the CSF-PR.","fileCount":"25","fileSizeKB":"10952340","spectra":"155942","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap;MS:1000031","modification":"MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:01090 - \\\"A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:01047 - \\\"A protein modification that effectively converts an L-lysine residue to a monohydroxylated lysine.\\\"","keywords":"Cerebrospinal fluid. homo sapiens;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Astrid Guldbrandsen","email":"astrid.guldbrandsen@biomed.uib.no","institution":"PROBE","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000655","task":"5d41113be0a648ffa743dabd304cbbae","id":"644"}, {"dataset":"MSV000098411","datasetNum":"98411","title":"Cellular- to ecosystem-scale consequences of phage-resistance mutations in marine Cellulophaga baltica ","user":"ajstai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751479378000","created":"Jul. 2, 2025, 11:02 AM","description":"The oceans teem with bacteria and viruses (phages), engaged in a battle of attack and resistance. While ecological theory predicts fitness-resistance trade-offs, the mechanisms and ecosystem consequences of resistance remain underexplored. Here we isolated 13 spontaneous, Cellulophaga baltica phage-resistant mutants that altered the cell surface or intracellular amino acid metabolism, and evaluated resistance mechanisms and ecological impacts. Mechanistically, surface mutants offered broad and complete extracellular resistance against multiple phages through decreased adsorption, while intracellular mutants resisted a single phage after viral DNA replication. For one intracellular mutant, resistance was shown to be lipid-mediated. Ecosystem impacts were three-fold: (i) surface mutants altered carbon utilization most; (ii) one intracellular mutant was predicted to secrete more metabolites (including experimentally-verified acetate); and (iii) all mutants were stickier with surface mutants also sedimenting faster. These findings illuminate how phage resistance drives fitness tradeoffs and quantifies cellular-to-ecosystem impacts, with direct linkages to marine carbon storage.","fileCount":"92","fileSizeKB":"21499620","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cellulophaga baltica (NCBITaxon:76594);Cellulophaga baltica phage phi18:4","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LCMS;Lipidomics;Bacteriophage;Resistance;DatasetType:Metabolomics","pi":[{"name":"Dr. Robert Hettich","email":"hettichrl@ornl.gov","institution":"Oak Ridge National Laboratory","country":"the United States of America"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"1b9e1e5a69dc455b8bfe674e65839556","id":"645"}, {"dataset":"MSV000098406","datasetNum":"98406","title":"Leishmania donovani co-fractionation","user":"AminAzimi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751474713000","created":"Jul. 2, 2025, 9:45 AM","description":"The dataset includes co-fractionation mass spectrometry data to support the identification of protein complexes and conserved interactions in L. donovani.","fileCount":"652","fileSizeKB":"197465596","spectra":"0","psms":"836599","peptides":"59353","variants":"74488","proteins":"5969","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Leishmania donovani BPK282A1 (NCBITaxon:981087)","instrument":"Q Exactive Plus","modification":"UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\";MOD:01160 - \\\"A protein modification that effectively results in the loss of an ammonia, usually by a process of vicinal dehydration, rearrangement, and rehydration with release of ammonia, resulting in a loss of nitrogen with no gain of oxygen.\\\"","keywords":"cofractionation;DatasetType:Proteomics","pi":[{"name":"Reza Salavati","email":"reza.salavati@mcgill.ca","institution":"Institute of Parasitology","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD065693","task":"73980d6b3d324600b00914a5d9b42e3f","id":"646"}, {"dataset":"MSV000098400","datasetNum":"98400","title":"GNPS - Greenwayodendron suaveolens stem barks","user":"mbeniddir","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751446001000","created":"Jul. 2, 2025, 1:46 AM","description":"Feature-based processing with MZmine3 of Greewayodendron suaveolens bark dichloromethane and methanol extract and chromatographic fractions.","fileCount":"5","fileSizeKB":"35109","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Greenwayodendron suaveolens (NCBITaxon:235734)","instrument":"Agilent 6546 Qtof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Annonaceae, Greewayodendron, suaveolens, sesquiterpene indole, alkaloids;DatasetType:Metabolomics","pi":[{"name":"Elvis Otogo N'Nang","email":"elvisotogonnang@gmail.com","institution":"Universite des Sciences de la Sante","country":"Gabon"},{"name":"Mehdi Beniddir","email":"mehdi.beniddir@u-psud.fr","institution":"Universite Paris-Saclay","country":"France"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"c5a5a71308fa43319c14c6f0f9402321","id":"647"}, {"dataset":"MSV000098399","datasetNum":"98399","title":"Deep and Quantitative Proteomic Profiling of Low Volume Mouse Serum Across the Lifespan","user":"deyamk","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751443501000","created":"Jul. 2, 2025, 1:05 AM","description":"We developed a nanoparticle-based LC-MS workflow optimized for low-volume mouse serum samples, enabling deep, quantitative, and reproducible proteome profiling. Applied to aging cohorts, the approach identified 3,992 protein groups across all samples and uncovered age-associated proteomic signatures in serum and linked to glucose and body composition. Complementary analysis using a 48-plex proximity extension assay (PEA) quantified an additional 39 cytokines not detected by MS, enhancing proteome coverage. This integrated platform supports robust biomarker discovery and systems-level insights in volume-limited preclinical studies.","fileCount":"259","fileSizeKB":"165142077","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Study of Longitudinal Aging in Mice (SLAM);Aging;Circulating biomarkers;Serum;Low volume;Nanoparticle (NP);Proteomics;Liquid Chromatography- Mass Spectrometry (LC-MS);Data-independent acquisition (DIA);Cytokines;Proximity extension assays (PEA);DatasetType:Proteomics","pi":[{"name":"Dr. Nathan Basisty","email":"nathan.basisty@nih.gov","institution":"NIH-National Institute on Aging, Baltimore, MD","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"45e490f16bad4edfae528dd52422c2aa","id":"648"}, {"dataset":"MSV000098395","datasetNum":"98395","title":"Proteomics analysis of plasma-derived exosomes extracted by thrombin pre-treated ExoQuick isolation","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751392940000","created":"Jul. 1, 2025, 11:02 AM","description":"Exosomes are very small nanosized, membrane-bound vesicles, ranging from 30 to 150 nm in size, are originated and released from a variety of cells from body fluids including blood plasma. The isolation of pure exosome from blood plasma is challenging since it is rich in various contaminants from diverse origins. We applied ExoQuick with thrombin for purification of plasma-derived exosome from healthy individual. Immunoassays confirmed the presence of proteins that are classically associated to exosomes (CD9, CD63 and CD81) but these proteins have not been detected by MS. We found several common proteins enriched in our data set compared with plasma-derived exosome markers from databases. Moreover, proteomics analysis and external database integration revealed an enrichment of those extracellular vesicles. The Gene Ontology data analyses determined the presence of proteins that are involved in catalytic, transporter functions and protein metabolism activities. These results allowed the detection of tetraspanin i.e. TSPAN14 in plasma where proteins were undetected by other studies. Furthermore, this study confirmed the detection of CD5L and LGALS3BP proteins. Although the undouble presence of plasma contaminants hamper MS analysis, still proteins with biomarker potential (TSPAN14, CD5L and LGALS3BP) are accessible in a reasonable sample processing frame that outperforms high-purity focused extraction methods e.g. SEC. The study suggests the use of TSPAN14, CD5L and LGALS3BP as new exosomal markers of plasma-derived exosomes in quantitative proteomics analysis.","fileCount":"39","fileSizeKB":"4258036","spectra":"83464","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Human;Exoquick;Plasma-derived exosomes;DatasetType:Proteomics","pi":[{"name":"Stefan Kalkhof","email":"stefan.kalkhof@izi.fraunhofer.de","institution":"Department Preclinical Development and Validation, Unit Proteomics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD028172","task":"582a3e53b0074e7aaeb89d26f87e789e","id":"649"}, {"dataset":"MSV000098392","datasetNum":"98392","title":"Chemical Crosslinking-MS Analysis of APOA1 WT and the p.K131del Variant Oligomers","user":"IvoD","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751386094000","created":"Jul. 1, 2025, 9:08 AM","description":"This dataset contains LC-MS\/MS data used to study the structural oligomeric alterations induced by the congenital APOA1 variant (p.K131del) also known as K107del. The analysis includes tryptic digests from crosslinked monomers, dimers, trimers, and tetramers by triplicates. mzML and sim-XL processed (csv) files are included. The dataset aims to support findings on the effect of the K107 deletion on APOA1 conformation and aggregation propensity.\n","fileCount":"73","fileSizeKB":"523753190","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Escherichia coli (NCBITaxon:562)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:00409 - \\\"A protein modification that effectively replaces a residue amino group with a formamido group.\\\"","keywords":"APOA1 self-association;Lipid-free APOA1;APOA1 oligomerization;APOA1 (p.K131del);cross-linking LC-MS;High-density lipoprotein (HDL);DatasetType:Proteomics","pi":[{"name":"John T. Melchior","email":"john.melchior@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f0d928ea628c4bcda35bfc0abffcb514","id":"650"}, {"dataset":"MSV000098391","datasetNum":"98391","title":"Intracellular Na+-overload induces a proteomic and metabolomic remodeling of atrial myocytes leading to atrial cardiomyopathy and fibrillation","user":"Kasarla04","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751359358000","created":"Jul. 1, 2025, 1:42 AM","description":"Aims\nTargeted therapies for atrial fibrillation (AF), the most common arrhythmia provoking heart failure and stroke, are urgently needed. However, the development of such therapies requires understanding of the cellular mechanisms that culminate in atrial cardiomyopathy (ACM) as a substrate for AF. Like in humans, increased persistent Na+ current leads to the development of ACM and spontaneous episodes of AF in mice. Here, we aim to identify and target the proteomic and metabolomic consequences of intracellular Na+-overload resulting in mitochondrial redox imbalance and contractile dysfunction of atrial myocytes (AMs).\nMethods and Results\nTransgenic mice expressing human gain-of-function mutant NaV1.5-F1759A channels in the fully redox-competent C57BL\/6N background presented intracellular Na+-overload leading to AM hypertrophy, left atrial (LA) enlargement, contractile dysfunction and episodes of AF at early ages. Hence, we employed mass spectrometry of NaV1.5-F1759A LA myocardium to reveal the proteomic and metabolomic nature of ACM. In total we quantified 3,294 proteins across individual LA samples, of which 440 were differentially regulated in transgenic mice, including functionally relevant enzymes of key metabolic pathways. Metabolomic analyses confirmed changes in glycolytic and anaplerotic substrates, and identified a significant decrease in the cardioprotective antioxidant glutathione. Transgenic expression of the redox biosensor Grx1-roGFP in NaV1.5-F1759A AMs showed an oxidized glutathione redox potential indicative of mitochondrial ROS production upon catecholaminergic stimulation and field-pacing, which was not observed in control cells. Finally, we targeted the decreased expression of the sarcoplasmic reticulum protein junctophilin-2 by transgenic overexpression in NaV1.5-F1759A animals, which recued AM hypertrophy, LA contractility and AF burden in intracellular Na+-overload.\nConclusions\nAtrial cardiomyopathy induced by intracellular Na+-overload in mice is characterized by profound cellular, proteomic and metabolomic changes culminating in mitochondrial redox imbalance and contractile dysfunction, which can be attenuated by restoring atrial junctophilin-2 expression.","fileCount":"88","fileSizeKB":"20042926","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Atrial fibrillation;atrial cardiomyopathy;intracellular sodium overload, junctophillin-2;proteomic and metabolomic profiling;reactive oxygen species;DatasetType:Metabolomics","pi":[{"name":"Dr. Prasad Phapale","email":"prasad.phapale@isas.de","institution":"Leibniz-Institut fuer Analytische Wissenschaften-ISAS-e.V.","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c70c589e9e59456785811ee59b324299","id":"651"}, {"dataset":"MSV000098389","datasetNum":"98389","title":"COVIDomics_plasma_2020_DDA-PASEF","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751330446000","created":"Jun. 30, 2025, 5:40 PM","description":"In order to investigate variations in the endotype of COVID19 patients, we completed an integrated analysis of 112 research participants, including 74 COVID19 patients versus 37 SARS-CoV-2 negative controls. COVID19 patients tested positive for SARS-CoV-2 infection by PCR and\/or antibody testing and were hospitalized due to COVID19 symptoms, but none of them had developed severe pathology requiring ICU admission at the time of blood collection. The control group was recruited from the same hospital system but tested negative for SARS-CoV-2 infection. Research blood draws were obtained from consented participants and analyzed by matched SARS-CoV-2 seroconversion assays, plasma proteomics using two alternative platforms [mass-spectrometry (MS), and SOMAscan assays], 82-plex cytokine profiling using Meso Scale Discovery (MSD) assays, and immune cell profiling via mass cytometry (MC).","fileCount":"493","fileSizeKB":"359797405","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"MS:1001535","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Multi-omics;Plasma;Covid-19;DatasetType:Proteomics","pi":[{"name":"Kirk Hansen","email":"kirk.hansen@cuanschutz.edu","institution":"Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD022817","task":"674c2aa1a3b245f2ae06c463feaed474","id":"652"}, {"dataset":"MSV000098387","datasetNum":"98387","title":"Comparative evaluation of analytical methods for CSF proteomics","user":"TKislinger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751312491000","created":"Jun. 30, 2025, 12:41 PM","description":"Mass spectrometry based proteomics data from cerebrospinal fluid samples, systematically comparing MStern, Seer, N-glycopeptide capture (N-Gp), and two extracellular vesicle fractions (P20-EV and P150-EV)","fileCount":"183","fileSizeKB":"182915375","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";UNIMOD:621 - \\\"Asn->Asp substitution.\\\"","keywords":"cerebrospinal fluid;proteomics;Mass spectrometry;MStern;N-glycoproteomics;extracellular vesicles;Seer;Method comparison;CNS lymphoma;DatasetType:Proteomics","pi":[{"name":"Dr. Thomas Kislinger","email":"thomas.kislinger@utoronto.ca","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aaec0b51fb4542d2a690c254912b94fa","id":"653"}, {"dataset":"MSV000098386","datasetNum":"98386","title":"Multivalent Interactions with CCR4-NOT and PABPC1 Determine mRNA Repression Efficiency by Tristetraprolin","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751310771000","created":"Jun. 30, 2025, 12:12 PM","description":"Tristetraprolin family of proteins regulate mRNA stability by binding to specific AU-rich elements in transcripts. This binding promotes the shortening of the mRNA poly(A) tail, or deadenylation, initiating mRNA degradation. The CCR4-NOT complex plays a central role in deadenylation, while the cytoplasmic poly(A)-binding protein PABPC1 typically protects mRNAs from decay. Here, we investigate how tristetraprolin interacts with CCR4-NOT and PABPC1 to control mRNA stability. Using purified proteins and in vitro assays, we find that tristetraprolin engages CCR4-NOT through multiple interaction sites and promotes its activity, emphasizing the importance of multivalent binding for efficient deadenylation. Phosphorylation of tristetraprolin does not affect its interaction with CCR4-NOT or its deadenylation activity, but is essential for tristetraprolin binding to PABPC1. We propose that tristetraprolin promotes the processive deadenylation activity of CCR4-NOT on mRNAs containing AU-rich elements, with phosphorylation-dependent interactions with PABPC1 potentially enhancing deadenylation and promoting regulated mRNA decay.","fileCount":"16","fileSizeKB":"6780495","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Tristetraprolin (TTP), CCR4-NOT complex, PABPC1, mRNA deadenylation, phosphorylation, multivalent interactions, AU-rich elements (AREs), mRNA stability, RNA-binding proteins, post-translational modifications.;DatasetType:Proteomics","pi":[{"name":"Eugene Valkov","email":"eugene.valkov@nih.gov","institution":"NIH\/NCI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d5bee79aa709450aa4575bf5bee1551c","id":"654"}, {"dataset":"MSV000098385","datasetNum":"98385","title":"ASPPs multimerize protein phosphatase 1 ","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751301033000","created":"Jun. 30, 2025, 9:30 AM","description":"Protein samples were analyzed by Multidimensional Protein Identification Technology (MudPIT), as described previously. Briefly, precipitated proteins were resuspended in 30uL of 100mM Tris pH 8.5 with 8M urea to denature proteins. Cysteines were reduced and alkylated prior to digestion with recombinant LysC and modified trypsin. Reactions were quenched by the addition of formic acid to the final concentration of 5%. After digestion, peptide samples were pressure-loaded onto 100 um fused silica microcapillary columns packed first with 9 cm of reverse phase material, followed by 3 cm of 5um Strong Cation Exchange material, followed by 1 cm of 5um C18 RP. The loaded microcapillary columns were placed in-line with a 1260 Quartenary HPLC. The application of a 2.5 kV distal voltage electrosprayed the eluting peptides directly into Elite orbi-trap mass spectrometers equipped with a custom-made nano-LC electrospray ionization source. Full MS spectra were recorded on the eluting peptides over a 400 to 1600 m\/z range at 60,000 resolution, followed by fragmentation in the ion trap on the first to 15th most intense ions selected from the full MS spectrum. Dynamic exclusion was enabled for 90 s. Mass spectrometer scan functions and HPLC solvent gradients were controlled by the XCalibur data system.\nRAW files were extracted into .ms2 file format using RawDistiller v. 1.0, in-house developed software. RawDistiller D(g, 6) settings were used to abstract MS1 scan profiles by Gaussian fitting and to implement dynamic offline lock mass using six background polydimethylcyclosiloxane ions as internal calibrants. MS\/MS spectra were first searched using ProLuCID with a mass tolerance of 10 ppm for peptide and fragment ions. Trypsin specificity was imposed on both ends of candidate peptides during the search against a protein database. Human protein database contained 81592 human proteins (NCBI 2020-11-23 release), as well as 426 common contaminants such as human keratins, IgGs and proteolytic enzymes. C. elegans protein data base included 28,127 C. elegans proteins (NCBI 2020-05-30 release), as well as 426 common contaminants. To estimate false discovery rates (FDR), each protein sequence was randomized (keeping the same amino acid composition and length) and the resulting \"shuffled\" sequences were added to the database, for a total search space of 163,860 amino acid sequence for human datasets and 57,106 amino acid sequences for C. elegans datasets. Masses of 57.0215 Da was differentially added to cysteine residues to account for alkylation by CAM and 15.9949 Da were differentially added to methionine residues.\nDTASelect v.1.9 was used to select and sort peptide\/spectrum matches (PSMs) passing the following criteria set: PSMs were only retained if they had a DeltCn of at least 0.08; minimum XCorr values of 1.8 for singly-, 2.1 for doubly-, and 2.5 for triply-charged spectra; peptides had to be at least 7 amino acids long. Results from each sample were merged and compared using CONTRAST. Combining all replicate runs, proteins had to be detected by at least 2 peptides and\/or 2 spectral counts. Proteins that were subsets of others were removed using the parsimony option in DTASelect on the proteins detected after merging all runs. Proteins that were identified by the same set of peptides (including at least one peptide unique to such protein group to distinguish between isoforms) were grouped together, and one accession number was arbitrarily considered as representative of each protein group. \nNSAF7 was used to create the final reports on all detected peptides and non-redundant proteins identified across the different run\n","fileCount":"132","fileSizeKB":"36132709","spectra":"0","psms":"308798","peptides":"1100","variants":"1397","proteins":"298","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"LTQ Orbitrap Elite","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"C. elegans;APE-1;MudPIT;DatasetType:Proteomics","pi":[{"name":"Laurence Florens","email":"proteomicslab@stowers.org","institution":"Stowers Institute for Medical Research Institute","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD065626","task":"2a1f45a1761541f08700fcfcdb233aa2","id":"655"}, {"dataset":"MSV000098383","datasetNum":"98383","title":"Upstream open reading frames regulate proto-oncogene translation and encode HLA-presented immunogenic tumor antigens","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751283865000","created":"Jun. 30, 2025, 4:44 AM","description":"Upstream open reading frames (uORFs) represent translational control elements within eukaryotic transcript leader sequences. Recent data showed that uORFs can encode for biologically active proteins and human leucocyte antigen (HLA)-presented peptides and suggest their potential role in cancer cell development and survival. However, it is so far unclear if uORF-encoded peptides could serve as tumor-associated antigen targets and thus also play a role in cancer immune surveillance. Combining mass spectrometry-based immunopeptidome analysis in primary tumor and healthy tissues and evaluation of proto-oncogene-associated uORF-mediated translational control we here identified a panel of HLA-presented tumor-associated uORF-derived antigens. These uORF-derived tumor antigens were further shown to induce multifunctional antigen-specific T cells, validating their suitability as antigen targets for T cell-based cancer immunotherapy. Our data further unravel the role of uORF-encoded peptides in malignant disease, suggesting uORF-derived tumor-associated antigens as targets for anti-cancer immune surveillance and immunotherapy development.","fileCount":"648","fileSizeKB":"299159591","spectra":"5902221","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;LTQ Orbitrap","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\"","keywords":"Cancer;Uorf;Immunotherapy;Immunopeptidomics;Hla peptides;DatasetType:Proteomics","pi":[{"name":"Juliane S. Walz","email":"juliane.walz@med.uni-tuebingen.de","institution":"Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital T\uFFFDbingen, T\uFFFDbingen, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD025716","task":"5d9de341502a4f7e9925ce7ed6d2c9aa","id":"656"}, {"dataset":"MSV000098382","datasetNum":"98382","title":"GNPS - SLC25A45 is required for mitochondrial uptake of methylated basic amino acids and de novo carnitine biosynthesis","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751276895000","created":"Jun. 30, 2025, 2:48 AM","description":"Methylated amino acids accumulate upon the degradation of methylated proteins and are implicated in diverse metabolic and signalling pathways. Consequently, disturbed methylated amino acid homeostasis is associated with cardiovascular disease and renal failure. Mitochondria are core processing hubs in conventional amino acid metabolism but how they interact with methylated amino acids is unclear. Here, we reveal that the orphan mitochondrial solute carrier SLC25A45 is required for the mitochondrial uptake of methylated amino acids. SLC25A45 binds with dimethylarginine and trimethyllysine but has no affinity for unmethylated arginine and lysine. A non-synonymous mutation of human SLC25A45 (R285C) stabilises the carrier by limiting its proteolytic degradation by the m-AAA protease and associates with altered methylated amino acids in human plasma. Metabolic tracing of trimethyllysine in cancer cells demonstrates that SLC25A45 drives the biosynthesis of the key metabolite carnitine. Furthermore, depletion of SLC25A45 limits the proliferation and survival of ovarian cancer cells upon glucose deprivation. SLC25A45 is therefore an essential mediator of compartmentalised methylated amino acid metabolism with diverse cellular roles.","fileCount":"270","fileSizeKB":"33188757","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mitochondria;solute carriers;metabolite transport;carnitine biosynthesis;DatasetType:Metabolomics","pi":[{"name":"David Sumpton","email":"d.sumpton@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Marilia Meira Dias","email":"m.dias@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Thomas MacVicar","email":"thomas.macvicar@glasgow.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"605e94e94c0f4252b358a861905e8655","id":"657"}, {"dataset":"MSV000098380","datasetNum":"98380","title":"Mass spectrometry-based analysis on the impact of iron status and whole blood donation on the global plasma proteome","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751268597000","created":"Jun. 30, 2025, 12:29 AM","description":"Blood donation is generally considered to be safe, however to ensure blood donor health it is important to monitor the impact of a whole blood donation. Study design and methods Here, we used quantitative mass spectrometry to assess the global plasma proteomic impact of longitudinal whole blood donation in 5 new and 4 regular donors over a period of 180 days as well as the effect on iron status, by selecting 78 donors based on high levels of ferritin and hemoglobin. The majority of plasma proteins were stable between whole blood donors and demonstrated a low coefficient of variation, irrespective to iron status or donors status (new or regular). Longitudinal analysis showed limited differences between the plasma proteomes of regular and new upon a whole blood donation, apart from a consistent and significant short-term decrease in fibronectin. Plasma protein levels measured with MS highly correlated with blood count and lipid parameters, validating our MS-approach. Based on protein co-expression, we observed protein complexes of diverse biological processes, platelet and neutrophil signatures, complement and immune responses with a highly correlating cluster of IGHM, IGJ and CD5L. We showed higher inter- than intra-individual variation, most notably of immunoglobulins and allelic variants for alpha-1 antitrypsin. Overall, this study shows that whole blood donation has limited impact for both new and regular donors apart from short-term decreases in fibronectin and that varying iron statuses do not affect the global plasma proteome. We showed that individual specific signatures were reflected on the plasma proteome as well as detection of allelic variants","fileCount":"293","fileSizeKB":"529705806","spectra":"19847716","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Proteomics;Plasma profiling;Massspectrometry;Whole blood donors;DatasetType:Proteomics","pi":[{"name":"M van den Biggelaar","email":"m.vandenbiggelaar@sanquin.nl","institution":"department molecular hematology","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD035447","task":"4d14ebf3c27c40149ac0420a0c3b384f","id":"658"}, {"dataset":"MSV000098378","datasetNum":"98378","title":"Deep undepleted human serum proteome profiling toward biomarker discovery for Alzheimer\u2019s disease","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751252303000","created":"Jun. 29, 2025, 7:58 PM","description":"Alzheimer's disease (AD) is a neurodegenerative disease, the most common cause of dementia in elderly persons. Accumulation of amyloid plaques in the brain is a characteristic of AD. The requirements for a biomarker include the ability to measure a pathologic process, predict outcome, distinguish disease or measure a pharmacological response to a drug treatment or therapeutic intervention. However, there are no reliable blood based biomarkers for AD. Serum-based protein measurement is a routine practice for biomarkers in human disease, but comprehensive profiling of serum proteome is often masked by the twenty most abundant proteins and impacted by large dynamic range. The commonly used depletion method can alleviate the challenge but introduce additional experimental variation. Here we present a deep analysis of un-depleted human serum proteome by combining 11-plex TMT labeling, exhaustive 2D liquid chromatography fractionation, and high resolution tandem mass spectrometry. This platform is capable of identifying 4,500 protein components, covering 6 orders of dynamic range, representing one of the deepest serum proteome datasets. Finally, a subset of proteins, show statistically significant difference between AD and control samples, which may serve as biomarker candidates.","fileCount":"891","fileSizeKB":"400928869","spectra":"8035679","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Proteomics;Alzheimer\u2019s disease;Human blood;Mass spectrometry;Plasma;Serum;Proteome;Tandem mass tag;Biomarker;DatasetType:Proteomics","pi":[{"name":"Junmin Peng","email":"junmin.peng@stjude.org","institution":"St. Jude Children's Research Hospital","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD011482","task":"afa5c8dd3c2e4458aa110e1e4bc6a407","id":"659"}, {"dataset":"MSV000098376","datasetNum":"98376","title":"Quantitative proteomic analysis of plasma in major mental disorders","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751251832000","created":"Jun. 29, 2025, 7:50 PM","description":"Emerging high-throughput proteomic technologies have recently been considered as a powerful means of identifying substrates involved in mood disorders. We performed proteomic profiling using liquid chromatography-tandem mass spectrometry to identify dysregulated proteins in plasma samples of 44, 49, and 50 patients with major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia , respectively, in comparison to 51 healthy controls (HCs).","fileCount":"340","fileSizeKB":"285436741","spectra":"4972358","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Human;Schizophrenia;Plasma;Bipolar disorder;Mood depression disorder;DatasetType:Proteomics","pi":[{"name":"Dohyun Han","email":"hdh03@snu.ac.kr","institution":"Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD028841","task":"2ffc1f1613b7424c8d66a41d1973e202","id":"660"}, {"dataset":"MSV000098375","datasetNum":"98375","title":"Comparison of proteome composition of serum enriched in extracellular vesicles isolated from polycythemia vera patients and healthy controls","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751219712000","created":"Jun. 29, 2025, 10:55 AM","description":"Extracellular vesicles (EVs), e.g., exosomes and microvesicles, are one of the main networks of intercellular communication. In myeloproliferative disorders, such as polycythemia vera (PV), excess of EVs originating from overabundant blood cells can directly contribute to thrombosis through their procoagulant activity. However, proteomic composition of these vesicles in PV patients has not been investigated before. In this work, we examined proteomic composition of serum exosomes of PV patients in comparison to healthy controls. We processed exosome-enriched serum samples using Multiple Enzyme Filter Aided Sample Preparation approach (MED-FASP), conducted LC-MS\/MS measurements on a Q-Exactive HF-X mass spectrometer, and quantitatively analyzed the absolute concentrations of identified proteins by Total Protein Approach (TPA). 38 proteins were present at statistically significant different concentrations between PV patients\u2019 study group and healthy controls\u2019 group. The main protein components deregulated in PV were primarily related with excessive amounts of cells (TFRC, SELL, GP5), increased platelet activation (SERPINE1, MMRN1), elevated immune and inflammatory response (HPSE, CAMP, LYZ, SELL, LTF), and high concentrations of procoagulant and angiogenetic agents (ANG, HPSE). Our study provides the first quantitative analysis of the serum exosomes\u2019 proteome in PV patients. Acquired knowledge can be beneficial to understanding of the mechanism of PV disease and further development of diagnostic or therapeutic procedures.","fileCount":"110","fileSizeKB":"92930269","spectra":"3029486","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human plasma;Extracellular vesicles;Vesicles;DatasetType:Proteomics","pi":[{"name":"Jacek R Wisniewski","email":"jwisniew@biochem.mpg.de","institution":"Max Planck Institute of Biochemistry, Martinsried, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD013234","task":"601505dbb39745c5ad093b2051f299fb","id":"661"}, {"dataset":"MSV000098374","datasetNum":"98374","title":"Unraveling Metabolic Alterations in Avian Influenza Exposed Individuals A Non Targeted Metabolomics Approach ","user":"maoshuoqin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751169414000","created":"Jun. 28, 2025, 8:56 PM","description":"Avian influenza poses a continuous public health threat, particularly to individuals with occupational exposure to poultry such as farm workers, live animal market employees, and processing plant staff. To investigate the systemic metabolic effects of such exposure, we applied an untargeted liquid chromatography mass spectrometry (LC MS) based metabolomics approach to analyze serum samples from occupationally exposed individuals and healthy controls. Multivariate statistical analysis revealed clear separation between the two groups, with stable clustering of quality control samples indicating high analytical reproducibility. Pathway enrichment and topology analyses identified several significantly altered metabolic pathways in the exposed group, most notably alanine, aspartate and glutamate metabolism and tryptophan metabolism, both of which are closely linked to immune regulation, energy metabolism, and host-pathogen interactions. In addition, lipidomic profiling revealed a pronounced increase in lysophosphatidylcholine (LPC) levels and a concurrent decrease in phosphatidylcholine (PC) species in exposed individuals, suggesting inflammation-associated lipid remodeling. These findings provide novel insights into the metabolic disruptions associated with avian influenza exposure and highlight potential serum biomarkers for early detection and health risk assessment in high risk occupational populations.","fileCount":"524","fileSizeKB":"55017107","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;DatasetType:Proteomics","pi":[{"name":"maoshuoqin","email":"maoshuoqin2006@163.com","institution":"China capital medical school","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1ab7ea1bd4de4030aa58771ba50ecff1","id":"662"}, {"dataset":"MSV000098373","datasetNum":"98373","title":"Discovery of non-canonical translation initiation sites through mass spectrometric analysis of protein N-termini","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751167544000","created":"Jun. 28, 2025, 8:25 PM","description":"Translation initiation generally occurs at AUG codons in eukaryotes although it has been shown that non-AUG or non-canonical translation initiation can also occur. However, the evidence for non-canonical translation initiation sites (TISs) is largely indirect and based on ribosome profiling studies. Here, using a strategy specifically designed to enrich N-termini of proteins, we demonstrate that many human proteins are translated at non-canonical TISs. The large majority of TISs that mapped to 5\u2019 untranslated regions were non-canonical and led to N-terminal extension of annotated proteins or translation of upstream small open reading frames (uORF). There has been little controversy on whether the corresponding amino acid to the start codon is incorporated at TIS or methionine is still incorporated. Notably, methionine was incorporated at almost all non-canonical TISs identified in this study. Comparison of the TISs determined through mass spectrometry with ribosome profiling data revealed that about two-thirds of the novel annotations were indeed supported by ribosome profiling data. The sequence orthology analysis and relative translation frequency analysis of non-canonical TISs over canonical ones suggests that those non-canonical TISs are not leaky but they can have certain biological functions. Overall, this study provides evidence of protein translation initiation at non-canonical TISs and indicates that further studies are required for elucidation of functional implications of such non-canonical translation initiation.","fileCount":"436","fileSizeKB":"270227213","spectra":"4076921","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;LTQ Orbitrap Elite","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\"","keywords":"Human;Non-canonical;Tails;DatasetType:Proteomics","pi":[{"name":"Akhilesh Pandey","email":"pandey@jhmi.edu","institution":"Department of Biological Chemistry Johns Hopkins University School of Medicine USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD006633","task":"62baa0bf3cd844899996f9ffa9831ac0","id":"663"}, {"dataset":"MSV000098372","datasetNum":"98372","title":"Plasma proteome profiling reveals global and specific changes of inflammatory and lipid homeostasis markers after bariatric surgery","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751167409000","created":"Jun. 28, 2025, 8:23 PM","description":"Obesity-related diseases now affect half of the global population, and bariatric surgery is one of the few interventions with long lasting weight loss and cardio-metabolic effects. Here, we investigated the effect of Roux-en-Y gastric bypass surgery on the plasma proteome, hypothesizing that specific proteins or protein patterns may serve as key mediators and markers of the metabolic response. We performed MS-based proteomics on two longitudinal studies encompassing 47 morbidly obese patients, generating quantitative information on more than 1700 proteins. A global correlation matrix incorporating about 200,000 relationships revealed functional connections between proteins and assigned them to physiological processes. The main classes of significantly altered proteins were markers of systemic inflammation and those involved in lipid metabolism, and our data highlight robust correlative and anti-correlative behavior to each other and to clinical parameters. A group of inflammation-related proteins showed distinct inverse relationships to proteins consistently associated with insulin sensitivity.","fileCount":"1417","fileSizeKB":"749159260","spectra":"9301199","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Biomarker \/ diabetes \/ mass spectrometry \/ obesity \/ plasma proteome profiling \/ serum \/ gastric bypass surgery \/ global correlation profiles;DatasetType:Proteomics","pi":[{"name":"Matthias Mann","email":"mmann@biochem.mpg.de","institution":"Proteomics and Signal Transduction Max Planck Institute of Biochemistry","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD009348","task":"b1551058179745e58712859c6c31a643","id":"664"}, {"dataset":"MSV000098371","datasetNum":"98371","title":"Proteomics of iPSC derived enteric neural lineages from Parkinson Disease patients ","user":"brghirotto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751145351000","created":"Jun. 28, 2025, 2:15 PM","description":"Gastrointestinal (GI) dysfunction precedes motor symptoms in Parkinson disease (PD), implicating the enteric nervous system (ENS) in early disease pathogenesis. However, how the PD-associated protein alpha synuclein (alpha syn) contributes to ENS dysfunction, and whether this is influenced by inflammation, remains unresolved. Here, we show that tumor necrosis factor alpha (TNF alpha) increases alpha syn accumulation at mitochondria, disrupts the malate-aspartate shuttle (MAS), and induces a metabolic shift toward glutamine oxidation in iPSC derived enteric neural lineages (ENLs) from PD patients carrying alpha syn gene triplications. This metabolic rewiring leads to mitochondrial dysfunction, NAD+ depletion, and oxidative stress. Targeting glutamate metabolism with Chicago Sky Blue 6B restores mitochondrial function and reverses TNF alpha induced metabolic impairment. Combined transcriptomic and histological analyses of human gut tissue show that inflammation-associated MAS suppression and alpha syn upregulation are not confined to PD but are general hallmarks of intestinal inflammation. These findings highlight a conserved metabolic vulnerability in the ENS and establish iPSC ENLs as a powerful platform for modeling early inflammatory disease mechanisms.","fileCount":"28","fileSizeKB":"36705857","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"iPSC;Parkinson;Enteric Nervous System;DatasetType:Proteomics","pi":[{"name":"Beate Winner","email":"beate.winner@fau.de","institution":"Friedrich Alexander Universitat Erlangen Nurnberg","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"a5457c2288564fc99305baa0c3b5b0f3","id":"665"}, {"dataset":"MSV000098370","datasetNum":"98370","title":"Robust micro-flow LC-MS\/MS for proteome analysis \u2013 38,000 runs and counting","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751079133000","created":"Jun. 27, 2025, 7:52 PM","description":"Micro-flow liquid chromatography tandem mass spectrometry (µLC\u2013MS\/MS) is increasingly becoming an alternative to nano-LC\u2013MS\/MS for the analysis of proteomes. We have recently demonstrated the potential of a µLC\u2013MS\/MS system operating with a 1 mm i.d.?×?150?mm column and at a flow rate of 50?µl\/min for high-throughput applications. Based on the analysis of ~38,000 samples measured on two instruments over the past two years, we show that the approach is extremely robust. Up to 1,500 analysis were performed within one month and >14,000 samples could be analyzed on a single column without loss of chromatographic performance. Samples included proteomes of cell lines, animal tissue and human body fluids, which were analyzed either with or without prior peptide fractionation or stable isotope labeling. We show that the µLC\u2013MS\/MS system is capable of measuring ~2,700 proteins from human plasma and ~5,200 proteins from human urine within one day, demonstrating its potential for in-depth as well as high-throughput clinical application.","fileCount":"261","fileSizeKB":"88354434","spectra":"3527100","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Micro-flow lc;Plasma;Proteomics;Urine;1.0 mm id column;DatasetType:Proteomics","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, Technische Universitaet Muenchen","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD023650","task":"ee145dcbbfe54a5a9ca7dcf4c00600c1","id":"666"}, {"dataset":"MSV000098369","datasetNum":"98369","title":"Online-2D nanoLC-MS for crude serum proteome profiling: assessing sample preparation impact on proteome composition","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751074905000","created":"Jun. 27, 2025, 6:41 PM","description":"Although current LC-MS technology permits scientists to efficiently screen clinical samples in translational research, e.g. steroids, biogenic amines and even plasma or serum proteomes, in a daily routine, maintaining the balance between throughput and analytical depth is still a limiting factor. A typical approach to enhance the proteome depth is employing offline 2-dimensional (2D) fractionation techniques before nanoLC-MS\/MS analysis. These additional sample preparation steps usually require extensive sample manipulation, which could result in sample alteration and sample loss. The consequent results variability increase the risk of false discovery, regardless of time-intensive sample preparation workload. Here we present and compare 1D-nanoLC-MS with an automated online-2D high-pH RP x low pH RP separation method for deep proteome profiling using a nanoLC system coupled to a high-resolution accurate-mass mass spectrometer. The proof-of-principle study permitted the identification of ca. 500 proteins with ~10,000 peptides in 15 enzymatically digested crude serum samples collected from healthy donors in 3 laboratories across Europe. The developed method identified 60% more peptides in comparison with conventional 1D nanoLC-MS\/SM analysis with ca. 4 times lower throughput while retaining the quantitative information. Serum sample preparation artifacts were revealed by applying unsupervised classification techniques, and, therefore, must be taken into account while planning multicentric biomarker discovery and validation studies. Overall, this novel method reduces sample complexity and boosts the number of peptide and protein identifications without the need for extra sample handling procedures for samples equivalent to less than 1 µL of blood, which expands the space for potential biomarker discovery by looking deeper into the composition of biofluids.","fileCount":"109","fileSizeKB":"246827655","spectra":"4443838","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Peptide fractionation;Blood;Nanolc-ms;1d nanolc-ms;Proteome profiling;Crude serum;High-resolution accurate mass-spectrometry;Online-2d nanolc-ms;DatasetType:Proteomics","pi":[{"name":"Alexander Boychenko","email":"oleksandr.boychenko@thermofisher.com","institution":"Thermo Fisher Scientific","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD024893","task":"7311dbc7ed734929a1e908dee833cb9e","id":"667"}, {"dataset":"MSV000098366","datasetNum":"98366","title":"Metabolomics of iPSC derived enteric neural lineages from Parkinson Disease patients challenged with TNF alpha","user":"brghirotto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751053621000","created":"Jun. 27, 2025, 12:47 PM","description":"Gastrointestinal (GI) dysfunction precedes motor symptoms in Parkinson disease (PD), implicating the enteric nervous system (ENS) in early disease pathogenesis. However, how the PD-associated protein alpha synuclein (alpha syn) contributes to ENS dysfunction, and whether this is influenced by inflammation, remains unresolved. Here, we show that tumor necrosis factor alpha (TNF alpha) increases alpha syn accumulation at mitochondria, disrupts the malate-aspartate shuttle (MAS), and induces a metabolic shift toward glutamine oxidation in iPSC derived enteric neural lineages (ENLs) from PD patients carrying alpha syn gene triplications. This metabolic rewiring leads to mitochondrial dysfunction, NAD+ depletion, and oxidative stress. Targeting glutamate metabolism with Chicago Sky Blue 6B restores mitochondrial function and reverses TNF alpha induced metabolic impairment. Combined transcriptomic and histological analyses of human gut tissue show that inflammation-associated MAS suppression and alpha syn upregulation are not confined to PD but are general hallmarks of intestinal inflammation. These findings highlight a conserved metabolic vulnerability in the ENS and establish iPSC ENLs as a powerful platform for modeling early inflammatory disease mechanisms.","fileCount":"8","fileSizeKB":"9653132","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Dionex instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Parkinson;iPSC;enteric nervous system;TNF-alpha;DatasetType:Metabolomics","pi":[{"name":"Beate Winner","email":"beate.winner@fau.de","institution":"Friedrich Alexander Universitat Erlangen Nurnberg","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"85492deedc7c40a39a3568287f5d398b","id":"668"}, {"dataset":"MSV000098365","datasetNum":"98365","title":"Involvement of serum-derived exosomes of patients with low bone density in progressive failure of bone remodeling via alteration of intercellular signal transduction and integrin-mediated mechanosensation","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751052730000","created":"Jun. 27, 2025, 12:32 PM","description":"Exosomes are secreted into the blood by various types of cells. These small vesicles are involved in bone remodeling by mediation of intercellular communication in osteoblasts, osteoclasts or their precursors. Alterations in exosomal proteins are related to the failure of bone remodeling, which results in progressive loss of bone mass and poor quality of bone structure. However, the molecular changes in serum-derived exosomes (SDEs) from patients with low bone density and their functions in bone remodeling remain to be fully elucidated. We present a quantitative proteomics analysis of exosomes purified from the serum of patients with osteoporosis\/osteopenia and normal volunteers; these data are available via Proteome Xchange with the identifier PXDXXXXX. Overall, 1,371 proteins were identified with an overlap of 1,160 Gene IDs among the ExoCarta proteins. In vitro studies and bioinformatics analysis revealed that the main changes in the SDEs of osteoporosis patients were proteins playing critical roles in integrins-mediated mechanosensation and signaling cascades, which are implicated in aggravating the failure of bone remodeling, including the enhancement of osteoclast differentiation and inhibition of bone mineralization. In contrast, the main changes in SDEs of osteopenia patients were proteins known to facilitate both osteoclast differentiation and osteoblastic bone formation, which resulted in a compensatory elevation of bone remodeling. In addition, bioinformatics analysis indicated that SDEs from elderly volunteers mediate negative regulation of bone remodeling via selenium deficiency-associated oxidative stress. This information will be helpful in elucidating the pathophysiological functions of SDEs and aid in the development of osteoporosis diagnostics and therapeutics.","fileCount":"45","fileSizeKB":"56317344","spectra":"1032818","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:01720 - \\\"A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-126 reporter+balance group.\\\"","keywords":"Bone remodeling;Exosome;Osteoblasts;Osteoclast;Osteoporosis;Integrin;DatasetType:Proteomics","pi":[{"name":"Wei Ge","email":"wei.ge@chem.ox.ac.uk","institution":"National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD006463","task":"657c204223d341238dec08855560ba3c","id":"669"}, {"dataset":"MSV000098364","datasetNum":"98364","title":"An integrated genomic, proteomic and immunopeptidomic approach to discover treatment-induced neoantigens","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751048383000","created":"Jun. 27, 2025, 11:19 AM","description":"All nucleated mammalian cells express major histocompatibility complex (MHC) proteins that present peptides on cell surfaces for immune surveillance. These MHC-presented peptides (pMHC) can convey non-self antigens derived from pathogens or mutations to amount T-cell responses. Alterations in tumor-specific antigens \u2013 particularly mutation-bearing peptides (neoantigens) presented by MHC \u2014 can serve as potent substrates for anti-tumor immune responses. Here we employed an integrated genomic and proteomic antigen discovery strategy aimed at measuring interferon gamma (IFN-?) induced alterations to antigen presentation, using a lymphoma cell line. IFN-? treatment resulted in a set of differentially expressed proteins (2 % of all quantified proteins) including components of antigen presentation machinery or interferon signaling pathways. In addition, several proteasome subunits were found to be modulated, consistent with previous reports of immunoproteasome induction by IFN-? exposure. This finding suggests that a modest proteomic response to IFN-? could create larger alteration to cells antigen repertoires. Accordingly, by surveying immunopeptides, distinct peptide repertoires were exclusively observed in the IFN-? induced samples. Furthermore, an additional set of presented peptides distinguished control and the IFN-? samples by their altered relative abundances including neoantigens. Accordingly, we developed a classification system to distinguish peptides which are differentially presented due to altered expression from novel peptides resulting from changes in antigen processing. Taken together, these data demonstrate that IFN-? can re-shape antigen repertoires by identity and by abundance. Extending this approach to models with greater clinical relevance should help develop strategies by which immunopeptide repertoires are intentionally reshaped to improve endogenous or vaccine-induced anti-tumor immune responses and potentially anti-viral immune responses.","fileCount":"88","fileSizeKB":"10401512","spectra":"36946","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00765 - \\\"A protein modification that effectively converts an L-cysteine residue to S-(L-cysteinyl)-L-cysteine, forming a disulfide bond with free cysteine.\\\";MOD:00696 - \\\"A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate').\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Human;Mhc;Interferon gamma;Antigen presentation;Orbitrap;DatasetType:Proteomics","pi":[{"name":"Joshua E Elias","email":"josh.elias@czbiohub.org","institution":"Chan Zuckerberg Biohub, Stanford, CA, USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD020750","task":"be5fa89b2e664360afc66a7c06172160","id":"670"}, {"dataset":"MSV000098363","datasetNum":"98363","title":"MHC immunopeptidome of JY cells analysed by EThcD at Orbitrap Fusion after mild acid elution","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751047334000","created":"Jun. 27, 2025, 11:02 AM","description":"To understand and treat immunology-related diseases, a comprehensive, unbiased characterization of major histocompatibility complex (MHC) peptide ligands is of key importance. Preceding the analysis by mass spectrometry, MHC peptide ligands are typically isolated by MHC immunoaffinity chromatography (MHC-IAC). Less often, mild acid elution (MAE) is used to extract MHC class I peptide ligands. MAE may provide a cheap alternative to MHC-IAC for suspension cells, but it is thought to be hampered by the high number of contaminating peptides not derived from the MHC. Here, we optimized the MAE protocol yielding MHC peptide ligand purities of more than 80%. We discovered distinct cysteinylation frequencies at individual positions of MHC peptide ligands and propose that MAE conserves the native cysteinylation pattern of MHC peptide ligands better than MHC-IAC. Our improved and carefully documented MAE workflow represents a high-quality, cost-effective alternative to MHC-IAC for suspension cells and should be applicable also in laboratories not specialized in MHC peptide ligand analyses.","fileCount":"45","fileSizeKB":"15209238","spectra":"285099","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion ETD","modification":"MOD:00765 - \\\"A protein modification that effectively converts an L-cysteine residue to S-(L-cysteinyl)-L-cysteine, forming a disulfide bond with free cysteine.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Post-translational modification;Ethcd;Hla ligandome;Mild acid elution;Cysteinylation;Mhc bound peptides;DatasetType:Proteomics","pi":[{"name":"Albert J.R. Heck","email":"A.J.R.Heck@uu.nl","institution":"Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre, Utrecht, The Netherlands","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD012498","task":"6588209667aa4589b4ce68c3a88fc786","id":"671"}, {"dataset":"MSV000098362","datasetNum":"98362","title":"Class II Immunopeptidome of 9033 cells","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751037691000","created":"Jun. 27, 2025, 8:21 AM","description":"Cells were treated with either PBS (mock) or hydroxychloroquine (HCQ).","fileCount":"43","fileSizeKB":"21702298","spectra":"0","psms":"541114","peptides":"41202","variants":"54188","proteins":"4466","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"MS:1003123","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Immunopeptidomics;Hcq;9033;Class ii;Hla;DatasetType:Proteomics","pi":[{"name":"Anthony Wayne Purcell","email":"anthony.purcell@monash.edu","institution":"Deputy Head (Research), Department of Biochemistry and Molecular Biology Head Immunoproteomics Laboratory Infection and Immunity Program Room 214, level 2, 15 Innovation Walk Monash Biomedicine Discovery Institute Monash University, Clayton Campus Clayton 3800 Victoria Australia","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD029648","task":"6cf775a5634747a0a172f29e9d5549a0","id":"672"}, {"dataset":"MSV000098361","datasetNum":"98361","title":"Antigen Presentation Profiling Reveals T-cell Recognition of Lymphoma Immunoglobulin Neoantigens","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751036520000","created":"Jun. 27, 2025, 8:02 AM","description":"Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. Such neoantigens have been implicated in response to immunotherapies including immune checkpoint blockade, yet their identification and validation remains challenging. Here we discover neoantigens in human mantle cell lymphomas using an integrated strategy for genomic and proteomic tumor antigen discovery that interrogates peptides presented within the tumor major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically identify neoantigen peptides in diagnostic tumor specimens from 17 patients. Remarkably, the 52 discovered neoantigenic peptides were invariably derived from the lymphoma immunoglobulin (Ig) heavy or light chain variable regions. Although we could identify MHC presentation of private germline polymorphic alleles, no mutated peptides were recovered from non-Ig somatically mutated genes. The immunoglobulin variable region somatic mutations were almost exclusively presented by MHC-II. We found T-cells specific for an immunoglobulin-derived neoantigen in the blood of a patient using MHC-II tetramers, and these T-cell clones expanded in frequency following tumor vaccination. These results demonstrate that an integrative approach combining MHC isolation, peptide identification and exome sequencing is an effective platform to uncover tumor neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.","fileCount":"277","fileSizeKB":"38442652","spectra":"2817828","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00696 - \\\"A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate').\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Human;Mhc;Mantle cell lymphoma;Antigen presentation;Ltq orbitrap elite;DatasetType:Proteomics","pi":[{"name":"Joshua E Elias","email":"josh.elias@stanford.edu","institution":"Department of Chemical & Systems Biology Stanford University USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD004746","task":"8d858c6eec5441e1bf5000ac7d3e414e","id":"673"}, {"dataset":"MSV000098359","datasetNum":"98359","title":"Temperature induced change of the HLA ligandome","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751036118000","created":"Jun. 27, 2025, 7:55 AM","description":"Temperature induced change of the HLA ligandome and proteome in B-cells","fileCount":"89","fileSizeKB":"79808462","spectra":"1507851","psms":"157992","peptides":"17889","variants":"22696","proteins":"6809","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hla class ii ligandome;Hla class i ligandome;Immunopeptidome;Proteome;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Wei Wu","email":"w.wu1@uu.nl","institution":"Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD022930","task":"a236c3c39d964ec990047181232d60f4","id":"674"}, {"dataset":"MSV000098357","datasetNum":"98357","title":"Proteomic Profiling of Serum Exosomes from Patients with Metastatic Gastric Cancer","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751029011000","created":"Jun. 27, 2025, 5:56 AM","description":"Clinical management of metastatic gastric cancer (mGC) remains a major challenge due to a lack of specific biomarkers and effective therapeutic targets. Recently, accumulating evidence has suggested that exosomes play an essential role in cancer metastasis and can be an excellent reservoir of novel biomarkers and candidate therapeutic targets for cancer. Therefore, in this study, we aimed to reveal the proteomic profile of mGC-derived exosomes.Exosomes were isolated from pooled serum samples of 20 mGC patients and 40 healthy controls (HCs) by ultracentrifugation. Next, quantitative proteomic analyses were applied to analyze the protein profiles of the exosomes, and bioinformatic analyses were conducted on the proteomic data. Finally, the expression of exosomal protein candidates was selectively validated in individual subjects by western blot analysis. We isolated exosomes from serum samples. The size of the serum derived exosomes ranged from 30 to 150 nm in diameter. The exosomal markers CD9 and CD81 were observed in the serum exosomes. However, the exosomal negative marker calnexin, an endoplasmic reticulum protein, was not detected in exosomes. Overall, 443 exosomal proteins, including 110 differentially expressed proteins (DEPs) were identified by quantitative proteomics analyses. The bioinformatics analyses indicated that the upregulated proteins were enriched in the process of protein metabolic, whereas the downregulated proteins were largely involved in cell-cell adhesion organization. Surprisingly, ten highly vital proteins (UBA52, PSMA1, PSMA5, PSMB6, PSMA7, PSMA4, PSMA3, PSMB1, PSMA6, and FGA) were filtered from DEPs, most of which are proteasome subunits. Moreover, the validation data confirmed that PSMA3 and PSMA6 was explicitly enriched in the serum derived exosomes from patients with mGC. The present study provided a comprehensive description of the serum exosome proteome of mGC patients, which could be an excellent resource for further studies of mGC.","fileCount":"20","fileSizeKB":"3077144","spectra":"144697","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metastatic gastric cancer;serum exosomes;lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Jian Hua Tong","email":"jh_tong@126.com","institution":"Ruijin Hospital, Shanghai Jiao Tong\uFFFDUniversity School of Medicine, Shanghai, China","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD019387","task":"224f9a140e4140f5a3359726bf060d8c","id":"675"}, {"dataset":"MSV000098356","datasetNum":"98356","title":"Characterization of plasma circulating small extracellular vesicles in patients with metastatic solid tumors and newly diagnosed brain metastasis","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751028907000","created":"Jun. 27, 2025, 5:55 AM","description":"Brain metastases are critical for outcomes and quality of life in almost 50% of oncological patients, generally associated with a poor short-term prognosis. Early or preventive diagnosis of this complication represents an unmet need. There is a necessity of discovering new biomarkers that could aid to predict disease outcome. In this study, we analyzed plasma circulating extracellular vesicles (EVs) from a cohort of 92 patients with different solid tumors (lung, breast, kidney cancer and melanoma) and found that newly diagnosed patients with brain metastases presented lower number of circulating particles and a higher protein concentration in small extracellular vesicles (sEVs) compared to patients without brain metastases and healthy controls. Out of all groups analyzed, melanoma patients with brain metastases presented decreased STAT3 activation and increased PD-L1 levels in circulating sEVs compared to patients without central nervous system metastases. The data presented in this work suggest that circulating sEVs may represent the immunosuppressive status of newly diagnosed brain metastases characterized by the reduced phospho-STAT3 (pSTAT3) and increased PD-L1, although the origin of these molecules found in circulating sEVs remains to be uncovered.","fileCount":"27","fileSizeKB":"13194783","spectra":"419758","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Exosomes;Plasma;Human;Brain metastasis;DatasetType:Proteomics","pi":[{"name":"Pilar Xim\uFFFDnez-Emb\uFFFDn","email":"mpximenez@cnio.es","institution":"Proteomics Unit Spanish National Cancer Research Centre (CNIO) ProteoRed-ISCIII Melchor F\uFFFDrnandez Almagro, 3 28029 Madrid. SPAIN","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD032767","task":"c95d3c33c552487cb9564fd53bc8391d","id":"676"}, {"dataset":"MSV000098355","datasetNum":"98355","title":"HLA-DR ligands from BLCLs 9022 and 9087","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751028292000","created":"Jun. 27, 2025, 5:44 AM","description":"HLA-DR-bound peptides eluted from B-lymphoblastoid cell lines 9022 and 9087.","fileCount":"123","fileSizeKB":"18589109","spectra":"218325","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 5600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human;Blcl;Immunopeptidome;Hla class ii;Hla-dr;DatasetType:Proteomics","pi":[{"name":"Anthony Purcell","email":"anthony.purcell@monash.edu","institution":"Deputy Head (Research), Department of Biochemistry and Molecular Biology, Head Immunoproteomics Laboratory, Infection and Immunity Program Monash Biomedicine Discovery Institute, Monash University, Clayton Campus Clayton 3800 Victoria Australia","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD017682","task":"27b5d3bea59449d2ae51be152e0b288f","id":"677"}, {"dataset":"MSV000098354","datasetNum":"98354","title":"A single T cell epitope drives the neutralizing anti-drug antibody response to natalizumab in multiple sclerosis patients","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751026133000","created":"Jun. 27, 2025, 5:08 AM","description":"Natalizumab (NZM), a humanized monoclonal IgG4 antibody to ?4 integrins, is used to treat patients with relapsing-remitting multiple sclerosis (MS), but in about 6% of the cases persistent neutralizing anti-drug antibodies (ADAs) are induced leading to therapy discontinuation. To understand the basis of the ADA response and the mechanism of ADA-mediated neutralization, we performed an in-depth analysis of the B and T cell responses in two patients. By characterizing a large panel of NZM-specific monoclonal antibodies, we found that, in both patients, the response was polyclonal and targeted different epitopes of the NZM idiotype. The neutralizing activity was acquired through somatic mutations and correlated with a slow dissociation rate, a finding that was supported by structural data. Interestingly, in both patients, the analysis of the CD4+ T cell response, combined with mass spectrometry-based peptidomics, revealed a single immunodominant T cell epitope spanning the FR2-CDR2 region of the NZM light chain. Moreover, a CDR2-modified version of NZM was not recognized by T cells, while retaining binding to ?4 integrins. Collectively, our integrated analysis identifies the basis of T-B collaboration that leads to ADA-mediated therapeutic resistance and delineates an approach to design novel deimmunized antibodies for autoimmune disease and cancer treatment.","fileCount":"10","fileSizeKB":"5474128","spectra":"190236","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Antibody therapy;Mhc-ii peptidomics;Multiple sclerosis;Human;DatasetType:Proteomics","pi":[{"name":"Luca Piccoli","email":"luca.piccoli@irb.usi.ch","institution":"Institute for Research in Biomedicine, Universit\uFFFD della Svizzera italiana, Bellinzona, Switzerland.","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD013599","task":"10fd028611ed4ffd8ec4a75f35347eb1","id":"678"}, {"dataset":"MSV000098353","datasetNum":"98353","title":"The HLA-Ligand-Atlas. A resource of natural HLA ligands presented on benign tissues","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751025870000","created":"Jun. 27, 2025, 5:04 AM","description":"A use case of the benign HLA-Ligand-Atlas is the prioritization of tumor-associated targets for e.g. peptide vaccination. Based on three glioblastoma samples, we illustrated how many of these peptides are covered in the benign dataset. The experimental and computational workflow for the isolation and identification of the glioblastoma immunopeptidomes is the same, as for all samples included in the HLA Ligand Atlas. As the three glioblastoma samples are not included in the HLA Ligand Atlas dataset, they have been deposited under a separate submission.","fileCount":"83","fileSizeKB":"23712306","spectra":"452689","psms":"18696","peptides":"15722","variants":"16318","proteins":"7567","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human;Hla;Glioblastoma;Immunopeptidomics;DatasetType:Proteomics","pi":[{"name":"Hans-Georg Rammensee","email":"hgrhgr2017@gmx.de","institution":"Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University T\uFFFDbingen","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD020186","task":"95037d32ab334def95f5461cf2535892","id":"679"}, {"dataset":"MSV000098352","datasetNum":"98352","title":"MHCquant: Automated and reproducible data analysis for immunopeptidomics","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751023195000","created":"Jun. 27, 2025, 4:19 AM","description":"Personalized multi-peptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to find epitopes - short, immunogenic peptides - suitable to elicit an immune response, human leukocyte antigen-presented peptides from cancer tissue samples are purified using immunoaffinity purification and analyzed by high performance liquid chromatography coupled to mass spectrometry. Here we report on a novel computational pipeline to identify peptides from large-scale immunopeptidomics raw data sets. In the conducted experiments we benchmarked our workflow to other existing mass spectrometry analysis software and achieved higher sensitivity. A dataset of 38 HLA immunopeptidomics raw files of peripheral blood mononuclear cells (PBMCs) from 10 healthy volunteers and 4 JY cell lines was used to assess the performance of the pipeline at each processing step. In addition, 66 isotope labeled known HLA-presented peptides were spiked into the JY cell extracts decreasing in concentration by log10 steps from 100 fmol to 0.1 fmol.","fileCount":"162","fileSizeKB":"31450099","spectra":"877061","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Human;Mhc;Benchmark;DatasetType:Proteomics","pi":[{"name":"Professor Oliver Kohlbacher","email":"oliver.kohlbacher@uni-tuebingen.de","institution":"Dept. of Computer Science, University of T\uFFFDbingen Germany, Center for Bioinformatics, University of T\uFFFDbingen, Germany, Quantitative Biology Center, University of T\uFFFDbingen, Germany, Max Planck Institute for Developmental Biology, Germany,","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD011628","task":"ca2d2fbb2032469986024e75d6fb4564","id":"680"}, {"dataset":"MSV000098351","datasetNum":"98351","title":"Proteomics of cerebrospinal fluid (CSF) of acitretin treated patients","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751021848000","created":"Jun. 27, 2025, 3:57 AM","description":"Acitretin has been shown to increase ADAM10 expression. In a phase II clinical trial, Alzheimer's disease patients were treated with acitretin or placebo to increase ADAM10 levels to counteract amyloid beta production. Analysis of the cerebrospinal fluid of from 18 AD patients treated with the synthetic retinoid acitretin or placebo were analyzed by label-free quantitative LC-MS\/MS analysis.","fileCount":"74","fileSizeKB":"91619643","spectra":"1297111","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Alzheimer disease;Csf;Acitretin;DatasetType:Proteomics","pi":[{"name":"Stefan F. Lichtenthaler","email":"stefan.lichtenthaler@dzne.de","institution":"DZNE Munich Neuroproteomics Feodor-Lynen Str. 17 81377 Munich Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD010756","task":"efbb4b33557b4088aa369f6884b5f2b8","id":"681"}, {"dataset":"MSV000098350","datasetNum":"98350","title":"CSF proteome mapping: Human cerebrospinal fluid LC-MS\/MS, Part 1","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751021796000","created":"Jun. 27, 2025, 3:56 AM","description":"3 mL CSF from a pool of 21 neurologically healthy donors was separated into a bound and a depleted fraction using a MARS Hu-14 column. This experiment represents the bound fraction. Gel separation on a gradient gel (SDS-PAGE) followed and the gel lane was cut into 37 fractions. Each fraction was in-gel trypsin digested and analyzed separately by LC-MS\/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to CSF-PR.","fileCount":"80","fileSizeKB":"41507968","spectra":"542056","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap;MS:1000031","modification":"MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:01090 - \\\"A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\"","keywords":"Homo sapiens;Cerebrospinal fluid;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Astrid Guldbrandsen","email":"astrid.guldbrandsen@biomed.uib.no","institution":"PROBE","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000651","task":"f5daac9bc3a54e21ad8983238405a5a3","id":"682"}, {"dataset":"MSV000098348","datasetNum":"98348","title":"Plasma exosomal proteomic pattern in Hemophagocyticlymphohistiocytosis of a twin boy","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751018629000","created":"Jun. 27, 2025, 3:03 AM","description":"Background: Secondary HLH is closely related to EBV infection, protein changes in plasma exosomes may be related to the pathogenesis of HLH patient. In recent years quantitative proteomic has been used to clarify the relationship between basic medicine and clinical medicine. Methods: Exosomes were isolated from plasma samples of a HLH patient and his twin brother. Plasma samples were classified into three groups according to the clinical presentation, namely T1 (the acute HLH), T2 (during pharmacological treatments), Ctr (the healthy control). Herein, we used TMT-based LC-MS\/MS platform to identified and characterized HLH signatures before and during pharmacological treatments. Results: Exosomes\u2019 marker proteins- CD63, TSG101, HSP70 were identified by western blotting. Through GO analysis and KEGG analysis, we found that the signaling pathways and functions enriched by differentially expressed genes are very different. We focus on describing? the significantly up-regulated proteins-MSN, HSPA8, CD163, and the significantly down-regulated proteins- PLG, FGG, F2. The significant changes of these factors are related to the deterioration of the disease Conclusion: Our exploratory study shows that the clinical symptoms and pathophysiological changes of HLH driven by EBV might be reflected in patients\u2019 plasma exosomes. Plasma exosome proteomics provides new highlightinsights for into exploring the diagnostic and therapeutic biomarkers of HLH.","fileCount":"20","fileSizeKB":"3818024","spectra":"81732","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hemophagocyticlymphohistiocytosis? twins?exosomes?proteomic analysis;DatasetType:Proteomics","pi":[{"name":"Yan Xie","email":"1148452190@qq.com","institution":"1Department of Hematology, Xiangya Hospital, Central South University, Changsha 410080, China 2NHC Key Laboratory of Carcinogenesis, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha 410078, China","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD019088","task":"8cda7fdcb4ee4734bb3c09c3fd3f0708","id":"683"}, {"dataset":"MSV000098346","datasetNum":"98346","title":"CSF proteome mapping: Human Plasma LC-MS\/MS, Part 6","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751010125000","created":"Jun. 27, 2025, 12:42 AM","description":"40 µL plasma from a pool of 20 neurologically healthy donors was separated into a bound and a depleted fraction using a MARS Hu-14 column. This experiment represents the bound fraction. Sample was in-solution trypsin digested and peptides were fractionated into 10 fractions by mixed-mode reversed phase anion exchange (MM(RP-AX) using a Promix MP column. Each fraction was analyzed separately by LC-MS\/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to the CSF-PR.","fileCount":"25","fileSizeKB":"12742172","spectra":"185211","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap;MS:1000031","modification":"MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:01090 - \\\"A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:01047 - \\\"A protein modification that effectively converts an L-lysine residue to a monohydroxylated lysine.\\\"","keywords":"Plasma;Homo sapiens;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Astrid Guldbrandsen","email":"astrid.guldbrandsen@biomed.uib.no","institution":"PROBE","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000656","task":"514976c82d9947109d0e47565df44f8e","id":"684"}, {"dataset":"MSV000098345","datasetNum":"98345","title":"Quantitative Proteomics Reveals Transforming growth factor beta Axis Induced by Resveratrol and Hesperetin Coformulation in Endothelial Cells","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1751010123000","created":"Jun. 27, 2025, 12:42 AM","description":"The endothelium is the frontline target of multiple metabolic stressors and pharmacological agents. As a consequence, endothelial cells (ECs) display highly dynamic and diverse proteome profiles. We describe here the culture of human aortic ECs from healthy and type 2 diabetic donors, the treatment with a small molecular conformation of trans-resveratrol and hesperetin (tRES+HESP), followed by proteomic analysis of whole-cell lysate. A number of 3666 proteins were presented in all the samples and thus further analyzed. We found that 179 proteins had a significant difference between diabetic ECs vs. healthy ECs, while 81 proteins had a significant change upon the treatment of tRES+HESP in diabetic ECs. Among them, 16 proteins showed a difference between diabetic ECs and healthy ECs and the difference was reversed by the tRES+HESP treatment, with the top 5 drastically altered proteins being ACVRL1, ADAM9, ITGAV, PCCB, and TGFBR2. Follow-up functional assays identified ACVRL1 and TGFBR2 as the most pronounced mediator for tRES+HESP-induced protection of angiogenesis in vitro. Our study has revealed the global changes in proteins and biological pathways in ECs from diabetic donors, which are potentially reversible by the tRES+HESP formula. Furthermore, we have identified the TGF? signaling axis as a responding mechanism in ECs treated with this formula, shedding light for future studies for deeper molecular characterization","fileCount":"28","fileSizeKB":"18959127","spectra":"863957","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Endothelial cells;type 2 diabetes;trans-resveratrol;proteomics;transforming growth factor-beta;DatasetType:Proteomics","pi":[{"name":"Dr. Zhengping Yi","email":"zhengping.yi@wayne.edu","institution":"Integrated Biosciences; Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD036094","task":"2cbbcd26f189483fbfdebdddfc03f34d","id":"685"}, {"dataset":"MSV000098343","datasetNum":"98343","title":"CSF proteome mapping: Human cerebrospinal fluid LC-MS\/MS, Part 3","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750983067000","created":"Jun. 26, 2025, 5:11 PM","description":"3 mL CSF from a pool of 21 neurologically healthy donors was in-solution trypsin digested followed by Solid-phase enrichment of N-linked glycopeptides (SPEG) using hydrazide modified beads. Glycopeptides were further fractionated into 20 fractions by mixed-mode reversed phase anion exchange (MM(RP-AX) using a Promix MP column. Each fraction was analyzed separately by LC-MS\/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to the CSF-PR.","fileCount":"45","fileSizeKB":"19433451","spectra":"235148","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap;MS:1000031","modification":"MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:01090 - \\\"A protein modification that by reaction of iodoacetamide effectively replaces a residue alpha-amino- or alpha-imino-hydrogen with a carboxamidomethyl group.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Homo sapiens;Cerebrospinal fluid;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Astrid Guldbrandsen","email":"astrid.guldbrandsen@biomed.uib.no","institution":"PROBE","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000653","task":"4cbefea3312b43f487af310ec8515d94","id":"686"}, {"dataset":"MSV000098341","datasetNum":"98341","title":"Albuminome from human serum and CSF","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750981751000","created":"Jun. 26, 2025, 4:49 PM","description":"Albuminome from human serum was isolated using ProteaPrep HSA affinity spin columns and Vivapure anti-HSA spin columns. Albuminome from CSF was isolated using ProteaPrep HSA affinity spin columns. Isolated albuminome was trypsin digested and analyzed by LC-MS\/MS to determine serum and CSF albuminome proteins. All raw MS\/MS data originating from the Orbitrap Elite were batch searched based on albuminome isolation method (ProteaPrep vs. Vivapure). A total of 9 files were acquired for each albuminome analyzed (3 technical reps x 3 MS technical reps). All data were searched using the Sorcerer 2TM-SEQUEST algorithm (Sage-N Research, Milpitas, CA, USA) using default peak extraction parameters. Data were searched against the Human Uniprot database (July 2012) with an Xcorr cutoff of 1.7 using the following criteria: Fixed modification: +57 on C (carbamidomethyl); Variable modification: +16 on M (oxidation); Enzyme: Trypsin with 2 max missed cleavages; Parent Tolerance: 50 ppm; Fragment tolerance: 1.00 Da. Post-search analysis was performed using Scaffold 3 version 3.6.2 (Proteome Software, Inc., Portland, OR, USA) with protein and peptide probability thresholds set to 95% and 90%, respectively, and one peptide required for identification. Protein and peptide false discovery rates were calculated automatically using Scaffold\u2019s probabilistic method and were equal to or less than 0.5 % for all samples using the above thresholds. Data were imported in Protein Center (Proxeon\/ThermoFisher) and all data were clustered by indistinguishable proteins to remove protein redundancy within data sets. Only proteins that were observed in all three technical replicates were included in the final protein list, although proteins observed it at least two technical replicates were included in the on-line supplement for reference.","fileCount":"109","fileSizeKB":"16691005","spectra":"498562","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Albuminome;Cerebrospinal fluid;Serum;Csf;Albumin;DatasetType:Proteomics","pi":[{"name":"Ronald Holewinski","email":"rholewi1@jhmi.edu","institution":"Johns Hopkins University","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD000036","task":"6ad1612c7f2b45ab8803a3fcd7a41aba","id":"687"}, {"dataset":"MSV000098338","datasetNum":"98338","title":"Membrane-Associated Rhes Slc4a7 Complex Orchestrates Tunneling Nanotube Formation and Mutant Huntingtin Spread","user":"gcrynen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750962673000","created":"Jun. 26, 2025, 11:31 AM","description":"Tunneling nanotubes are membranous structures that mediate intercellular transfer of proteins, including the pathogenic mutant Huntingtin protein in Huntingtons disease. We previously identified the ras homolog enriched in the striatum (Rhes) as a key regulator of TNT formation and mHTT transmission however, the molecular components underlying this process remained unknown. Here, using unbiased Liquid chromatography tandem mass spectrometry LC MSMS analysis of membrane associated Rhes complexes, we identify Slc4a7 (Solute Carrier Family 4 Member 7), an intracellular pH sensor, as a top membrane binding partner of Rhes. Functional studies revealed that siRNA mediated depletion or pharmacological inhibition of Slc4a7 significantly reduced Rhes induced TNT formation and suppressed mHTT intercellular transfer. Mechanistically, Rhes directly interacts with Slc4a7 through both its N and C terminal domains and modulates intracellular pH to facilitate TNT formation. This interaction does not depend on the transporter activity of Slc4a7. However, inhibition of Rhes farnesylation a lipid modification that anchors Rhes to the membrane disrupts its binding to Slc4a7 and abolishes TNT formation. Importantly, Slc4a7 knockout mice showed markedly reduced cell to cell transmission of mHTT in the striatum in vivo. Together, these findings uncover a previously unrecognized Rhes Slc4a7 signaling axis critical for TNT mediated mHTT transmission and highlight Slc4a7 as a potential therapeutic target to limit disease spread in HD.","fileCount":"77","fileSizeKB":"94919452","spectra":"0","psms":"417262","peptides":"48149","variants":"84200","proteins":"5203","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion ETD","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"rhes;SLC4A7;Huntington disease;Neurodegeneration;protein protein interaction;tunneling nanotubes;DatasetType:Proteomics","pi":[{"name":"Srinivasa Subramaniam","email":"ssubramaniam@fau.edu","institution":"Florida Atlantic University (FAU), Stiles-Nicholson Brain Institute","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD065528","task":"2ad39c7d8fd249a5afe30f97910e9361","id":"688"}, {"dataset":"MSV000098337","datasetNum":"98337","title":"GNPS - Asaia species - average mass spectrum profiles","user":"sabipur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750954039000","created":"Jun. 26, 2025, 9:07 AM","description":"an in-house prepared average mass spectrum profile of Asaia krungthepensis CCM 7333T, Asaia lannensis BCC 15734 and Asaia siamensis CCM 7132T for the identification in the MALDI Biotyper Offline Classification software, samples prepared by the ethanol\/formic acid extraction method from freshly grown colonies cultured aerobically on Sabouraud dextrose agar (25 degrees Celsia, 72 hours), matrix: alfa-cyano-4-hydroxycinnamic acid (10 mg per microliter), spectra acquired using an Autoflex Speed mass spectrometer and FlexControl 3.4 software (both Bruker Daltonics, Bremen, Germany), single average mass spectrum profiles created from a total of 30 spectra (10 spectra from one independent experiment of five biological replicates by four technical replicates) using MALDI Biotyper software version 3.1 according to the manufacturer standard protocols (MALDI Biotyper Preprocessing Standard Method and MSP Creation Standard Method) (both Bruker Daltonics, Bremen, Germany)","fileCount":"4","fileSizeKB":"263","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Asaia species","instrument":"Autoflex Speed (Bruker Daltonics)","modification":"not known","keywords":"average mass spectrum profile;DatasetType:Proteomics","pi":[{"name":"Sabina Purkrtova","email":"Sabina.Purkrtova@vscht.cz","institution":"University of Chemistry and Technology, Prague","country":"Czechia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d1be065211664b96a7c6d79d407f4f79","id":"689"}, {"dataset":"MSV000098335","datasetNum":"98335","title":"A novel factor integrating transcription and repression of surface antigen genes in African trypanosomes","user":"aad100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750926593000","created":"Jun. 26, 2025, 1:29 AM","description":"Mass spectrometry data and proteomic results relating to the manuscript: A novel factor integrating transcription and repression of surface antigen genes in African trypanosomes","fileCount":"40","fileSizeKB":"115519858","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trypanosoma brucei (NCBITaxon:5691)","instrument":"timsTOF HT","modification":"UNIMOD:4 - 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\\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Plasma proteogenomics;DatasetType:Proteomics","pi":[{"name":"Janne Lehti\uFFFD","email":"janne.lehtio@ki.se","institution":"Cancer proteomics group, Science for Life Laboratory, Department of oncology and pathology, Karolinska Institutet","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD010899","task":"49311e878e6442d989c1e7fb3c3c7c1c","id":"691"}, {"dataset":"MSV000098333","datasetNum":"98333","title":"Proteome-wide evaluation of plasma depletion methods vis-à-vis fractionation techniques","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750914857000","created":"Jun. 25, 2025, 10:14 PM","description":"Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and\/or response to medical treatment to avoid unnecessary invasive biopsy. Data driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome, and in particular the enormous quantitative dynamic range, estimated to be between 9-13 orders of magnitude between the lowest and highest abundance protein. A major challenge is to identify workflows which can achieve depth of plasma proteome coverage, while minimizing the complexity of sample workup and maximizing sample throughput. In this study, we have performed intensive depletion of high abundant plasma proteins or enrichment of low abundant proteins using Hu6, Hu14 and ProteoMiner followed by SDS PAGE and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method which satisfies requirements for analysis of clinical samples, and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we have reported that gel-based prefractionation approaches can replace expensive and time-consuming chromatographic separation, thereby significantly accelerating analysis time. In addition, we showed that a variety of methodologies can achieve similarly high proteome coverage, allowing flexibility depending on project specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable and accurate diagnoses for the population as a whole.","fileCount":"1153","fileSizeKB":"428539358","spectra":"3146939","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00399 - \\\"A protein modification that is produced by reaction with iodoacetic acid, usually replacement of a reactive hydrogen with a methylcarboxy group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Electrophoresis;Plasma;Chromatography;Mass spectrometry;Prefractionation techniques;Label-free quantitation;Biomarkers;Proteome;DatasetType:Proteomics","pi":[{"name":"Gurjeet Kaur","email":"g.virk@student.unsw.edu.au","institution":"Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD022469","task":"3a3be663c16940da9dd99f237956fb6a","id":"692"}, {"dataset":"MSV000098332","datasetNum":"98332","title":"Proteomic Analysis in mouse CAD cells","user":"Ekkaphot","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750911633000","created":"Jun. 25, 2025, 9:20 PM","description":"As an in vitro model of neurons, catecholaminergic CAD cells have been selected because of their direct origin in the mouse central nervous system and their ability to undergo inducible differentiation, which is characterized by cell cycle exit and neurite outgrowth. This study aims to apply a label-free quantitative SWATH-MS proteomic approach to investigate the holistic aspects of protein expression in CAD cells upon differentiation.","fileCount":"82","fileSizeKB":"16438313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CAD cell line;Neuronal differentiation;SWATH-based proteomics;DatasetType:Proteomics","pi":[{"name":"Ekkaphot Khongkla","email":"ekkaphot.kho@mahidol.edu","institution":"Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University","country":"Thailand "}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"","task":"072106098b8943979bcd2c92fdf0c0e9","id":"693"}, {"dataset":"MSV000098331","datasetNum":"98331","title":"Proteome-wide analysis and surface protein isolation for secretome characterization reveal insights into the biology of the leaf-cutter ant Acromyrmex echinatior","user":"timohuangtw","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750907219000","created":"Jun. 25, 2025, 8:06 PM","description":"The leaf-cutter ant Acromyrmex echinatior secretes a protein layer that covers their exoskeleton and physically interacts with biotic and abiotic factors, including their symbiotic bacteria Pseudonocardia. In this study, in order to characterize both the global proteome and the externally-secreted cuticular protein layer of A. echinatior, we utilize a novel, dual-layered proteomic approach. Using diaPASEF, we quantified 4,428 proteins across four early adult stages, uncovering distinct age-dependent protein clusters enriched in muscle development, lipid metabolism, and immune-related responses. We then developed a novel acid-based extraction method to isolate the externally-secreted protein layer, identifying 323 secreted proteins via ddaPASEF acquisition, many of which were temporally upregulated and associated with various functions such as environmental stress response, microbial defense, and cuticle structural maturation. Notably, tropomyosin-family proteins were both highly enriched in the external-secretome and exhibited significant changes across the early adult timepoints, potentially linking these ion-binding molecules to the metal-enrichment processes that takes place during this crucial stage.","fileCount":"1267","fileSizeKB":"219867400","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Acromyrmex echinatior","instrument":"timsTOF fleX MALDI-2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Leaf-cutter ant, secretome, biomineralization;DatasetType:Proteomics","pi":[{"name":"Lingjun Li","email":"lingjun.li@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065473","task":"0e519c65b1f744ceb0c62854eb208797","id":"694"}, {"dataset":"MSV000098329","datasetNum":"98329","title":"SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750895753000","created":"Jun. 25, 2025, 4:55 PM","description":"Contains raw data and search results for manuscript titled \"SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics\".","fileCount":"54","fileSizeKB":"514926141","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mass spectrometry;Proteomics;Multiplexing;Data-Independent Acquisition;DatasetType:Proteomics","pi":[{"name":"Joshua J Coon","email":"jcoon@chem.wisc.edu","institution":"Department of Chemistry and Biomolecular Chemistry, University of Wisconsin, Wisconsin, USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065469","task":"f7d5f488e02945c08b8f71c035826002","id":"695"}, {"dataset":"MSV000098328","datasetNum":"98328","title":"Proteomic profiling of extracellular vesicles from virulent (vEV) and attenuated (aEV) Paracoccidioides brasiliensis isolate Pb18, as well as EVs released from virulent Pb18 exposed to oxidative (vEVOxi) and nitrosative (vEVNO) stress.","user":"CEOA","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750893217000","created":"Jun. 25, 2025, 4:13 PM","description":"This dataset supports a comparative proteomic analysis of extracellular vesicles (EVs) and whole-cell extracts from the pathogenic fungus Paracoccidioides brasiliensis isolate Pb18. The study investigates protein cargo differences between EVs derived from virulent (vEV) and attenuated (aEV) variants, including vEVs exposed to oxidative (vEVOxi) and nitrosative (vEVNO) stress. Characterization of EVs included NTA, DLS, and Zeta potential measurements. Proteins were enzymatically digested and analyzed via nano-flow LC-MS\/MS.\n","fileCount":"39","fileSizeKB":"49698783","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Paracoccidioides brasiliensis","instrument":"Bruker Impact II;Waters Synapt G2 HDMS","modification":"Carbamidomethyl (C, fixed);Oxidation (M, variable)","keywords":"Paracoccidioides brasiliensis;Extracellular vesicles;Nano LC-ESI-MS\/MS;Oxidative stress;Nitrosative stress;Fungal pathogen;DatasetType:Proteomics","pi":[{"name":"Rosana Puccia","email":"rosana.puccia@unifesp.br","institution":"Federal University of Sao Paulo (UNIFESP)","country":"Brazil"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD065468","task":"d7089fc432a0404fae754efefb3a4e46","id":"696"}, {"dataset":"MSV000098326","datasetNum":"98326","title":"GNPS Maloney lab LCMS Data 062325","user":"malonekn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750885321000","created":"Jun. 25, 2025, 2:02 PM","description":"Assorted extracts and fractions of assorted citrus bacteria and soil bacteria, along with media blanks","fileCount":"1647","fileSizeKB":"15432667","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not applicable","instrument":"6538 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Citrus bacteria;Soil bacteria;DatasetType:Metabolomics","pi":[{"name":"Katherine Maloney","email":"kmaloney@pointloma.edu","institution":"Point Loma Nazarene University - San Diego, CA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"262aa12fd8fb41849154c48887ae5fa5","id":"697"}, {"dataset":"MSV000098325","datasetNum":"98325","title":"Gut microbiota-derived metabolite Trimethylamine N-oxide alters the host epigenome through inhibition of S-adenosylhomocysteine hydrolase","user":"Jessica_Han","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750879755000","created":"Jun. 25, 2025, 12:29 PM","description":"Mouse proteomics, histone proteomics; cell culture histone proteomics","fileCount":"215","fileSizeKB":"191653006","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";UNIMOD:34 - \\\"Methylation.\\\"","keywords":"proteomics;DatasetType:Proteomics","pi":[{"name":"John Denu","email":"john.denu@wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"144c3cbdcd0048dc90e3430244372351","id":"698"}, {"dataset":"MSV000098322","datasetNum":"98322","title":"High-Throughput Screening of Amyloid Inhibitors via Covalent-Labeling Mass Spectrometry","user":"rwvachet","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750869727000","created":"Jun. 25, 2025, 9:42 AM","description":"MS spectra of DEPC modifications on beta-2-microglobulin (b2m) residues under amyloid-forming conditions, with or without 4-hydroxythalidomide.","fileCount":"6","fileSizeKB":"1275166","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"Diethylpyrocarbonate","keywords":"DEPC labeling;DatasetType:Proteomics","pi":[{"name":"Richard W. Vachet","email":"rwvachet@chem.umass.edu","institution":"Department of Chemistry, University of Massachusetts Amherst","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"acc276095b294cfcb5a44e5fac64d34c","id":"699"}, {"dataset":"MSV000098308","datasetNum":"98308","title":"GNPS - HSL chemical standards ","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750806851000","created":"Jun. 24, 2025, 4:14 PM","description":"HSL standards: N-(3-oxohexanoyl) L-homoserine lactone and N-octanoyl L-homoserine lactone. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA)","fileCount":"18","fileSizeKB":"578930","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"none","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HSL;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Margareth McFall-Ngai","email":"mcfallng@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5816403232f448ae8941b0606fb8ecc0","id":"700"}, {"dataset":"MSV000098307","datasetNum":"98307","title":"Discovery of novel binding molecules for plant-associated Proteobacterial LuxR solos (QS-derived)","user":"cbez","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750797197000","created":"Jun. 24, 2025, 1:33 PM","description":"Discovery of novel LuxR solo regulators and their cognate binding signal molecules from non-canonical biosynthetic gene clusters (BGCs). Untargeted LC-MS\/MS acquisition was performed in Positive mode on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"312","fileSizeKB":"12498918","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294);Pseudomonas japonica (NCBITaxon:256466);Pseudomonas brassicacearum (NCBITaxon:930166);Pseudomonas cichorii (NCBITaxon:36746);Paraburkholderia phenazinium (NCBITaxon:60549)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LuxR solos;Quorum sensing;signalling;plant-associated bacteria;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"05455ca0d2044f6cb7a72f247d2d2e37","id":"701"}, {"dataset":"MSV000098306","datasetNum":"98306","title":"GNPS - Metabolite-protein covariation architecture identified a cysteine shunt regulating liver cholesterol","user":"BingsenZhangDFCI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750790199000","created":"Jun. 24, 2025, 11:36 AM","description":"Metabolomics raw data for manuscript Xiao, H. et al. \"Metabolite-protein covariation architecture identified a cysteine shunt regulating liver cholesterol\".","fileCount":"903","fileSizeKB":"107755548","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X;Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"diversity outbred;cysteine;hypotaurine;CDO1;taurine;LRRC58;DatasetType:Metabolomics","pi":[{"name":"Edward T. Chouchani","email":"EdwardT_Chouchani@DFCI.HARVARD.EDU","institution":"Dana Farber Cancer Institue","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3df6707e36674d13b26639cbc7785def","id":"702"}, {"dataset":"MSV000098300","datasetNum":"98300","title":"Defective Olfactomedin-2 connects adipocyte dysfunction to obesity","user":"Wszymanski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750760776000","created":"Jun. 24, 2025, 3:26 AM","description":"Olfactomedin-2 (OLFM2) is a pleiotropic glycoprotein emerging as a regulator of energy homeostasis. We here show the expression of OLFM2 to be adipocyte-specific and inversely associated with obesity. OLFM2 levels increase during adipocyte differentiation and are suppressed in inflamed adipocytes. Functionally, OLFM2 deficiency impairs adipogenesis, while its over-production enhances the transformation of fat cell progenitors. Loss and gain of function experiments revealed that OLFM2 modulates key metabolic and structural pathways, including PPAR signaling, citrate cycle, fatty acid degradation, axon guidance and focal adhesion. On the molecular level, OLFM2 deficiency in adipocytes predominantly downregulates genes involved in cell cycle. Extending these findings in vivo, both whole-body Olfm2 knockout and adipose-specific Olfm2 depletion resulted in impaired adipose cell cycle gene expression, with the latter also displaying fat mass accretion and metabolic dysfunction. Collectively, our results underscore a critical role for OLFM2 in adipocyte biology, and support a causative link between reduced adipose OLFM2 and the pathophysiology of obesity.","fileCount":"8","fileSizeKB":"466891069","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Ultra;Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"dia;mouse;TimsTof Ultra;Dia-NN;uPAC;autonomics;DatasetType:Proteomics","pi":[{"name":"Francisco J. Ortega, Ph.D. ","email":"fortega@idibgi.org","institution":"Institut d'Investigacio Biomedica de Girona (IDIBGI)","country":"Spain"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD065388","task":"8f9891669d574c2da780daa6b4338783","id":"703"}, {"dataset":"MSV000098297","datasetNum":"98297","title":"Untargeted Metabolomics Reveals Distinct Serum Metabolic Profiles in Avian Influenza Occupational Exposure Populations","user":"maoshuoqin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750750010000","created":"Jun. 24, 2025, 12:26 AM","description":"Background and Objectives:Avian influenza poses a continuous public health threat, particularly to individuals with occupational exposure to poultry such as farm workers, live animal market employees, and processing plant staff. This study aimed to investigate the systemic metabolic effects of such exposure and to identify potential biomarkers for early detection and health risk assessment. Materials and Methods: An untargeted liquid chromatographymass spectrometry (LCMS)based metabolomics approach was applied to analyze serum samples from occupationally exposed individuals and healthy controls. Multivariate statistical analysis, pathway enrichment, and topology analysis were performed to identify significantly altered metabolites and metabolic pathways. The least absolute shrinkage and selection operator (LASSO) algorithm was employed to select key metabolites. Results: Multivariate statistical analysis revealed a clear separation between the exposure group and control, suggesting distinct metabolic profiles between the two populations. Pathway analysis indicated significant alterations in alanine, aspartate, and glutamate metabolism, as well as tryptophanmetabolism, which are closely linked to immune regulation, energy metabolism, and host pathogen interactions. LASSO feature selection and subsequent manual verification identified 17 key metabolites with strong discriminative power. Furthermore, lipidomic profiling revealed a pronounced increase in lysophosphatidylcholine (LPC) levels and a concurrent decrease in phosphatidylcholine (PC) species in exposed individuals. Conclusions: This study reveals metabolic disruptions associated with occupational avian influenza exposure and identifies potential serum biomarkers related to immune and lipid metabolism. These findings provide novel insights into host responses to avian influenza exposure and may support early detection and health risk assessment in highrisk occupational populations.","fileCount":"1050","fileSizeKB":"110161912","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"nontargeted metabolomics;DatasetType:Metabolomics","pi":[{"name":"maoshuoqin","email":"maoshuoqin@mail.ccmu.edu.cn","institution":"School of Basic Medical Sciences, Capital Medical University, Beijing","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc435a8aa3cd4e6b97e224d37c82e9e6","id":"704"}, {"dataset":"MSV000098295","datasetNum":"98295","title":"GNPS - Photosynthetic metabolite used for nitrogen fixation","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712612000","created":"Jun. 23, 2025, 2:03 PM","description":"Using 13C bicarbonate labelling, metabolites from photosynthesis will be identified and depletion of metabolites after 1hour of photosynthesis inhibition will reveal metabolites used for nitrogen fixation. Bicarbonate will be added at the beginning of the day, and samples will be taken after 5hours. Cells will be treated with DCMU (photosynthesis inhibitor) at this 5h timepoint and left for an additional 1h incubation. Final samples will be taken at 6h (1 hour after DCMU addition) to assess depletion of the photosynthetic metabolites.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008462) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"197","fileSizeKB":"17689007","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Epithemia clementina","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"13C labelling;photosynthesis;depletion;DatasetType:Metabolomics","pi":[{"name":"Ellen Yeh","email":"ellenyeh@stanford.edu","institution":"Stanford","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"47196ebe973e4715b6a832ac38816e9b","id":"705"}, {"dataset":"MSV000098294","datasetNum":"98294","title":"GNPS - Uptake ability of cyanobacteria","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712595000","created":"Jun. 23, 2025, 2:03 PM","description":"Using the NLDM we aim at charaterizing the uptake ability of C. subtropica and Synechocystis. Cultures will be washed with NLDM and then incubated either in the dark or in 12h light\/12h dark in NLDM media. After 24h cultures will be spin down and 1mL of supernatant will be flash frozen.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008462) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"244","fileSizeKB":"21691818","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crocosphaera subtropica; Synechocystis PCC 6804","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanobacteria;DatasetType:Metabolomics","pi":[{"name":"Ellen Yeh","email":"ellenyeh@stanford.edu","institution":"Stanford","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d5f4fc90bc3d45b29311ac0a0bd2d070","id":"706"}, {"dataset":"MSV000098293","datasetNum":"98293","title":"GNPS - Tyrosine-sulfated peptide hormone induces flavonol biosynthesis to control elongation and differentiation in Arabidopsis primary root","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712593000","created":"Jun. 23, 2025, 2:03 PM","description":"In Arabidopsis roots, growth initiation and cessation are organized into distinct zones. How regulatory mechanisms are integrated to coordinate these processes and maintain proper growth progression over time remains poorly understood. Here, we demonstrate that the peptide hormone PLANT PEPTIDE CONTAINING SULFATED TYROSINE 1 (PSY1) promotes root growth by controlling cell elongation. Higher levels of PSY1 lead to longer differentiated cells with a shootward displacement of characteristics common to mature cells. PSY1 activates genes involved in the biosynthesis of flavonols, a group of plant-specific secondary metabolites. Consistent with these transcriptional changes, untargeted metabolomics reveals an enrichment of features annotated as diverse flavonol glycosides upon PSY1 treatment. Using genetic and chemical approaches, we show that flavonols are required for PSY1 function. PSY1-mediated flavonol accumulation is localized to the differentiation zone. PSY1 signaling in this zone is associated with a reduction of reactive oxygen species (ROS) activity and a decrease in auxin accumulation. These findings support a model where PSY1 signals the developmental-specific accumulation of secondary metabolites to regulate the extent of cell elongation and progression to maturation.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008481) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"1116","fileSizeKB":"89297855","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Psy1;root growth;Arabidopsis;peptide hormone;flavonols;DatasetType:Metabolomics","pi":[{"name":"Pam Ronald","email":"pcronald@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8b56ad6d93e04c0aa3c2169fc0cc4f0a","id":"707"}, {"dataset":"MSV000098292","datasetNum":"98292","title":"GNPS - Soil depth shapes microbial community composition and function in a freshwater wetland","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712557000","created":"Jun. 23, 2025, 2:02 PM","description":"Wetland microbiomes play a crucial role in the global carbon cycle by modulating soil organic carbon (SOC) and greenhouse gas (GHG) emissions. Understanding how microbial communities respond to environmental changes is essential for predicting wetland carbon fluxes under future climate scenarios. Here, we investigated the biogeochemistry of a temperate lacustrine wetland across four seasons and three soil depths, integrating greenhouse gas flux measurements, porewater metabolite profiles, metagenomics, metabolomics, and metaproteomics. While seasonal shifts in GHG fluxes and porewater chemistry were evident, microbial community composition and function were primarily structured by soil depth, suggesting resilience to short-term seasonal fluctuations. Depth-correlated microbial taxa and metabolic pathways revealed distinct stratification: surface soils were enriched in metabolically versatile Gammaproteobacteria capable of oxygen and nitrate respiration, as well as methane and sulfur oxidation, whereas deeper layers favored strict anaerobic metabolism, with increasing abundances of Anaerolinea and Methanomicrobia. Metabolomics showed an enrichment of purine nucleotides and amino acids at the surface, while deeper soils accumulated amino sugars and phenolic compounds, highlighting differences in carbon processing. Metaproteomics confirmed active metabolic pathways, linking functional potential to microbial activity. By integrating multi-omics with biogeochemical measurements, this study provides a system-level view of wetland microbial function and resilience, contributing to predictive models of wetland carbon cycling under future climate change.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000490) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"184","fileSizeKB":"14428507","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"wetland soils microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"wetlands;biogeochemistry;metagenomics;metaproteomics;metabolomics;climate change;methane;nitrous oxide;DatasetType:Metabolomics","pi":[{"name":"Mari Winkler","email":"mwinkler@uw.edu","institution":"University of Washington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f15934bd9dec4969892c70703bcf88ec","id":"708"}, {"dataset":"MSV000098291","datasetNum":"98291","title":"GNPS - NLDM Set 2: Metabolomics of Chlamydomonas and Brevundimonas","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712540000","created":"Jun. 23, 2025, 2:02 PM","description":"Chlamydomonas and Brevundimonas, a bacterium co-isolated from wild Chlamydomonas, were grown separately and together in 3mL fresh NLDM, as well as 3mL of the other organism's spent media (separately only), at 28oC and 200RPM in a diel cycle of alternating 12 hours and light and dark for 24 hours, and samples were collected to understand their metabolic capacities and possible symbiotic relationship.\r\n\r\nThis research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:https:\/\/doi.org\/10.46936\/fics.proj.2021.60010\/60000390) and used resources at the DOE Joint Genome Institute (https:\/\/ror.org\/04xm1d337) and the Environmental Molecular Sciences Laboratory (https:\/\/ror.org\/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).","fileCount":"769","fileSizeKB":"69710981","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chlamydomonas reinhardtii CC5390; Brevundimonas sp.","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"phototroph-heterotroph symbioses;DatasetType:Metabolomics","pi":[{"name":"Sabeeha Merchant","email":"sabeeha@berkeley.edu","institution":"UC Berkeley","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8d8f41b82bc8475cabaabdcc6d7b5c89","id":"709"}, {"dataset":"MSV000098290","datasetNum":"98290","title":"GNPS - Heat sensitivity in the Antarctic green alga Chlamydomonas priscui","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712504000","created":"Jun. 23, 2025, 2:01 PM","description":"Chlamydomonas priscui (previously sp. UWO241) is a green alga isolated from the ice-covered Antarctic Lake Bonney, where it thrives in a permanently cold, low light and hypersaline environment. We propose a multi-omics approach to investigate how this obligate cold extremophile (psychrophile) responds to high temperature stress stress. We will examine the role of salinity and light intensity on temperature resilience in C. priscui. We have shown that C. priscuii acclimated to high salinity and low light (HS-LL; similar to its natural habitat) exhibits significantly slower rates of heat-induced cell death, when compared to cultures acclimated to predicted climate change conditions accompanied with increased light or decreased salinity. We will examine the molecular basis of this response. Algae will be grown photoautotrophically at 4°C with continuous light to mimic the polar day and acclimated to the four defined conditions, adjusting salinity and light. Mid-log phase cultures will be exposed to short-term stress at 24°C for 12h, followed by 24h recovery at 4°C.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008464) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"820","fileSizeKB":"118838793","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chlamydomonas sp. UWO241","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"heat stress;multi-omics;Antarctic;Lake Bonney;salinity;lipidomics;DatasetType:Metabolomics","pi":[{"name":"Marina Cvetkovska","email":"mcvetkov@uottawa.ca","institution":"U of Ottawa","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d3564affe2664a369369856845eb63a4","id":"710"}, {"dataset":"MSV000098289","datasetNum":"98289","title":"GNPS - Decoding the specificity between MCP chemotaxis receptors and root exudates of plants","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712504000","created":"Jun. 23, 2025, 2:01 PM","description":"33 total samples. \r\n* 1 is seed exudates (30 sprouts in nutrient water, 24 hours, ~30 mL). \r\n* 28 are from EcoFabs (14, 15, 16 and 17 days with 7 total individual plant replicates, ~8-10 mL each)\r\n* 4 are from \"magenta box\" hydroponics plants grown to 42 days old (2 replicates) and 48 days old (2 replicates). All of them were collected in sterile nutrient water, replaced 24 hours before I harvested, filter sterilized and flash frozen.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008098) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"467","fileSizeKB":"30766646","spectra":"879127","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Solanum lycopersicum root exudate","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"chemotaxis receptors;tomato;EcoFAB;DatasetType:Metabolomics","pi":[{"name":"Tiffany Lowe-Power","email":"tlowepower@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"74a58e0c51e040b78c673298c15f1d35","id":"711"}, {"dataset":"MSV000098288","datasetNum":"98288","title":"The influence of nutrients on microbial interactions and secondary metabolites in toxic cyanobacterial blooms","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712488000","created":"Jun. 23, 2025, 2:01 PM","description":"We describe metabolomics from microbial communities of western Lake Erie, a valuable model system for the impacts of nutrient cycling and microbial interactions on cyanobacterial blooms and secondary metabolites in freshwater ecosystems. We will assess the role of associated bacteria and viruses in cycling nutrients, exchanging metabolites, and influencing secondary metabolite production of these cyanobacteria.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008110) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"313","fileSizeKB":"26917213","spectra":"504927","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudoanabaena","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"nutrient cycling;cyanobacterial blooms;DatasetType:Metabolomics","pi":[{"name":"Gregory Dick","email":"gdick@umich.edu","institution":"University of Michigan","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"99db40412c7148038dae003f93b60127","id":"712"}, {"dataset":"MSV000098287","datasetNum":"98287","title":"GNPS - Metabolic barriers controlling root microbiota assembly","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750712470000","created":"Jun. 23, 2025, 2:01 PM","description":"Plant roots are an essential plant organ, which is functionally related to nutrient and water uptake. These functions are conditioned by their morphology since water and nutrients infiltrate the root from the soil through different tissue layers to reach the central vasculature. We have revealed that microbial composition affects root morphology complexity. Importantly, we also found that the presence of the microbiota changes morphological traits in the root under low nutrient conditions, suggesting an unexplored coordination between root morphology complexity and microbial communities with consequences for plant health. Using Synthetic Communities (Syncom), we identified three bacteria that are capable of modifying plant root morphogenesis. So, in this experiment, we exposed duckweed plants to a bacterial Syncom as well as three alternative Syncoms, each of which excludedimportant bacteria. Additionally, we also exposed the plants to single bacteria.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60012307) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"528","fileSizeKB":"55881453","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Spirodela polyrhiza","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Duckweed;Root complexity;Syncom;DatasetType:Metabolomics","pi":[{"name":"Gabriel Castrillo","email":"gabriel.castrillo@nottingham.ac.uk","institution":"University of Nottingham","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0d6c03d4c50b4d10ae5ecf4b263a6299","id":"713"}, {"dataset":"MSV000098286","datasetNum":"98286","title":"GNPS - Lemonade Creek soil heterotrophy experiment","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750711960000","created":"Jun. 23, 2025, 1:52 PM","description":"Lemonade Creek soil samples. Algae colonize the soil just below the surface. Samples were taken in quadruplicate at four time points starting at 7:30 am (~30 min prior to sunrise) and finished at 8:00 pm (dark). Each replicate sample has both a pellet and supernatant. Soil material was scraped from the green layer beneath the surface, suspended in 10 mls sterile ultrapure water and shaken vigorously to suspend all biomass. Soil mineral material was allowed to settle (~10-15 sec), the supernatant was decanted to a fresh 15 ml Falcon tube, and then centrifuged (2100 x g, 5 minutes). Supernatant was poured off to a fresh tube and then it and the pellet (soil biomass plus some silt materials) were flash frozen in ethanol \u2013 dry ice bath and then stored on dry ice until transferred to -80°C freezer.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000481) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"510","fileSizeKB":"35024475","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"soil microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"algae;Lemonade Creek;heterotrophy;algal biofilms;DatasetType:Metabolomics","pi":[{"name":"Debashish Bhattacharya","email":"debash.bhattacharya@gmail.com","institution":"Rutgers University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2f6e62b3b0b84de7bf941be68ef65fa1","id":"714"}, {"dataset":"MSV000098285","datasetNum":"98285","title":"GNPS - Plant-mycorrhizal-decomposer interactions under climate change: the role of shifting plant carbon allocation","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750711893000","created":"Jun. 23, 2025, 1:51 PM","description":"Our work focuses on an economically and societally important plant-EMF system that dominates coniferous forests in U.S. and abroad; plants in the Pinaceae and their EMF symbionts in the genus Suillus. Pinaceae forests cover ~30% of U.S. land area and store approximately 57.8 billion tons of C. Pines have also been introduced to over 5 million Ha of land in the Southern Hemisphere, where populations of non-native Pinaceae species are escaping from original plantations and co- invading with their EMF symbionts, with unknown consequences to ecosystem biogeochemistry. At the DOE-funded Duke Free-Air CO2 Enrichment (FACE) experiment in North Carolina, U.S., Pinus taeda trees accumulated biomass quickly under elevated CO2, using unknown mechanisms for mining soil N to support rapid growth. Our analysis of the Suillus-Pinus system will generate molecular data on these responses, providing insight into the prospects for sustained plant productivity \u2013 and ecosystem C storage \u2013 under elevated CO2. By linking our molecular data with development of an ecosystem model, our proposed work directly meets DOE BER\u2019s mission of translating genomics data into digestible units that can improve our predicative understanding of terrestrial biogeochemistry.\r\n\r\nThis research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:https:\/\/doi.org\/10.46936\/fics.proj.2020.51536\/60000208) and used resources at the DOE Joint Genome Institute (https:\/\/ror.org\/04xm1d337) and the Environmental Molecular Sciences Laboratory (https:\/\/ror.org\/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).","fileCount":"692","fileSizeKB":"49753008","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pinus taeda\\\/Suillus","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"biogeochemistry;ectomycorrhizal fungi;pine;carbon storage;DatasetType:Metabolomics","pi":[{"name":"Jennifer Bhatnagar","email":"jmtalbot@bu.edu","institution":"Boston University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"70530ba438494529994960becc66c2d3","id":"715"}, {"dataset":"MSV000098284","datasetNum":"98284","title":"GNPS - Elucidation of plant-microbe interactions mechanisms in the rhizosphere","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750711059000","created":"Jun. 23, 2025, 1:37 PM","description":"Scientific rationale. The plant microbiome includes beneficial microbiota that provide the plant host protection from pathogens, increased nutrient availability and resilience against abiotic stress. It is well established that the well characterized plant root-colonizing, growth-promoting rhizobacterium Pseudomonas simiae WCS417 conveys benefit to plant host Arabidopsis thaliana, but the mechanisms of this microbially mediated enhancement remains underexplored. In a pilot in vitro investigation, we observed that only providing root exudates in the absence of the plant failed to result in bacterial growth, suggesting that a key component of an in vivo plant-microbe interaction is essential. Here, we propose to use novel plant propagation techniques, namely fabricated ecosystems via ecoBoxes, to facilitate controlled and reproducible plant-microbe interaction over a four-week period. Through metabolomics analyses, we aim to identify the presence\/absence of key metabolites observed in experimental treatments. \r\nSpecific aim. Experimental characterization of root colonization mechanisms. Col-0 seeds will be surface sterilized and plated on mesh and ½ MS medium in square plates and left at 4oC for approximately 48 hours to allow for stratification. Two to 3-day old seedlings will be added to ecoBoxes and let to grow for 1-2 weeks with 60 ml 1\/5 MS media (pH adjusted to ~ 5.7). Pseudomonas simiae WCS417 fluorescent strain, SB642 will be added to \u2018with bacterium\u2019 treatment and all samples will be subsequently collected at ~ 4 weeks. Each treatment will have 5 corresponding replicates. Exudate media will be processed for metabolomic analysis (15 samples total) while Arabidopsis will be used for confocal microscopy of plant root colonization (15 plants total).\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008794) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"298","fileSizeKB":"22583680","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plant microbiome;root colonization;fabricated ecosystems;rhizobacterium;DatasetType:Metabolomics","pi":[{"name":"Jonelle Basso","email":"JBasso@lbl.gov","institution":"Lawrence Berkeley National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"07c28c49ed4747b9acbab478e6dfa394","id":"716"}, {"dataset":"MSV000098283","datasetNum":"98283","title":"A multiorgan proteomic atlas of mouse aging","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750700609000","created":"Jun. 23, 2025, 10:43 AM","description":"Fifteen tissues were harvested from multiple male and female Blac6 wild type mice from early and late in the aging process. A 2 stage method was employed to generate metabolomic and proteomic data from each respective tissue. This repository contains the proteomics data. Proteins were reduced with DTT and alkylated with iodoacetamide prior to S-Trap digestion. 400ng of peptides were analyzed using an EvoSep One system running the 30SPD method and linked to a TIMSTOF Flex running a diaPASEF method. All downstream data was analyzed with SpectroNaut 19. ","fileCount":"1941","fileSizeKB":"208294630","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Mouse aging;Multi-organ;Sex-linked proteomics alterations;DatasetType:Proteomics","pi":[{"name":"Ben Orsburn","email":"orsburn@pitt.edu","institution":"University of Pittsburgh","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"15253666adc44daaac82d247e33efab1","id":"717"}, {"dataset":"MSV000098282","datasetNum":"98282","title":"Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750696578000","created":"Jun. 23, 2025, 9:36 AM","description":"Aging hampers the regenerative potential of intestinal epithelium across species including humans, yet the underlying causes remain elusive. Here, using proteomic and metabolomic profiling of intestinal tissues together with functional assays, we characterized the temporal dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent. Comparison of regeneration dynamics in mice of different ages revealed the emergence of proteostasis stress and increased levels of polyamines following injury exclusively in old epithelia. We show that delayed regeneration is an intrinsic feature of aged epithelial cells that display reduced protein synthesis and accumulation of ubiquitylated proteins. Inhibition of the polyamine pathway in vivo further delays regeneration in old mice, while its activation by dietary intervention or supplementation of polyamines is sufficient to enhance the regenerative capacity of aged intestines. Our findings highlight promising epithelial targets for interventions aimed at tackling the decline in tissue repair mechanisms associated with aging.\n","fileCount":"45","fileSizeKB":"81181857","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"polyamines, regeneration, protein homeostasis, intestine;DatasetType:Proteomics","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD065349","task":"c444ee42844e4d5aa439d0e4fed9d6a2","id":"718"}, {"dataset":"MSV000098281","datasetNum":"98281","title":"Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750696427000","created":"Jun. 23, 2025, 9:33 AM","description":"Aging hampers the regenerative potential of intestinal epithelium across species including humans, yet the underlying causes remain elusive. Here, using proteomic and metabolomic profiling of intestinal tissues together with functional assays, we characterized the temporal dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent. Comparison of regeneration dynamics in mice of different ages revealed the emergence of proteostasis stress and increased levels of polyamines following injury exclusively in old epithelia. We show that delayed regeneration is an intrinsic feature of aged epithelial cells that display reduced protein synthesis and accumulation of ubiquitylated proteins. Inhibition of the polyamine pathway in vivo further delays regeneration in old mice, while its activation by dietary intervention or supplementation of polyamines is sufficient to enhance the regenerative capacity of aged intestines. Our findings highlight promising epithelial targets for interventions aimed at tackling the decline in tissue repair mechanisms associated with aging.\n","fileCount":"19","fileSizeKB":"39409064","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"polyamines, regeneration, intestines, protein homeostasis;DatasetType:Proteomics","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD065348","task":"f1508b2a13854ba782c645d557387a07","id":"719"}, {"dataset":"MSV000098275","datasetNum":"98275","title":"A conserved role for the Zinc binding ZZ domain of the ORB2 CPEB2 RNA binding protein in translational repression of target transcripts in Drosophila S2 cells and embryos","user":"Sichun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750439175000","created":"Jun. 20, 2025, 10:06 AM","description":"RNA binding proteins RBPs are key components of the post transcriptional regulatory machinery. We show that the ORB2 RBP, the Drosophila ortholog of vertebrate Cytoplasmic Polyadenylation Element Binding Protein 2 CPEB2, binds to hundreds of maternally provided mRNAs in early embryos, these transcripts are translationally repressed and unstable during the maternal to zygotic transition MZT. We identify a U rich motif enriched in ORB2 targets, which confers ORB2 binding and repression to a luciferase reporter mRNA in S2 tissue culture cells. ORB2 and its human homolog CPEB2 but not ORB and CPEB1 repress translation. The C terminal Zinc binding ZZ domain of ORB2 is necessary and sufficient for repression. We mapped regions of ORB2 ZZ domain that, when substituted into the same region of ORB ZZ domain, converts the non repressive domain into a repressor. ORB2 interacts with a suite of post-transcriptional regulators in early embryos; a subset of these interactions is lost upon deletion of the ZZ domain, notably with the Cup repressive complex. Analysis of the early embryo translatome in the presence or absence of the endogenous ZZ domain, shows that ORB2 targets move onto polysomes upon ZZ domain deletion, indicating that this domain mediates translational repression of ORB2 targets during the MZT. Together, our results assign a function to the ZZ domain and support a significant role for ORB2 in post transcriptional regulation of maternal mRNAs during the Drosophila MZT.","fileCount":"182","fileSizeKB":"49456759","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila (NCBITaxon:7215)","instrument":"QE-HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"ORB2, Cytoplasmic Polyadenylation Element Binding Protein CPEB, RNA binding protein, translational regulation, post transcriptional regulation, Drosophila, embryo, maternal to zygotic transition, S2 cell, CPEB, Cup, Trailer hitch TRAL, ME31B, Belle BEL, Smaug SMG;DatasetType:Proteomics","pi":[{"name":"Howard Lipshitz","email":"howard.lipshitz@utoronto.ca","institution":" University of Toronto","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065275","task":"843e675042b14ed1a140977c810c427e","id":"720"}, {"dataset":"MSV000098273","datasetNum":"98273","title":"GNPS - Stieleria Neptunia Enr13 Stieleriacines D-E + knock out studies, Total Synthesis Stieleriacine C + derivatives","user":"Sballuff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750429868000","created":"Jun. 20, 2025, 7:31 AM","description":"Crude extract datasets used for the analysis of of Stieleria neptunia Enr13 wild-type and N-acyl amino acid synthases (NASs) knock-out strains. Additional datasets for synthetic stieleriacine C and derivatives.","fileCount":"79","fileSizeKB":"2519411","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Stieleria neptunia Enr13","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Planctomycetota, Stieleria neptunia, Stieleriacines, Total Synthesis, Synthetic Library;DatasetType:Metabolomics","pi":[{"name":"Christine Beemelmanns","email":"christine.beemelmanns@helmholtz-hips.de","institution":"Helmholtz Institute for Pharmaceutical Research Saarland","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4e59e6003a4344afad431f7b9b36f050","id":"721"}, {"dataset":"MSV000098272","datasetNum":"98272","title":"Larval ascariasis elicits a prominent IgA and IgG1\/2 antibody response to adult Ascaris excretory\/secretory antigens in pigs","user":"benjamin_hempel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750417006000","created":"Jun. 20, 2025, 3:56 AM","description":"Roundworm infections result in morbidity, causing significant health and economic concerns in humans and pigs, respectively. We investigated the humoral responses of A. suum infected pigs before and after transition from larval to adult stage and confirmed our previous report on the diagnostic value of human Ascaris-specific antibodies. We evaluated the systemic and mucosal humoral responses in Ascaris infected pigs at 14- and 35-days post-infection (dpi). Ascaris-specific antibodies against larval and adult worm antigens and adult excretory\/secretory (ES) products in serum, broncho-alveolar lavage fluid and intestinal mucus were quantified by ELISA. IgA+ B cells in jejunal\/ileal mesenteric lymph nodes (mLNs) were investigated using flow cytometry.","fileCount":"13","fileSizeKB":"5935786","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ascaris suum (NCBITaxon:6253)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Ascaris;Antibody;IgA;Somatic Antigens;DatasetType:Proteomics","pi":[{"name":"Susanne Hartmann","email":"susanne.hartmann@fu-berlin.de","institution":"Freie University Berlin","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065260","task":"066ba4d319014678bdb61706edb254ef","id":"722"}, {"dataset":"MSV000098269","datasetNum":"98269","title":"Drosophila melanogaster miPEP8 regulates cell size through its interaction with ref(2)P\/p62","user":"bertrandfabre31","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750408476000","created":"Jun. 20, 2025, 1:34 AM","description":"Affinity purifications were performed on Schneider 2 cells transfected with either EGFP, EGFP-miPEP8 or EGFP-miPEP8mt (miPEP8 mutated on a short linear motif) and the eluted proteins were reduced, alkylated and digested in gel with trypsin. The resulting peptides were injected on either an LTQ Orbitrap Velos Pro or a Q Exactive Plus.\nA proteome analysis was also performed on Schneider 2 cells transfected with either EGFP or EGFP-miPEP8 sorted by FACS. After reduction and alkylation, the proteins were digested in solution with trypsin. The desalted peptides were injected on a TimsTOF SCP.","fileCount":"345","fileSizeKB":"67252745","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"timsTOF SCP;LTQ Orbitrap Velos Pro;Q Exactive Plus","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Microproteins;miPEP;ref(2)P\/p62;Cell size;DatasetType:Proteomics","pi":[{"name":"Bertrand Fabre","email":"Bertrand.Fabre@ipbs.fr","institution":"IPBS\/CNRS","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2228aa49f5284f70b502d38d5c595ad6","id":"723"}, {"dataset":"MSV000098268","datasetNum":"98268","title":"Extended NGN2 Expression in iPSCs Dramatically Enhances Purity of Neuronal Cultures ","user":"jymbcrc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750378482000","created":"Jun. 19, 2025, 5:14 PM","description":"iPSC-derived neuronal cultures can provide valuable insights into the pathogenesis of neurological disease. However, single cell iPSC clones with NGN2 and mCherry show spontaneous loss of mCherry fluorescence, leading to questions about the homogeneity of neurons derived from apparently heterogeneous iPSCs. We find that mCherry silencing does not influence iNeurons with two lines of evidence. First, using single-cell proteomics, we found that spontaneous mCherry silencing does not drive heterogeneity in iPSCs. Second, bulk proteomics and immunofluorescence analysis indicated that iNeurons from iPSCs expressing or lacking mCherry both resemble cortical glutamatergic neurons. The primary confounding factor in iNeuron generation was that suboptimal neuronal conversion led to cell aggregates comprised of actively proliferating neuronal progenitor cells and astrocytes as the culture developed. Our results indicate that extended NGN2 dosage substantially improves neuron purity","fileCount":"21994","fileSizeKB":"713970106","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"IPSCs;Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral;timsTOF Pro","modification":"No","keywords":"neuronal cultures, proteomics, single-cell, NGN2 Expression;DatasetType:Proteomics","pi":[{"name":"jesse meyer","email":"jesse.meyer@cshs.org","institution":"cedars sinai medical center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d6565d9ff321400097c66d4aab254610","id":"724"}, {"dataset":"MSV000098264","datasetNum":"98264","title":"E3 ubiquitin ligase TRIP12 controls protein translation and promotes cancer cell survival via a potential mTOR\/G3BP1 nexus","user":"aad100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750330896000","created":"Jun. 19, 2025, 4:01 AM","description":"Mass spectrometry data and proteomic results relating to the manuscript: E3 ubiquitin ligase TRIP12 controls protein translation and promotes cancer cell survival via a potential mTOR\/G3BP1 nexus","fileCount":"34","fileSizeKB":"18545753","spectra":"0","psms":"229505","peptides":"75123","variants":"95411","proteins":"20781","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:188 - \\\"13C(6) Silac label.\\\"","keywords":"TRIP12;protein translation;mTOR;G3BP1;cancer;DatasetType:Proteomics","pi":[{"name":"Omar Khan","email":"okhan@hbku.edu.qa","institution":"College of Health and Life Sciences, Hamad Bin Khalifa University","country":"Qatar"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD065213","task":"add97367e29946f59f33d82fcf529bc7","id":"725"}, {"dataset":"MSV000098263","datasetNum":"98263","title":"GNPS - Ion Mobility-Reframe Drug Library","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750298228000","created":"Jun. 18, 2025, 6:57 PM","description":"Crude standards of reframe drug mixtures were analyzed on a TimsTOF Pro2 coupled to Agilent LC system for library generation. ","fileCount":"27788","fileSizeKB":"50365371","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"library;ion mobility;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5094dadc7b754e98b01c718ca09dac84","id":"726"}, {"dataset":"MSV000098260","datasetNum":"98260","title":"Enhanced Levels of MYHCA peptides in Mediastinal Lymph Nodes Following Myocardial Infarction","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750270057000","created":"Jun. 18, 2025, 11:07 AM","description":"A total of 14 lymph node samples were collected from 7 mice, with 8 samples obtained from the MI group and 6 from the sham-operated group. Each mouse contributed two lymph node samples: the mediastinal lymph node, MedLN and the sub-iliac lymph node, siLN. Supplementary Table 1 provides a detailed breakdown of sample distribution across the experimental groups. ","fileCount":"19","fileSizeKB":"50996863","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Myocardial infarction;MYHCA;Cardiac myosin heavy chain alpha;Lymph nodes;MMP-2;DatasetType:Proteomics","pi":[{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"},{"name":"Richard Schulz","email":"rschulz@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065173","task":"60edfe0a4a0c4103b298d88f6cda564e","id":"727"}, {"dataset":"MSV000098258","datasetNum":"98258","title":"AAV2 induced RPA exhaustion generates cellular DNA damage and restricts viral gene expression","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750268422000","created":"Jun. 18, 2025, 10:40 AM","description":"In Gel Digestion\nEach lane sample was then cut into small rectangular pieces and divided into two fractions: fraction 2 containing the streptavidin band and fraction 1 containing the remaining proteins. For in gel digestion, both fractions were subjected to several rounds of washing to remove salts and Coomassie. Specifically, gel pieces were incubated for 15 min in 25 mM ammonium bicarbonate, 50% ethanol 60 C for strongly stained pieces, and the supernatant was discarded. This wash step was repeated 2 3 times or until gel pieces were destained completely. Next, in preparation for cysteine reduction & alkylation, fractions were incubated in 100% ethanol for 10 min to dehydrate the gel pieces.\nCysteine residues were reduced by incubating fractions for 20 min at room temperature in 20 mM DTT, 50 mM ammonium bicarbonate. After discarding the supernatant, cysteine residues were alkylated by a 20 min incubation in 80 mM chloroacetamide, 50 mM ammonium bicarbonate. Alkylation compounds were removed with successive 10 min washes in i 50 mM ammonium bicarbonate, ii 25 mM ammonium bicarbonate, 50% ethanol, and iii 100% ethanol. Gel pieces were subsequently dried in a vacuum concentrator.\nFor overnight digestion at 37 C, trypsin solution 0.25 ug trypsin Promega in 50 ul of 50 mM ammonium bicarbonate was added to each fraction. On the following day, peptides were extracted by two sequential 15 min elutions in 150 ul of elution solution 80% acetonitrile, 0.2% formic acid under sonication. The resulting eluates were pooled and evaporated to dryness in a vacuum concentrator.\nLC MS analysis\nFor LC MS analysis, a Vanquish Neo UHPLC system Thermo Fisher Scientific was coupled to an Orbitrap Ascend mass spectrometer Thermo Fisher Scientific via a Nanospray Flex ionization source. A 40 cm in house prepared fused silica C18 column was maintained at 50 C using a custom built column heater. The source voltage was set to 2 kV, and the ion transfer tube was held at 275 C. Peptide samples from streptavidin containing fractions were injected at a total amount of 500 ng, whereas 1 ug of peptides was loaded for all other samples. Peptides were separated at a flow rate of 300 nL per min with a 73 min active gradient from 5% to 46% solvent B solvent A: 0.2% FA; solvent B: 80% acetonitrile with 0.2% FA.\nOrbitrap Ascend parameters were as follows: MS1 scans were acquired at a resolution of 240k scan range 300 1350 m per z, with a maximum injection time of 50 ms, an automatic gain control AGC target of 1 x 106, a normalized AGC target of 250%, and an RF lens percentage of 30. Data dependent acquisition employed a 1 s cycle time. MIPS monoisotopic peak determination was set to peptide, and the isolation window center was set to most abundant peak. Charge states 2 5 were included, and dynamic exclusion was set to 20 s with a 5 ppm mass tolerance. MS2 spectra were recorded in the ion trap using an isolation window of 0.8 m per z, a normalized HCD collision energy of 24%, an ion trap scan rate set to Turbo, a scan range of 150 1350 m per z, a normalized AGC target of 250%, and a maximum injection time of 12 ms.\nProteomics data analysis\nRAW files generated from the LC MS runs were analyzed with MaxQuant version 2.4.2.0, searching against a UniProt human FASTA file containing both SwissProt and TrEMBL entries. Adeno associated virus 2 proteins Rep68 P03132 and Rep78 Q89268 were added to this database. Unless otherwise specified, all MaxQuant parameters were set to their default values.\nGel fractions originating from the same lane were assigned identical experiment names but treated as separate fractions in MaxQuant. In the Group specific parameters tab, Type was set to multiplicity = 2, and Arg10 and Lys8 were checked. Under Misc., Re quantify was enabled. In the Global parameters tab, the FASTA files described above were specified under Sequences. Under Protein quantification, Label min. ratio count was set to 1, and under Identification, Min. unique peptides was set to 1 with Match between runs enabled. Finally, under Label free quantification, iBAQ was enabled.\n","fileCount":"18","fileSizeKB":"7418216","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Adeno-associated virus 2 Srivastava\\\/1982 (NCBITaxon:648242)","instrument":"Orbitrap Ascend","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"iPOND;AAV2;In-Gel Digestion;DatasetType:Proteomics","pi":[{"name":"Joshua J. Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065171","task":"9af93a72528349cdb401ae12c4a3cdba","id":"728"}, {"dataset":"MSV000098257","datasetNum":"98257","title":"GNPS - Shifts in Zostera marina metabolites with heat stress exposure","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750266286000","created":"Jun. 18, 2025, 10:04 AM","description":"Zostera marina plants were exposed to ambient, +3 Celsius, or +6 Celsius temperatures for five weeks. Following exposure, root exudates and plant compartments were collected for metabolite extraction. This study aims to investigate metabolic shifts in Z. marina under heat stress and their implications for host physiology and associated microbiomes. Untargeted LC-MS\/MS acquisition was performed in Positive mode on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1271","fileSizeKB":"63801778","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Zostera marina (NCBITaxon:29655)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Seagrass;MSCollaboratory;Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Maggie Sogin","email":"esogin@ucmerced.edu","institution":"University of California Merced","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6fbd5edec48a41fe864b38201fbc444c","id":"729"}, {"dataset":"MSV000098254","datasetNum":"98254","title":"GNPS_Metabolomic_Profiling_Allium_cepa_var_aggregatum_Negative","user":"chitival","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750257855000","created":"Jun. 18, 2025, 7:44 AM","description":"Analysis of metabolomic profiles of nine onion cultivars including Ocanera cultivars (local materials and materials conserved from plant germplasm banks) and Peruvian onions, using LC-MS-QTOF (-)","fileCount":"87","fileSizeKB":"6630453","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Allium cepa var. aggregatum (NCBITaxon:28911)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Onion;Shallot;Metabolomic fingerprinting;Allium cepa var. aggregatum;DatasetType:Metabolomics","pi":[{"name":"Juan Camilo Henao Rojas","email":"jhenao@agrosavia.co","institution":"Agrosavia","country":"Colombia"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"392e6ffb59be486bb9ba599e3621a957","id":"730"}, {"dataset":"MSV000098253","datasetNum":"98253","title":"The reaction of yeast sumo(smt3) and Cu(II)","user":"xsj1109","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750252582000","created":"Jun. 18, 2025, 6:16 AM","description":"In this study, ESI-MS and IM-MS data were collected from the reaction products of yeast SUMO with different copper ions, and the SUMO conjugated with one Cu(II) was analyzed by top-down spectrometry.","fileCount":"2","fileSizeKB":"653824","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Waters Synapt G2 instrument (Waters, Milford);Exactive Plus orbitrap mass spectrometer (Thermo Fisher Scientific)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sumo;smt3;copper;DatasetType:Other (protein)","pi":[{"name":"Yangzhong Liu","email":"liuyz@ustc.edu.cn","institution":"University of Science and Technology of China","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"34193b91bdcf49588b8b20f78c6b6b79","id":"731"}, {"dataset":"MSV000098245","datasetNum":"98245","title":"Protein corona formed on lipid nanoparticles compromises delivery efficiency of mRNA cargo","user":"evoke10195","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750202967000","created":"Jun. 17, 2025, 4:29 PM","description":"Proteomics to characterize the protein corona for lipid nanoparticles","fileCount":"1024","fileSizeKB":"573511878","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si;ACQUITY UPLC","modification":"MS:1002864 - 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Cells were seeded at the same density from the same parent passage. Samples are named, e.g., P1_A5N1_3. P1 represents Plate 1, P2 represents Plate 2. The middle code represents conditions, e.g., grown in antibiotics-containing media for 5 passages then switched to non-antibiotic containing media for 1 passage. The final code represents the replicate (e.g., well #3 of a six well plate for this passage). KFB just represents a blank containing only beads during SP3 sample prep, no lysate. R represents reference (pooled) sample. Blanks represent just 0.1% formic acid in water. 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Fecal samples were extracted with 50:50 (MeOH:H2O) and analyzed using the LC-MS\/MS method on the Thermo Orbitrap Q Exactive.","fileCount":"596","fileSizeKB":"115507114","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fecal;Diet_study;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"70271eec650646109ff55bd634832e7d","id":"734"}, {"dataset":"MSV000098241","datasetNum":"98241","title":"An increase of NPY1 expression leads to inhibitory phosphorylation of PIN-FORMED (PIN) proteins and suppression of pinoid (pid) null mutants","user":"zhouxinshen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750189580000","created":"Jun. 17, 2025, 12:46 PM","description":"The PINOID (PID) protein kinase is required for flower initiation in Arabidopsis. The pid mutants fail to initiate flowers on inflorescences, a phenotype that is mimicked by disrupting either the NAKED PINS IN YUC MUTANTS (NPY) gene family or PIN FORMED 1 (PIN1). Both PID and NPY1 have been reported to positively modulate PIN-mediated polar auxin transport. Here, we show that overexpression of NPY1 (NPY1 OE) completely suppressed pid null mutants, demonstrating that NPY1 functions downstream of PID. NPY1 OE triggered phosphorylation of PIN proteins at multiple sites that are mostly different from the previously characterized phosphorylation sites regardless of the presence of PID. Phosphorylation of the newly identified PIN sites in NPY1 OE plants likely leads to the inhibition of PIN functions, as we previously showed that pid is suppressed by decreasing PIN1 gene dosage or decreasing PIN1 activity. Furthermore, we show that the Ser\/Thr rich C-terminal motif in NPY1 is phosphorylated and is required for pid suppression by NPY1 OE. Overexpression of NPY1 that lacked the C-terminal motif (NPY1-noC) failed to rescue pid, but overexpression of NPY1-noC was still able to trigger phosphorylation of PIN proteins including PIN2, which is known to cause agravitropic roots when mutated. NPY1-noC overexpression plants displayed a complete loss of root gravitropic response, likely caused by PIN2 phosphorylation. Our results suggest a pathway for auxin mediated-flower initiation, in which PID regulates NPY1 accumulation and\/or activity, and subsequently, NPY1 triggers phosphorylation of PIN proteins and inhibition of PIN functions.","fileCount":"84","fileSizeKB":"100058348","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phosphorylation;NAKED PINS IN YUC MUTANTS (NPY);PIN FORMED 1 (PIN1);PINOID (PID);Auxin;DatasetType:Proteomics","pi":[{"name":"Steven P Briggs","email":"sbriggs@ucsd.edu","institution":"UCSD","country":"USA"},{"name":"Yunde Zhao","email":"yundezhao@ucsd.edu","institution":"University of California San Diego","country":"UCSD"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f37785fcf1dc438a80c09067e1543e22","id":"735"}, {"dataset":"MSV000098239","datasetNum":"98239","title":"Proteomic mapping of MYHCA cleavage sites by MMP-2","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750187564000","created":"Jun. 17, 2025, 12:12 PM","description":"Myosin S1(S1) fragments were incubated with full-length MMP-2, the catalytic domain of MMP-2, or APMA activated MMP-2 under similar conditions. 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Mullowney, Angelica Moran, Antonio Hernandez, Mary McMillin, Amber R. Rose, David Moran, Jessica Little, Ann B. Nguyen, Bhakti K. Patel, Christopher J. Lehmann, Matthew A. Odenwald, Eric G. Pamer, Kiang-Teck J. Yeo, Ashley M. Sidebottom.","fileCount":"7528","fileSizeKB":"240586938","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"5975C GC\\\/MS(Agilent instrument model);6546 Q-TOF LC\\\/MS (Agilent instrument model);QTRAP 6500","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbiome;human gut microbiome;clinical diagnositic;deoxycholic acid;butyrate;clinical screen;DatasetType:Metabolomics","pi":[{"name":"Ashley M. Sidebottom","email":"asidebottom@bsd.uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"40c8299e7cd54b0fb7dc64cb2c2af885","id":"737"}, {"dataset":"MSV000098237","datasetNum":"98237","title":"CM4AI: SEC-MS of MDA-MB468 following vorinostat or paclitaxel treatment","user":"aforget","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750181402000","created":"Jun. 17, 2025, 10:30 AM","description":"SEC-MS profiling of MDA-MB468 breast cancer cell line following treatment with vorinostat or paclitaxel. Each SEC-MS set is composed of 72 fractions.","fileCount":"20020","fileSizeKB":"955068215","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"breast cancer;MDA-MB468;SEC-MS;Vorinostat;Paclitaxel;CM4AI;B2AI;DatasetType:Proteomics","pi":[{"name":"Antoine Forget","email":"antoine.forget@ucsf.edu","institution":"UCSF","country":"USA"},{"name":"Nevan J. Krogan","email":"nevan.krogan@ucsf.edu","institution":"University of California, San Francisco","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065123","task":"ad8b8084f5b14af5bafac70fdd42a577","id":"738"}, {"dataset":"MSV000098236","datasetNum":"98236","title":"Arylsulfamates inhibit colonic Bacteroidota growth through a sulfatase-independent mechanism","user":"trl1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750174344000","created":"Jun. 17, 2025, 8:32 AM","description":"Untargeted lipidomics analysis of Bacteroides thetaiotaomicron in the absence (control) or presesence (test) of sublethal doses of arylsulfamate ","fileCount":"40","fileSizeKB":"5068649","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides thetaiotaomicron (NCBITaxon:818)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arylsulfamates, lipidomics, Bacteroides;DatasetType:Metabolomics","pi":[{"name":"Alan Cartmell","email":"alan.cartmell@york.ac.uk","institution":"University of York","country":"UK"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"66dff9557bb74a6c842f179b911981f1","id":"739"}, {"dataset":"MSV000098235","datasetNum":"98235","title":"Nucleosome context regulates chromatin reader preference","user":"leeal0011","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750172484000","created":"Jun. 17, 2025, 8:01 AM","description":"Raw .MS files for the manuscript, \"Nucleosome context regulates chromatin reader preference\"","fileCount":"3","fileSizeKB":"575","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive UHMR","modification":"UNIMOD:34 - 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Helichrysum data, Helichrysum italicum, Helichrysum splendidum, Helichrysum petiolare","user":"Mots","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750155162000","created":"Jun. 17, 2025, 3:12 AM","description":"Helichrysum extracts for three medicinal species (H. italicum, H. petiolare, and H. splendidum) for natural product research.","fileCount":"26","fileSizeKB":"2811025","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Helichrysum italicum (NCBITaxon:261786);Helichrysum splendidum (NCBITaxon:261804);Helichrysum petiolare (NCBITaxon:261796)","instrument":"LCMS-9030","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Helichrysum italicum, Helichrysum splendidum, Helichrysum petiolare, natural products;DatasetType:Metabolomics","pi":[{"name":"Fidele Tugizimana","email":"Fidele.Tugizimana@omnia.co.za","institution":"University of Johannesburg & Omnia Nutriology","country":"South Africa"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a21755d761c445239606e89f1b1cb6d5","id":"743"}, {"dataset":"MSV000098225","datasetNum":"98225","title":"Indentification of interacting proteins of AS160","user":"S_Chen6","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750130072000","created":"Jun. 16, 2025, 8:14 PM","description":"This study was to identify the interacting proteins of AS160 in H293t cells with Flag-AS160 overexpression through Flag beeds pull down.","fileCount":"25","fileSizeKB":"229790","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 5600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"AS160, protein interactors;DatasetType:Proteomics","pi":[{"name":"Shuai Chen","email":"chenshuai@nju.edu.cn","institution":"Model Animal Research Center, Nanjing University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD065080","task":"954870423f3548c680638bac8c0cfb1e","id":"744"}, {"dataset":"MSV000098222","datasetNum":"98222","title":"GNPS - aging_mice_study_positive_(liver,fecal)","user":"jypark","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750115161000","created":"Jun. 16, 2025, 4:06 PM","description":"Metabolomic analysis of fecal and liver samples from 2-, 6-, 12-, and 18-month-old mice.","fileCount":"120","fileSizeKB":"4980054","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"aging;mice;fecal;liver;DatasetType:Metabolomics","pi":[{"name":"Heejung Yang","email":"heejyang@kangwon.ac.kr","institution":"Kangwon National University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cbd0d69351b74f7a9b31c2feb6951303","id":"745"}, {"dataset":"MSV000098219","datasetNum":"98219","title":"Proteomic analysis of breast cancer cell lines MCF_7 and MDA_MB_468 treated with melatonin","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750098378000","created":"Jun. 16, 2025, 11:26 AM","description":"Breast cancer (BC) is the most prevalent and lethal tumor among women worldwide.\nAlthough the antitumor effects of melatonin are well documented, its precise molecular\nmechanisms in specific breast cancer subtypes remain unclear. This dataset provides\nproteomic data from total protein extracts of two breast cancer cell lines [MCF-7\n(ER+and PR+) and MDA-MB-468 (triple negative) treated with melatonin. The aim of\nthe study was to identify melatonin-induced changes in global protein expression and to\nassess its potential as a therapeutic modulator in hormone-responsive and triple-negative\nbreast cancer.","fileCount":"25","fileSizeKB":"16869964","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive (Thermo Fisher)","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Breast cancer;Melatonin;Proteomics;DatasetType:Proteomics","pi":[{"name":"Debora Aparecida Pires de Campos Zuccari","email":"debora.zuccari@famerp.br","institution":"Faculty of Medicine of Sao Jose do Rio Preto (FAMERP)","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Program in Tropical Diseases and in Medical Biotechnology, Botucatu Medical School (FMB)\/Biotechnology Institute (IBTEC), UNESP, Botucatu, SP","country":"Brazil"},{"name":"Luiz Gustavo de Almeida Chuffa ","email":"luiz-gustavo.chuffa@unesp.br","institution":"Department of Structural and Functional Biology, Institute of Biosciences, UNESP, Botucatu, SP","country":"Brazil"},{"name":"Roberta Carvalho Cesario ","email":"roberta.cesario@unesp.br","institution":"Department of Structural and Functional Biology, Institute of Biosciences, UNESP, Botucatu, SP","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"efc8697129854ff2bb2693fbd35287c5","id":"746"}, {"dataset":"MSV000098218","datasetNum":"98218","title":"GNPS - Extracto etanolico de Parkia pendula - Completo - Venezuela","user":"Darrieche","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750096815000","created":"Jun. 16, 2025, 11:00 AM","description":"Analisis metabolomico del extracto etanolico de Parkia pendula, recolectado en Venezuela","fileCount":"2","fileSizeKB":"19222","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Parkia pendula (NCBITaxon:1905032)","instrument":"Bruker Daltonics instrument model","modification":"Not modifications","keywords":"Parkia pendula, analisis metabolomico, extracto etanolico;DatasetType:Metabolomics","pi":[{"name":"Dioni Arrieche","email":"dioniarrieche@gmail.com","institution":"Universidad Tecnica Federico Santa Maria","country":"Chile"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4ba6e2feef8247b1bb339257f67e150f","id":"747"}, {"dataset":"MSV000098216","datasetNum":"98216","title":"Variability of Micrurus venom from Bahia_Brazil","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750086592000","created":"Jun. 16, 2025, 8:09 AM","description":"Coral snakes represent a highly diversified group of elapids in the New World. However, little is known about the diversity of coral snakes in the state of Bahia, making it essential to map their distribution and gain a better understanding of the variability in their venoms. Such knowledge is crucial not only for evolutionary and ecological studies but also for improving antivenom production and the clinical management of envenomations caused by these snakes. The MS data demonstrated in this study, the variation in the composition and activities of Micrurus venoms from the state of Bahia, Brazil, evidencing their diversity. Analysis through proteomic and functional studies of three different venom samples reveals differences in protein composition, which correlate with biological and enzymatic activities, as well as varying lethal potencies. ","fileCount":"7","fileSizeKB":"12841028","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Micrurus (NCBITaxon:8634)","instrument":"Q-Exactive (Thermo Fisher)","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Micrurus venom;Coral snakes;Variability;Mass spectrometry;DatasetType:Proteomics","pi":[{"name":"Ilka Borges Biondi","email":"ilkabiondi@gmail.com","institution":"Universidade Estadual de Feira de Santana (UEFS), Bahia (BA)","country":"Brazil"},{"name":"Luciana Casais-e-Silva","email":"luciana.casais@ufba.br","institution":"Department of Bioregulation, Institute of Health Sciences (ICS), Federal University of Bahia, Salvador, BA","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Graduate Programs in Tropical Diseases and in Medical Biotechnology, Botucatu Medical School (FMB)\/Biotechnological Institute (IBTEC), Sao Paulo State University (UNESP)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1c9af4d2ef854f26a95b150186d66c25","id":"748"}, {"dataset":"MSV000098215","datasetNum":"98215","title":"GNPS - MAB_CDA_014_1323_02_S_active_fraction","user":"clemencemandel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750080690000","created":"Jun. 16, 2025, 6:31 AM","description":"Acrostalgmus luteoalbus strain grown on PDA. 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Cell lysate containing 1 mg protein was added to 100 microlitre each of 100 micromolar PolyP8-agarose, PolyP3-agarose, Pi agarose, and hydroxy agarose. The volume was made up to 1ml using lysis buffer. The beads were kept overnight at 4 degree C for overnight mixing on an end-over-end mixer, washed using lysis buffer, and boiled at 95 degree C for 5 mins in 1X Laemmli buffer. The proteins were run on 12% SDS-Polyacrylamide gels for 20 mins so that the dye front moves to about 0.8 cm in the resolving gel. The gel was stained using the Coomassie blue stain (0.25%) for half an hour. Later, the gel was destained using a destaining solution to remove excess stain. 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A standard sample containing 11 purified compounds (5 with one or two chlorine atoms and 2 with a bromine atom), with masses ranging from 238.0509 to 1447.4300 Da, were prepared. Then, varying amounts of the standard sample were mixed with F1 and M3 culture mediaand analyzed via UPLC-HRMS\/MS, generating the IN-house STandards Spiked in Culture Media dataset (INST_SCM).","fileCount":"50","fileSizeKB":"5331465","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"standards","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Halogenates;Standards;DeepHalo;DatasetType:Metabolomics","pi":[{"name":"Yunying Xie","email":"xieyy@imb.pumc.edu.cn","institution":"Institute of Medicinal Technology, CASM","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e40ea43599f04e4a8c3d44c507313979","id":"753"}, {"dataset":"MSV000098203","datasetNum":"98203","title":"GNPS - he IN-house STandards dataset (INST) for evaluating the performance of DeepHalo","user":"xyying","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750029892000","created":"Jun. 15, 2025, 4:24 PM","description":"To evaluate the effectiveness of DeepHalo in identifying chlorine- or bromine-containing compounds in real-world complex samples, a series of LC-HRMS\/MS analyses were acquired using UPLC-QTof (Supplementary Information). A standard sample containing 11 purified compounds (5 with one or two chlorine atoms and 2 with a bromine atom), with masses ranging from 238.0509 to 1447.4300 Da, was analyzed at low, medium, and high concentrations using UPLC-HRMS\/MS. Each concentration was analyzed with one to three replicates, resulting in 14 LC-HRMS runs, collectively referred to as the IN-house STandards dataset (INST).","fileCount":"26","fileSizeKB":"1623057","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Standards","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Halogenates;DeepHalo;Standards;DatasetType:Metabolomics","pi":[{"name":"Yunying Xie","email":"xieyy@imb.pumc.edu.cn","institution":"Institute of Medicinal biotechnology","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"79114a13d3ed442eb36becb49c23d764","id":"754"}, {"dataset":"MSV000098202","datasetNum":"98202","title":"GNPS - Lychnophora plant family crude extracts","user":"Anelize","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1750015896000","created":"Jun. 15, 2025, 12:31 PM","description":"LC-MS\/MS of plant crude extracts from Brazil. 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Brown algae have evolved independently from other major eukaryotic lineages, such as the Opistokonts (animals, fungi) or Archaeplastida (land plants, green and red algae). Within this lineage, there is considerable variation between species, which differ in ecology, diversity and evolutionary features, suggesting specific adaptations in their changing marine environment. In this context, several questions remain concerning the evolution of brown algal metabolism, and in particular, the response to oxidative stress. This study explored the consequences of copper stress on two brown algae from the Ectocarpales order: the free-living Ectocarpus sp7 and the endophytic Laminarionema elsbetiae. Using PAM-based fluorescence measurements, we revealed that high copper exposure reduces the photosynthetic capacity and activity of the endophyte. Through a cutting-edge untargeted metabolomic approach using UHPLC-HRMS profiling, we detected metabolic alterations induced by short-term exposure to moderate copper concentration in both free-living and endophytic Ectocarpales. The metabolite-regulated response appears to be substantial in Ectocarpus sp7 compared to L. elsbetiae, as a greater number of up- and down-regulated features were detected. Among the discriminant ions identified by tandem mass spectrometry, our results showed that copper exposure triggers the metabolism of algal defense signaling, primarily through the upregulation of oxylipins, mainly in Ectocarpus sp 7. Altogether, our findings suggest that in Ectocarpales, fine metabolic adaptation may have altered the metabolism linked to defense signaling, such as the oxylipin pathway, particularly in ecological niches like endophytic life.","fileCount":"132","fileSizeKB":"9321983","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ectocarpus (NCBITaxon:2879);Laminarionema elsbetiae (NCBITaxon:64929)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Brown Algae;Copper Stress;LCMS;Reverse Chromatography;Ectocarpus;Holobiont;Laminarionema elsbetiae;DatasetType:Metabolomics","pi":[{"name":"Dr. Catherine Leblanc","email":"catherine.leblanc@sb-roscoff.fr","institution":"Biologie Integrative des Modeles Marins, LBI2M (Sorbonne Universite\/CNRS), Station Biologique de Roscoff (SBR)","country":"France"},{"name":"Dr. Gabriel Markov","email":"gabriel.markov@sb-roscoff.fr","institution":"Biologie Integrative des Modeles Marins, LBI2M (Sorbonne Universite\/CNRS), Station Biologique de Roscoff (SBR)","country":"France"},{"name":"Dr. Marine Vallet","email":"mvallet@ice.mpg.de","institution":"Friedrich Schiller University Jena, Max Planck Institute for Chemical Ecology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d17e53d82bc447a3b5be73ae30f18d3a","id":"756"}, {"dataset":"MSV000098196","datasetNum":"98196","title":"GNPS_2025_Batch1_WT,OE,ko,WTwithOE","user":"JyotiAgg5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1749895007000","created":"Jun. 14, 2025, 2:56 AM","description":"Batch 1 includes WT, ko, and OE lines under Fe sufficient and deficient conditions for rice germinated and grown for 10 days.","fileCount":"101","fileSizeKB":"1311247","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Oryza sativa (NCBITaxon:4530)","instrument":"6545XT Q-TOF LC\\\\\\\/MS (Agilent Instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Batch1 includes WT, ko and OE lines under Fe sufficient and deficient conditions;DatasetType:Metabolomics","pi":[{"name":"Kuo-Chen Yeh","email":"kcyeh@gate.sinica.edu.tw","institution":"Agricultural Biotechnology Research Center","country":"Taiwan"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"2c258baa5d4145adaff27baa08b4342c","id":"757"}, {"dataset":"MSV000098195","datasetNum":"98195","title":"High-resolution ion mobility as an alternative to quadrupole-based precursor isolation for reducing chimeric fragmentation spectra in bottom-up proteomics ","user":"isabelroseuribe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1749867624000","created":"Jun. 13, 2025, 7:20 PM","description":"100 ng HeLa digest analyzed at a throughput of 200 samples per day on a prototype Q-TOF equipped with a MOBIE platform capable of parallel-accumulation mobility-aligned fragmentation.","fileCount":"197","fileSizeKB":"28340210","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6546 Q-TOF LC\\\/MS (Agilent) with MOBIE platform (MOBILion)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"chimeric fragmentation;ion mobility;quadrupole;mobility-aligned fragmentation;DatasetType:Proteomics","pi":[{"name":"Daniel DeBord","email":"daniel.debord@mobilionsystems.com","institution":"MOBILion Systems, Inc.","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6cace8b753a24b0ea3cb4181ee77d52b","id":"758"}, {"dataset":"MSV000098191","datasetNum":"98191","title":"GNPS - Human tissue cultures if HT29 and HepG2, 48hr incubation with small molecules","user":"hgouda","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1749838162000","created":"Jun. 13, 2025, 11:09 AM","description":"Human colon adenocarcinoma cells (HT29) and liver hepatocytes (HepG2) cultured with incubation of small molecules for 48hrs. The tissues were extracted using 50:50 (MeOH:H2O) for metabolomics analysis.","fileCount":"1452","fileSizeKB":"60128998","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HT29;HepG2;Bile acids;N-acyl lipids;Diet;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7db312c463c54f68acd31e3755601d80","id":"759"}, {"dataset":"MSV000098188","datasetNum":"98188","title":"\"Microscale\" Salinispora spp. strains (NSSP)","user":"g6castro","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1749829152000","created":"Jun. 13, 2025, 8:39 AM","description":"While our previous evolutionary analyses of Salinispora and its BGCs have focused on 118 strains isolated from worldwide marine sediment samples, the aim of this study was to isolate, genome-sequence, and characterize the biosynthetic potential of a \"microscale\" collection of Salinispora strains isolated from a 1-m^2 quadrat in Fiji, thus allowing us to compare taxonomic and BGC diversity at different spatial scales. This MassIVE data set contains LCMS runs of the ethyl acetate extracts produced from liquid cultures of 99 microscale Salinispora strains (96 are classified as S. arenicola, 2 as S. pacifica, and 1 as S. oceanensis) grown in A1 media, along with two media controls. The extracts were analyzed on a Agilent 1260 Infinity Series LC system coupled to a 6530 Series Q-TOF mass spectrometer, using a C18 Phenomenex Luna column (5 um, 100 mm x 4.6 mm) with a 10 min solvent gradient from 10% to 100% MeCN (0.1% FA) in water (0.1% FA) with 1.0 mL min-1 flow rate. LCMS parameters: positive mode, source ionization 0 eV, CID 30 eV and a 100-1700 Da detection window. Raw .d and converted .mzxml file formats are included. 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Simultaneously, the ubiquitin ligase Anaphase-Promoting Complex\/Cyclosome (APC\/C)-Cdh1 remains active, allowing origin licensing and blocking premature DNA replication. Paradoxically, glycolysis is reduced by APC\/CCdh1 through the degradation of key glycolytic enzymes, raising the question of how cells coordinate these mutually exclusive events to ensure proper cell division. Here we show that cells resolve this paradox by transiently inactivating the APC\/C during cell cycle entry, which allows a transient metabolic shift favoring glycolysis. Upon mitogen stimulation, rapid mTOR-mediated phosphorylation of the APC\/C adapter protein Cdh1 at the N-terminus causes it to partially dissociate from the APC\/C. This partial inactivation of the APC\/C leads to the accumulation of PFKFB3, a rate-limiting enzyme for glycolysis, promoting a metabolic shift towards glycolysis. Delayed accumulation of phosphatase activity later removes Cdh1 phosphorylation, restoring full APC\/C activity, and shifting cells back to favoring oxidative phosphorylation. Thus, cells coordinate the simultaneous demands of cell cycle progression and metabolism through an incoherent feedforward loop, which transiently inhibits APC\/C activity to generate a pulse of glycolysis that is required for mammalian cell cycle entry.","fileCount":"10","fileSizeKB":"102437","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TSQ Quantiva","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mTOR, cdh1, cell cycle regulation, glycolysis, APC\/C, quiescence;DatasetType:Metabolomics","pi":[{"name":"Steven D. 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Highresolution mass spectra (HRMS) were recorded on a Waters Premier GC-TOF, Waters G2-XS\/APGC and\r\nAgilent-6520 Q-TOF mass spectrometer","fileCount":"43","fileSizeKB":"5402750","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Waters Premier GC-TOF;Waters G2-XS\\\/APGC;Agilent-6520 Q-TOF","modification":"none","keywords":"P450BM3;Terpene Synthesis;DatasetType:Other (HRMS)","pi":[{"name":"JIAN Li","email":"jianlizcz@sjtu.edu.cn","institution":"Shanghai Jiao Tong University","country":"CHINA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5ad055ccf6d648ca8224a85de928d4a7","id":"788"}, {"dataset":"MSV000098129","datasetNum":"98129","title":"Calu-6 (SMARCA4-WT) PRT3789 Global Proteomics ","user":"mhulse","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1749676360000","created":"Jun. 11, 2025, 2:12 PM","description":"Calu-6 (SMARCA4-WT) cell line treated with PRT3789 for 6 hr and 48 hr.","fileCount":"42","fileSizeKB":"48810088","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Q-Exactive HF","modification":"Static: TMTPro (lysine and peptide N-termini), Carbamidomethyl (C) Dynamic: Oxidation (M)","keywords":"TMT18, quantitative proteomics, Orbitrap, mass spectrometry, data-dependent acquisition, DDA, HCD, SEQUEST, peptide labeling, human, LC-MS\/MS, protein identification;DatasetType:Proteomics","pi":[{"name":"Michael Hulse","email":"mhulse@preludetx.com","institution":"Prelude Therapeutics","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD064894","task":"9bf05e7322a749da9087f45d4e5fc287","id":"789"}, {"dataset":"MSV000098126","datasetNum":"98126","title":"PERK protein kinase facilitates keratinocyte collective cell migration by engagement with cell adhesion molecules independent of its kinase activity ","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1749669237000","created":"Jun. 11, 2025, 12:13 PM","description":"Proximity labeling experiments (BioID) were performed on Human NTERT keratinocytes depleted of PERK (EIF2AK3, PERK-KO) re-expressing a WT PERK containing a C-terminal UltraID tag.\n\nPERK-KO and PERKUltraID cells were treated with differentiation medium containing 50 uM of exogenous Biotin for 6 h, washed three times with ice-cold PBS and harvested on ice with a modified RIPA buffer solution (25mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA, 1x HALT protease\/phosphatase inhibitor cocktail). Samples were then sonicated and incubated at 4C with rotation for 30 minutes, followed by centrifugation step to pellet cell debris. Total protein concentration was measured, and the samples were normalized to 1 mg\/ml to a final volume of 1 ml. Normalized samples were incubated with 40uL of trypsin-resistant streptavidin beads with rotation overnight at 4C. The next day, the beads were collected by magnetic separation and washed three times with an IP wash solution (25 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.5% Triton X-100), followed by two washes with PBS. Finally, the beads were resuspended with 100 ul of PBS and submitted on ice for preparation and mass spectrometry analysis by the Indiana University School of Medicine Center for Proteome Analysis.","fileCount":"26","fileSizeKB":"8227700","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"BioID;MS;proteomics;NTERT;DatasetType:Proteomics","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"},{"name":"Dan F. Spandau","email":"dspanda@iu.edu","institution":"Indiana University School of Medicine","country":"United States"},{"name":"Ronald C. 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We show here that the widespread harmful algal bloom (HAB) species Microcystis aeruginosa, threatening freshwater aquatic ecosystems globally, releases a complex mixture of thiamin antivitamins, including bacimethrin and methoxythiamin, which induce thiamin deficiency in the model green alga Chlamydomonas reinhardtii. Putative biosynthetic genes for bacimethrin were upregulated in M. aeruginosa when grown in co-culture resulting in greater production of bacimethrin. Bacimethrin, methoxythiamin, oxidized forms of thiamin and methoxythiamin, and a novel structural homolog of bacimethrin were all found at elevated levels in the co-culture exometabolome extracts and were all inhibitory to the growth of C. reinhardtii individually at very low concentrations and as a mixture in culture medium extracts. The thiamin-requiring mutant C. reinhardtii, CC-25, was much more sensitive to bacimethrin and methoxythiamin than the wildtype. Thiamin addition largely rescued the inhibitory effects of exposure to antivitamins in both the wildtype and mutant strain. Finally, we determined that bacimethrin is present in aquatic environments and is elevated during Microcystis blooms. Thus, allelopathic suppression of competitors, particularly those that are auxotrophic for thiamin, by M. aeruginosa via the production of antivitamins in environments where thiamin availability is low, could help this species to become dominant and form blooms","fileCount":"53","fileSizeKB":"723685","spectra":"24120","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Microcystis aeruginosa NIVA-CYA 118\\\/2 (NCBITaxon:59621);Chlamydomonas reinhardtii (NCBITaxon:3055)","instrument":"X500R QTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"thiamin;antivitamin;DatasetType:Metabolomics","pi":[{"name":"Beth Ahner","email":"baa7@cornell.edu","institution":"Cornell University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"561dfd078ca9446c81fbd015732667e4","id":"813"}, {"dataset":"MSV000098017","datasetNum":"98017","title":"Desulfovibrio marinus single-subunit oligosaccharyltransferase and its human IgG substrates","user":"YungstedtUGA","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1748451282000","created":"May. 28, 2025, 9:54 AM","description":"Glycoproteomics data about glycan attachment of human IgG catalyzed by a previously uncharacterized single-subunit oligosaccharyltransferase (ssOST) from the bacterium Desulfovibrio marinus, namely DmPglB. 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The spectra were collected at Wageningen Food Safety Research, part of Wageningen University and Research (The Netherlands), using an Orbitrap IQ-X tribrid mass spectrometer in ESI+ mode. The library contains all classes of PAs, including the 35 PAs regulated in the EU.","fileCount":"310","fileSizeKB":"22065197","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"Orbitrap IQ-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Food safety;Plant toxins;Pyrrolizidine Alkaloids;Spectral library;DatasetType:Metabolomics","pi":[{"name":"Federico Padilla Gonzalez","email":"federico.padillagonzalez@wur.nl","institution":"Wageningen Food Safety Research","country":"Netherlands"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3b4a3d51da7b44e497b61d88a474fe33","id":"816"}, {"dataset":"MSV000098007","datasetNum":"98007","title":"GNPS - Indonesia Streptomyces crude extract","user":"nestor_serna","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1748389880000","created":"May. 27, 2025, 4:51 PM","description":"Crude extracts of Streptomyces isolated from Indonesia","fileCount":"3","fileSizeKB":"942306","spectra":"286","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces sp. 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See associated publication for details.","fileCount":"111","fileSizeKB":"21810853","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli K-12 (NCBITaxon:83333)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Escherichia coli;FIA;DatasetType:Metabolomics","pi":[{"name":"Julian Trouillon","email":"jtrouillon@ethz.ch","institution":"ETH Zurich","country":"Switzerland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"1d6bd60363be47a0a14fe431e76afc4c","id":"819"}, {"dataset":"MSV000097998","datasetNum":"97998","title":"Early microglia progenitors colonize the embryonic CNS via integrin-mediated transmigration from the pial surface","user":"oliver_schilling","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1748335222000","created":"May. 27, 2025, 1:40 AM","description":"Microglia progenitors initially colonize the developing central nervous system (CNS) around embryonic day (E) 9.5 in the mouse. Even though their ontogeny from early erythromyeloid progenitors in the yolk sac is well defined, the molecular machinery needed to enter the developing CNS is so far not resolved. Here, we combined unbiased transcriptomic and proteomic approaches to screen for potential factors. We identified a distinct and dynamic integrin expression profile on microglial progenitors, whereas in parallel the developing CNS peaks in the production of extracellular matrix (ECM) molecules. We found that this ECM is deposited along the pial surface between CNS and mesenchyme, where microglial progenitors interact with deposited ECM along the barrier zone of the CNS, pointing to a mesenchyme-to-CNS transmigration route of microglial progenitors. Loss of the integrin adaptor molecule Tln1 in microglia progenitors led to a reduced capacity to enter the developing CNS, whereas their numbers in the surrounding mesenchyme remained unchanged. However, deficiency of Itgb1 or Itgb2 alone was not sufficient to affect this migration. Our data revealed an essential role of a complex integrin expression profile on microglia progenitors to equip these cells to interact with ECM at the pial surface of the developing CNS and facilitate their entrance from the surrounding mesenchyme. 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Prenatal exposure to the antiepileptic drug valproate (VPA) is associated with an increased risk of neurodevelopmental disorders, including congenital malformations and autism spectrum disorder. VPA-treated animal models and neural organoids proposed defects in intracellular mechanisms such as Wnt signaling underlying VPA-induced neurodevelopmental adversities. However, the influence of extracellular mechanisms on these defects remains unexplored. Here, we showed that VPA treatment disrupted ventricular-like regions, suggesting defects in cell-cell and cell-matrix interactions. Transcriptomics analyses confirmed the disruption of ECM secretion as well as intracellular processes related to microenvironment sensing, such as cellular mechanosensing and Hippo-YAP\/TAZ signaling pathway. Finally, proteomics analysis corroborated that VPA alters the microenvironment of the human dorsal forebrain organoids by disrupting the secretion of extracellular matrix (ECM) proteins. Altogether, our study suggests VPA-treated dorsal forebrain organoids serve as a model to investigate the role of extracellular processes in brain development and to understand how their disruptions might contribute to neurodevelopmental disorders. 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All processing and analysis steps are fully documented in the companion GitHub repository (https:\/\/github.com\/paleobiotechnology\/pptase_ddiscoideum).\r\n","fileCount":"408","fileSizeKB":"30879107","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Dictyostelium discoideum (NCBITaxon:44689)","instrument":"Q-Exactive Plus Orbitrap","modification":"NA","keywords":"social amoebae;phosphopantetheinyl transferase;polyketide synthases;secondary metabolism;DatasetType:Metabolomics","pi":[{"name":"Pierre Stallforth","email":"pierre.stallforth@leibniz-hki.de","institution":"Leibniz-HKI, Jena","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a174bc208d1242ed95691f37e9cc4ba8","id":"828"}, {"dataset":"MSV000097984","datasetNum":"97984","title":"GNPS - Untargeted Metabolomic Profiling of Streptomyces and Nocardia from Oligotrophic Ecosystems","user":"froz9","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1748047388000","created":"May. 23, 2025, 5:43 PM","description":"We conducted an untargeted metabolomic analysis of Streptomyces and Nocardia strains isolated from two contrasting oligotrophic environments: Cuatro Cienegas and Calakmul. Metabolomic profiling was performed using liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-HR-MS\/MS). Data acquisition was carried out in positive ionization mode under a Data-Dependent Acquisition (DDA) strategy. The analysis included samples cultivated under two distinct culture conditions: ISP2 and ISP5 media. Metabolites were extracted using a solvent mixture of acetonitrile, methanol, and ethyl acetate in a 1:1:1 ratio","fileCount":"147","fileSizeKB":"1752374","spectra":"208044","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces (NCBITaxon:1883);Nocardia (NCBITaxon:1817)","instrument":"6530A Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Actinobacteria;Microbial Ecology;Chemical Ecology;DatasetType:Metabolomics","pi":[{"name":"Aldo Moreno Ulloa","email":"amoreno@cicese.mx","institution":"Centro de Investigacion Cientifica y de Educacion Superior de Ensenada ","country":"Mexico"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"8ff83c737e0b4786b377cbfc753a348b","id":"829"}, {"dataset":"MSV000097981","datasetNum":"97981","title":"GNPS-Osteobag samples for metabolomics","user":"hgouda","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1748024464000","created":"May. 23, 2025, 11:21 AM","description":"Osteobag samples extracted with 50:50 methanol\/water containing sulfadimethoxine as internal standard prior to LC-MS\/MS analyses. 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However, combined PFAS exposure, which more closely reflects real-world environmental conditions, remains poorly understood. In this study, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) were exposed to three common PFAS compounds-perfluorohexanesulfonic acid (PFHxS), perfluorooctanoic acid (PFOA), and perfluorodecanoic acid (PFDA), individually or in combination. Compared with single PFAS compounds, combined PFAS exposure induced synergistic cytotoxicity, significantly reducing hiPSC-CM viability after 5 or 10 days. Combined PFAS exposure for 10 days reduced mitochondrial membrane potential and content in a dose-dependent manner and caused a shift in cysteine metabolism, potentially indicative of an adaptive response to oxidative challenges. Following 14 days of exposure, combined PFASs increased vimentin, a fibroblast marker, along with reduced NK2 Homeobox 5 (NKX2.5), alpha-actinin, and cardiac troponin T (cTnT), key markers of cardiomyocytes, as detected by immunocytochemistry. In addition, proteomic profiling identified that combined PFASs upregulated proteins related to extracellular matrix organization, cholesterol metabolism, and antioxidant defense, and downregulated proteins related to mitochondrial function. These results underscore the importance of evaluating PFAS mixtures to better understand cardiac risks associated with environmental exposure.","fileCount":"19","fileSizeKB":"13234175","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Per- and polyfluoroalkyl substances;cardiotoxicity;hiPSC-derived cardiomyocytes;mitochondrial dysfunction;extracellular matrix;metabolism;proteomics;DatasetType:Proteomics","pi":[{"name":"Chunhui Xu","email":"chunhui.xu@emory.edu","institution":"Department of Pediatrics, Emory University School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"87dcff4b1b474974b79de075ad3a19e6","id":"831"}, {"dataset":"MSV000097978","datasetNum":"97978","title":"E3 ubiquitin ligase TRIP12 catalyzes non-canonical lysine-independent ubiquitin-ubiquitin linkages in vitro","user":"aad100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1748011584000","created":"May. 23, 2025, 7:46 AM","description":"Mass spectrometry raw data and proteomic results relating to: E3 ubiquitin ligase TRIP12 catalyzes non-canonical lysine-independent ubiquitin-ubiquitin linkages in vitro","fileCount":"13","fileSizeKB":"2229973","spectra":"0","psms":"2649","peptides":"408","variants":"523","proteins":"65","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:23 - \\\"Dehydration.\\\";UNIMOD:6 - \\\"Iodoacetic acid derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"E3 ubiquitin ligase TRIP12;ubiquitin;non-canonical modification;Ubiquitination;DatasetType:Proteomics","pi":[{"name":"Omar Khan","email":"okhan@hbku.edu.qa","institution":"College of Health and Life Sciences, Hamad Bin Khalifa University","country":"Qatar"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD064242","task":"d1bc54bf7b9d4743a72fd458c0fe62fb","id":"832"}, {"dataset":"MSV000097977","datasetNum":"97977","title":"Extracellular Matrix Alterations in Chronic Ischemic Cardiomyopathy Revealed by Quantitative Proteomics ","user":"htrogers","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747956635000","created":"May. 22, 2025, 4:30 PM","description":"Ischemic cardiomyopathy (ICM) is a leading cause of heart failure characterized by extensive remodeling of the cardiac extracellular matrix (ECM). While initially adaptive, ECM deposition following ischemic injury eventually turns maladaptive, promoting adverse cardiac remodeling. The strong link between the extent of fibrosis and adverse clinical outcomes has led to growing interest in ECM targeted therapies to prevent or reverse maladaptive cardiac remodeling in ICM; yet, the precise composition of the ECM in ICM remains poorly defined. In this study, we employed a sequential protein extraction enabled by the photocleavable surfactant Azo to enrich ECM proteins from left ventricular tissues of patients with end-stage ICM (n=16) and nonfailing donor hearts (n=16). High-resolution mass spectrometry-based quantitative proteomics identified and quantified over 6,000 unique protein groups, including 315 ECM proteins. We discovered significant upregulation of key ECM components, particularly glycoproteins, proteoglycans, collagens, and ECM regulators. Notably, LOXL1, FBLN1, and VCAN were among the most differentially expressed. Functional enrichment analyses revealed enhanced TGFB signaling, integrin-mediated adhesion, and complement activation in ICM tissues, suggesting a feedback loop driving continued ECM deposition in the end-stage failing heart. Together, our findings provide a comprehensive proteomic landscape of ECM alterations in the end-stage ICM myocardium and identify promising molecular targets for therapeutic intervention.","fileCount":"2630","fileSizeKB":"497470494","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Bottom-Up Proteomics;Ischemic Cardiomyopathy;Extracellular Matrix;DatasetType:Proteomics","pi":[{"name":"Ying Ge","email":"ying.ge@wisc.edu","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD064211","task":"0616d4059530444a90138acd05d5a5b3","id":"833"}, {"dataset":"MSV000097976","datasetNum":"97976","title":"GNPS - Different Collision Energies on QExactive","user":"cbez","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747943765000","created":"May. 22, 2025, 12:56 PM","description":"This dataset was generated using 12 different acquisition methods on a Thermo Q Exactive mass spectrometer, each employing varying collision energies and AGC settings. Samples included two each from feces, serum, brain tissue, two distinct bile acid standard mixtures, and one mixed food matrix. MS\/MS data were acquired in positive ionization mode, with chromatographic separation performed on a Phenomenex Polar C18 column.","fileCount":"231","fileSizeKB":"12377993","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"different CE, AGC, feces, brain tissue, bile-acid mix, food-mix, serum;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cc083654ae6f4119815f32d13ebfeb36","id":"834"}, {"dataset":"MSV000097975","datasetNum":"97975","title":"Vibrio cholerae colony metabolomics","user":"eolder","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747941066000","created":"May. 22, 2025, 12:11 PM","description":"Untargeted metabolomics of V. cholerae wild type and delta-GluP mutant colonies. Extracted with ACN and analyzed by LC-MS\/MS. 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The metabolic composition of root exudates varies according to plant developmental stage, nutrient availability, (a)biotic stresses and interaction with the root-associated microbiota, including arbuscular mycorrhizal fungi (AMF), which play a key role in plant mineral nutrition and stress tolerance. While it is well established that AMF can perceive plant root exudate compounds, little is known about plant root exudate modifications in response to AMF inoculation. Here, we developed an aeroponic-based culture system suitable for the analysis of maize root exudates during symbiosis with the AMF Rhizophagus irregularis while controlling nutrient availability. We validated the functionality of the system by monitoring both maize root colonization by the AMF and the expression profile of symbiotic root marker genes. We then investigated the composition of root exudates (strigolactones and specialized metabolites) from mycorrhizal and non-mycorrhizal plants grown under different N and P regimes. Comparisons of specialized metabolite profiles from root exudates, root tissues, and fungal extracts allowed us to identify candidate metabolic features specifically accumulating in mycorrhizal root exudates. Thus, we provide an innovative method to better understand the role of root exudate metabolites in shaping the microbiota of mycorrhizal plants.","fileCount":"2867","fileSizeKB":"105601773","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Zea mays (NCBITaxon:4577)","instrument":"impact II","modification":"ND","keywords":"Maize;Specialized metabolites;aeroponic conditions;Rhizophague irregularis;arbuscular mycorrhizal;symbiosis;root exudates;DatasetType:Metabolomics","pi":[{"name":"Boutet stephanie","email":"stepahnie.boutet@inrae.fr","institution":"INRAE","country":"france"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"e1841ca070834af6ba280f79a586eb33","id":"836"}, {"dataset":"MSV000097968","datasetNum":"97968","title":"PSMtags improve peptide sequencing and throughput in sensitive proteomics","user":"madamo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747918957000","created":"May. 22, 2025, 6:02 AM","description":"Mass spectrometry-based proteomics enables comprehensive characterization of protein abundance, function, and interactions. Label-free approaches are simple to implement but challenging to scale to thousands of samples per day. Multiplexed techniques, such as plexDIA, can address these limitations but remain restricted by the lack of mass tags optimized for data-independent acquisition (DIA) workflows. Here, we present a systematic approach screening a library of 576 compounds that identifies several small molecules that, when conjugated to peptides, improve their detection and sequence identification by mass spectrometry. The lead molecule, PSMtag, substantially increases the detection of fragment b-ions, which increases the confidence of sequence identification and enhances de novo sequencing. PSMtags allow 9-plexDIA, using only stable isotopes of carbon, oxygen and nitrogen. As a result, it allows simultaneously increasing proteome coverage and sample throughput for plexDIA workflows without compromising quantitative accuracy. We demonstrate 240 samples-per-day with 9-plexDIA, while acquiring 28,359 protein data points in the same time label-free methods acquire 4,340. Our approach constitutes an expandable framework for designing mass tags to overcome existing limitations in multiplexed proteomics and provides plexDIA reagents capable of analyzing over 1,000 samples per day when using 10 minute runs. By facilitating higher throughput and improved identification, this innovation holds significant potential for accelerating proteomic studies across diverse biological and clinical applications.","fileCount":"2080","fileSizeKB":"91399860","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Astral;timsTOF SCP;Orbitrap Exploris 240","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"mass tag;multiplexing;DIA;fragmentation;throughput;DatasetType:Proteomics;single-cell","pi":[{"name":"Nikolai Slavov","email":"n.slavov@northeastern.edu","institution":"Northeastern University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD064191","task":"4906b9cefe1c4aa29bfca03a27fb6a65","id":"837"}, {"dataset":"MSV000097967","datasetNum":"97967","title":"GNPS - In vitro Gut Untargeted metabolomics dataset","user":"Lamichhane2025","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747903511000","created":"May. 22, 2025, 1:45 AM","description":"The Enteromix model of the human large intestine. In summary, each simulator unit consists of four connected glass vessels that are fed semi-continuously every third hour. The four vessels in the simulator (V1toV4) model different compartments of the human colon from the proximal (V1) to the distal part (V4), each having a different controlled pH and flow rate. 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We performed proximity labeling experiments using the TurboID system to label intracellular proteins that are in close proximity to GAB2, NPM1wt, NPM1cA, DNMT3Awt or DNMT3AR882H protein (baits), in primary murine HSPCs. We used a TurboID cDNA fused in frame to the N- or C-terminus of each bait in an MSCV-based retroviral vector, and transduced these vectors into primary murine bone marrow HSPCs from relevant genotypes. TurboID cDNA alone was used as a control for non-specific biotin labeling. Cells were lysed and labeled proteins were captured using streptavidin beads, followed by on-bead digest and mass spectrometry. 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Ley","email":"timley@wustl.edu","institution":"Washington University in St. Louis","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD064174","task":"7442566d365b4c6d8ae3d39e296ba160","id":"839"}, {"dataset":"MSV000097965","datasetNum":"97965","title":"GNPS - Salmonella infection on different diets - gallbladder","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747874765000","created":"May. 21, 2025, 5:46 PM","description":"Mice infected with Salmonella (gallbladder) run on Q-Exactive. 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With increasing realisation that the M1\/M2 paradigm does not reflect the complexity of macrophage phenotypes in cancer patients, an urgent need has arisen to develop improved, translatable in vitro models for human TAMs. To address this gap, we have screened conditioned media from a panel of tumour cell lines for their ability to induce suppressive marker upregulation on human monocyte-derived macrophages (hMDMs), as well as active T-cell immunosuppression. We performed secretome characterization of these tumour-conditioned media (TCM) to shed light on cancer cell-derived soluble factors that may contribute to TAM polarisation. Furthermore, we characterized the proteomic and transcriptomic signatures of macrophages exposed to either TCM or primary ascites fluid from ovarian cancer patients and performed bioinformatics analysis to determine the most translationally relevant models of TAMs. In summary, our work provides mechanistic insights on tumour-macrophage crosstalk in the context of establishing suppressive TAM phenotypes and addresses the long-standing gap of defining translationally relevant human in vitro TAM models. 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Dataset includes spectra for hiPSC-CMs (cell count: 50k cells) cultured as monocultured on non-patterned PDMS (Monoculture Monolayer), hiPSC-CMs cultured as co-cultures (with hiPSC-CFs) on non-patterned PDMS (Coculture Monolayer), and hiPSC-CMs co-cultured (with hiSPC-CFs) on patterned PDMS (Micropattern). Additionally, we have included data files from method development using 100k hiPSC-CMs: (A-C) treated with 25% HFIP, (D-F) treated with 25% HFIP and pulse-sonication, (G-I) treated with 90% HFIP, and (J-L) treated with 90% HFIP and pulse sonication.","fileCount":"3138","fileSizeKB":"101373844","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)","instrument":"impact II;nanoACQUITY UPLC","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Top-down proteomics;hiPSC-CM maturation;sensitivity;cardiac model;arrhythmia;DatasetType:Proteomics","pi":[{"name":"Lee L. Eckhardt","email":"lle@medicine.wisc.edu","institution":"University of Wisconsin-Madison","country":"United States of America"},{"name":"Ying Ge","email":"ge2@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"02ab7c09e14049da8987a78f6356b21e","id":"891"}, {"dataset":"MSV000097860","datasetNum":"97860","title":"Androgenic Effects of 11-oxyandrogens in Castration-Resistant Prostate Cancer","user":"microu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747168100000","created":"May. 13, 2025, 1:28 PM","description":"Investigations of CRPC cell models demonstrate that 11-ketotestesterone (11KT) and 11-hydroxytestosterone (11OHT) drive robust AR-mediated proliferative responses and significantly modulate gene and protein expression profiles, paralleling canonical androgens. They also exhibit unique transcriptional and post-transcriptional effects that include potential AR-independent pathways. Furthermore, the AR antagonist enzalutamide effectively inhibits their androgenic actions, suggesting they are primarily AR-mediated.","fileCount":"45","fileSizeKB":"543007393","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\"","keywords":"DIAnn;CRPC proteomics;11-oxygenated androgens;androgen receptor;enzalutamide;DatasetType:Proteomics","pi":[{"name":"Chantal Guillemette","email":"chantal.guillemette@crchudequebec.ulaval.ca","institution":"CHU de Quebec Research Center - Universite Laval","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD063893","task":"9f3c175e8b3b43898794a4402b01eafe","id":"892"}, {"dataset":"MSV000097859","datasetNum":"97859","title":"Establishment of a murine model of beta-parvalbumin-induced fish allergy and proteomic profiling of immune cell activation using DIA-based ZenoSWATH-MS","user":"robertstr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747168100000","created":"May. 13, 2025, 1:28 PM","description":"Food allergy is an immune-mediated condition caused by hypersensitivity to food allergens, with fish allergens, particularly beta-parvalbumins (beta-PRVBs), being the most significant. While the only effective treatment is avoidance of the food allergen, the intracellular mechanisms of immune activation during allergen exposure are not well understood.\n\nThis study aimed to investigate critical insights into immune cell activation in a newly proposed beta-PRVB-induced fish allergy model, with a particular focus on to explore the proteomic phenotype of splenocytes and T cell activation in response to the allergen.\n\nTo establish a robust allergic response, mice were sensitized to beta-PRVB using aluminium hydroxide, a Th2-skewing adjuvant, (intraperitoneal injection) and subsequently challenged orally with beta-PRVB . This carefully designed protocol was designed to induce a Th2-type immune response, which was confirmed by detecting allergen-specific antibodies and cytokines. For proteomic analysis of the immune response, high-resolution quantitative proteomics data were generated using an advanced DIA-based ZenoSWATH-MS technology.","fileCount":"124","fileSizeKB":"25821871","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"ZenoTOF 7600","modification":"ALKYKATION;Carbamidomethyl on cysteine C2H3NO [C] +57Da","keywords":"fish allergy;parvalbumin;proteomics;SWATH;immunoproteasome;DatasetType:Proteomics","pi":[{"name":"Monica Carrera","email":"mcarrera@iim.csic.es","institution":"Spanish Research Council_CSIC","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5192394b7ff14d869a68cefe59962ad0","id":"893"}, {"dataset":"MSV000097856","datasetNum":"97856","title":"Site-specific TMT O-GlcNAc proteomics","user":"ChiulabUCD","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1747167858000","created":"May. 13, 2025, 1:24 PM","description":"The liver circadian clock and hepatic transcriptome are highly responsive to metabolic signals generated from feeding-fasting rhythm. Previous studies have identified a number of nutrient-sensitive signaling pathways that could interpret metabolic input to regulate rhythmic hepatic biology. Here, we investigated the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) in mediating metabolic regulation of rhythmic biology in the liver. We observed daily oscillation of global nuclear protein O-GlcNAcylation in the liver of mice subjected to night-restricted feeding (NRF). Among 449 O-GlcNAcylated proteins we identified, 64 proteins are rhythmically O-GlcNAcylated over a 24-hour day-night cycle. Proteins involved in gene expression were enriched among rhythmically O-GlcNAcylated nuclear proteins, suggesting rhythmic O-GlcNAcylation may directly shape the daily rhythmicity of the hepatic transcriptome. We also identified xxx O-GlcNAcylation sites, demonstrating day-night differences of site-specific O-GlcNAcylation. Furthermore, we showed that rhythmic O-GlcNAcylation can also indirectly modulate the hepatic transcriptome by interacting with phosphorylation. Specifically, several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. We show that O-GlcNAcylation occur at a phospho-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), thus regulating its stability and transcriptional output. Finally, we report that day-restricted feeding (DRF) in the nocturnal mouse dampens O-GlcNAcylation rhythm. This suggests the dysregulation of daily nuclear protein O-GlcNAcylation rhythm could partially contribute to the disruption in liver transcriptomic rhythm previously observed in DRF condition, despite not the primary driver. In summary, our results provide new mechanistic insights into metabolic regulation of daily hepatic transcriptomic rhythm via interplay between O-GlcNAcylation and phosphorylation and shed light on the deleterious effects of improper mealtimes.","fileCount":"11","fileSizeKB":"5456386","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"nanoUPLC-MS\\\/MS","modification":"UNIMOD:934 - \\\"Photocleavable Biotin + GalNAz on O-GlcNAc.\\\"","keywords":"O-GlcNAcylation;Liver;Circadian rhythm;DatasetType:Proteomics","pi":[{"name":"Joanna Chiu","email":"jcchiu@ucdavis.edu","institution":"University of California Davis","country":"The United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a2bcb46bd364442995d457889c508fed","id":"894"}, {"dataset":"MSV000097853","datasetNum":"97853","title":"Proteomics of ovarian cancer stem like cells A2780: Monolayer vs Spheroid","user":"RAJUM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746865356000","created":"May. 10, 2025, 1:22 AM","description":"Proteomics of ovarian cancer cell line A2780 in 2D monolayer and in 3D spheroid culture.","fileCount":"22","fileSizeKB":"11967104","spectra":"0","psms":"109773","peptides":"21732","variants":"28045","proteins":"12885","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Spheroid;Monolayer;Ovarian cancer;Proteomics;DatasetType:Proteomics","pi":[{"name":"Raju Mukherjee","email":"raju.mukherjee@labs.iisertirupati.ac.in","institution":"Indian Institute of Science Education and Research, Tirupati","country":"India"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD063832","task":"e63454c29356465eacc6b21f6445a7be","id":"895"}, {"dataset":"MSV000097846","datasetNum":"97846","title":"GNPS - LC-MS\/MS data collected on producers of Trestatin B","user":"hmohiman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746829770000","created":"May. 9, 2025, 3:29 PM","description":"LC-MS\/MS data collected on producers of trestatin-B","fileCount":"5","fileSizeKB":"10746","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinomyces (NCBITaxon:1654)","instrument":"6210 Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Trestatin producers;DatasetType:Metabolomics","pi":[{"name":"Hosein Mohimani","email":"hoseinm@andrew.cmu.edu","institution":"Carnegie Mellon University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"be6e870005e94ecb9a74d92d05c3e9e4","id":"896"}, {"dataset":"MSV000097845","datasetNum":"97845","title":"GNPS - Alzheimer's Bacteroides HILIC Fecal","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746817583000","created":"May. 9, 2025, 12:06 PM","description":"Wildtype and transgenic mice were treated with or without Bacteroides fragilis and fecal samples were extracted for untargeted LC-MS analysis. 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File descriptions are as follows: MALDI-TIMS-MS1: 250321_JB182_Pen12.d; MALDI iprm-PASEF with precursor list 1- 250321_JB182_Pen12_Precursors1.d; MALDI iprm-PASEF with precursor list 2- 250321_JB182_Pen12_Precursors2.d; MALDI iprm-PASEF with precursor list 3- 250321_JB182_Pen12_Precursors3.d. imzML versions of each of the raw data files can be found with the corresponding file names in the Supplementary Files Folder.","fileCount":"13","fileSizeKB":"5918410","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Glutamicibacter arilaitensis (NCBITaxon:256701);Penicillium solitum (NCBITaxon:60172)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"iprm-PASEF;MALDI-MSI;DatasetType:Metabolomics;DatasetType:Other (MALDI iprm-PASEF)","pi":[{"name":"Laura M. 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File descriptions are as follows: \nMALDI-TIMS-MS1: 250321_JB182_Pen12.d\nMALDI iprm-PASEF with precursor list 1: 250321_JB182_Pen12_Precursors1.d\nMALDI iprm-PASEF with precursor list 2: 250321_JB182_Pen12_Precursors2.d\nMALDI iprm-PASEF with precursor list 3: 250321_JB182_Pen12_Precursors3.d\n\nimzML versions of each of the raw data files can be found with the corresponding file names in the Supplementary Files Folder. ","fileCount":"181","fileSizeKB":"6102497","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Glutamicibacter arilaitensis (NCBITaxon:256701);Penicillium solitum (NCBITaxon:60172)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"iprm-PASEF;MALDI-MSI;DatasetType:Metabolomics;DatasetType:Other (iprm-PASEF Imaging)","pi":[{"name":"Laura M. 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Multivariable analysis indicated older age, female sex, Black race\/ethnicity, and higher BMI were associated with at least one measure of better barrier function: older age was associated with better dynamic barrier function (beta=-0.141, p=0.034) and barrier permeability (beta=-0.158, p=0.018); female participants had superior dynamic barrier function (beta=0.164, p=0.027) and increased barrier recovery (beta=-0.239, p=0.001); black participants also had better dynamic barrier function (beta=-0.200, p=0.006) and higher barrier integrity (beta=0.256, p<0.001); and higher BMI was associated with better barrier integrity (beta=0.131, p=0.033). Protein expression from tape strips analyzed by mass spectrometry among a sub-sample of 20 participants showed that protein families linked to barrier composition and insult response were higher among participants with above-median barrier function (p<0.01). Our results provide a framework for future research on epidermal barrier function and suggest additional measures are needed to differentiate age-associated barrier decline.","fileCount":"44","fileSizeKB":"41085452","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"skin;skin barrier;Baltimore Longitudinal Study of Aging;Aging;DatasetType:Proteomics","pi":[{"name":"Katrina Abuabara","email":"katrina.abuabara@ucsf.edu","institution":"University of California, San Francisco, Department of Dermatology","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD063780","task":"68b762f00a9b4710864d88bb88eab1b7","id":"903"}, {"dataset":"MSV000097830","datasetNum":"97830","title":"Data from New collagen peptide markers from New Guinea fauna: Identifying archaeological bone in the tropics","user":"AnnetteOertle","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746712495000","created":"May. 8, 2025, 6:54 AM","description":"Raw MS\/MS files for new collagen peptide markers from New Guinea fauna. 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The coral life stages in the experiment include egg bundles sampled on spawning night, larvae, settled recruit corals, and finally recruits containing their endosymbiotic Symbiodiniaceae. Exudate samples were concentrated and desalted with solid phase extraction (SPE), using three different types of cartridge (PPL, HLB and ENVI-Carb) at two different pHs (2 and native). With untargeted MS we want to understand the differences in the chemical composition between samples treated with different SPE methods, and coming from different juvenile coral life stages.. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA) ","fileCount":"437","fileSizeKB":"19835093","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Acropora millepora (NCBITaxon:45264);Symbiodiniaceae (NCBITaxon:252141)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;MSCollaboratory;Coral;Endosymbiotic;Symbiodiniaceae;DatasetType:Metabolomics","pi":[{"name":"Roman Stocker","email":"omanstocker@ethz.ch","institution":"ETH Zurich","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f9dd49ec7fea4e59b4074b007209d38e","id":"907"}, {"dataset":"MSV000097814","datasetNum":"97814","title":"GNPS - Algal induction from a spotted salamander host dataset 2 NEG","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746563090000","created":"May. 6, 2025, 1:24 PM","description":"Follow up study. Samples corresponding to sterile filtered metabolites from before and after the bloom period of development of blastopore of neurulating Ambystoma maculatum (spotted salamander) hosts. Algal species (Oophila amblystomatis) bloom outside the blastopore of the host. Pond water and rearing media samples are also included. Untargeted LC-MS\/MS acquisition (negative mode) was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"433","fileSizeKB":"16020916","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ambystoma maculatum (NCBITaxon:43114);Oophila amblystomatis (NCBITaxon:1008953)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Salamander;Algal induction;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Ryan Kerney","email":"rkerney@gettysburg.edu","institution":"Gettysburg College","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"57a68dea2af84ccbac520d1181d93ccd","id":"908"}, {"dataset":"MSV000097813","datasetNum":"97813","title":"GNPS - Algal induction from a spotted salamander host dataset 2 POS","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746562855000","created":"May. 6, 2025, 1:20 PM","description":"Follow up study. Samples corresponding to sterile filtered metabolites from before and after the bloom period of development of blastopore of neurulating Ambystoma maculatum (spotted salamander) hosts. Algal species (Oophila amblystomatis) bloom outside the blastopore of the host. Pond water and rearing media samples are also included. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA)","fileCount":"575","fileSizeKB":"25166763","spectra":"758295","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ambystoma maculatum (NCBITaxon:43114);Oophila amblystomatis (NCBITaxon:1008953)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Salamander;Algal induction;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Ryan Kerney","email":"rkerney@gettysburg.edu","institution":"Gettysburg College","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e3c16077530a465cad4826f2e5a2d586","id":"909"}, {"dataset":"MSV000097810","datasetNum":"97810","title":"Characterization of cytokine treatment on human pancreatic islets by top-down proteomics","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1746556167000","created":"May. 6, 2025, 11:29 AM","description":"Top-down proteomic data from 6 human islet donors; islets were treated with interferon gamma (IFN-gamma) and interleukin-1 beta (IL-1 beta). 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This transition to a quiescent state occurred in the absence of substantial proteome re-modelling but broad changes of protein phosphorylation and ubiquitylation. The transition also included the participation of ubiquitylation -mediated inhibition of E1 ubiquitin activating and E2 ubiquitin conjugating enzymes. 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The TFA dataset breaks the crosslinker in a solution of pyrrolidine and TFA; normally guanidine\/formic acid is used.","fileCount":"7","fileSizeKB":"666416","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"butylpyrrolidine","keywords":"crosslinking, intrinsic disorder;DatasetType:Proteomics","pi":[{"name":"Eric Weiss","email":"elweiss@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"792073f0c859427da6ac66f595b27e1c","id":"950"}, {"dataset":"MSV000097736","datasetNum":"97736","title":"Increasing mass spectrometry throughput using time-encoded sample multiplexing","user":"jderks","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745693871000","created":"Apr. 26, 2025, 11:57 AM","description":"Liquid chromatography-mass spectrometry (LC-MS) can enable precise and accurate quantification of analytes at high-sensitivity, but the rate at which samples can be analyzed remains limiting. Throughput can be increased by multiplexing samples in the mass domain with plexDIA, yet multiplexing along one dimension will only linearly scale throughput with plex. To enable combinatorial-scaling of proteomics throughput we developed a complementary multiplexing strategy in the time domain, termed `timePlex'. timePlex staggers and overlaps the separation periods of individual samples. This strategy is orthogonal to isotopic multiplexing, which enables combinatorial multiplexing in mass and time domains when paired together and thus multiplicatively increased throughput. We demonstrate this with 3-timePlex and 3-plexDIA, enabling the multiplexing of 9 samples per LC-MS run, and 3-timePlex and 9-plexDIA exceeding 500 samples \/ day with a combinatorial 27-plex. Crucially, timePlex supports sensitive analyses, including of single cells. These results establish timePlex as a methodology for label-free multiplexing and for combinatorially scaling the throughput of LC-MS proteomics. We project this combined approach will eventually enable an increase in throughput exceeding 1,000 samples \/ day.","fileCount":"38","fileSizeKB":"147558248","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Exploris 240;Orbitrap Exploris 480","modification":"UNIMOD:888 - \\\"MTRAQ light.\\\"","keywords":"DIA;plexDIA;timePlex;Single-cell;DatasetType:Proteomics","pi":[{"name":"Nikolai Slavov","email":"nslavov@parallelsq.org","institution":"Parallel Squared Technology Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD063357","task":"7193ea0d007741c680f22ec005718e2b","id":"951"}, {"dataset":"MSV000097735","datasetNum":"97735","title":"GNPS - Corals Metabolomic Profile to Establish Coral Cell Culture","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745621527000","created":"Apr. 25, 2025, 3:52 PM","description":"Samples from Pocillopora demicornis were collected by airbrushing, frozen, lyophilized and extracted with methanol-water (4:1). Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"131","fileSizeKB":"5469841","spectra":"162403","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pocillopora damicornis (NCBITaxon:46731)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coral;Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Nikki Traylor-Knowles","email":"ntraylorknowles@earth.miami.edu","institution":"University of Miami","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"97e589fa277b4acbb46d32a6ce901ab2","id":"952"}, {"dataset":"MSV000097732","datasetNum":"97732","title":"Unknown source in the nature based on iriomote","user":"viqqikurnianda","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745602005000","created":"Apr. 25, 2025, 10:26 AM","description":"This unknown organisms to understanding the protein","fileCount":"3","fileSizeKB":"22794","spectra":"420","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"unknown symbiotic dinoflagellate (NCBITaxon:75304)","instrument":"LCMS-IT-TOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Organic, organisms;DatasetType:Metabolomics","pi":[{"name":"Viqqi Kurnianda","email":"viqqikurnianda@yahoo.co.id","institution":"University of the Ryukyus","country":"Japan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d2f8521dd9bb456bba23e71f9579bed7","id":"953"}, {"dataset":"MSV000097731","datasetNum":"97731","title":"GNPS GCMSMS Dataset creation for crude extracts of two fungal endophytes having antibacterial activity (without zlib compressed files)","user":"AbhiBeck_1914","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745588817000","created":"Apr. 25, 2025, 6:46 AM","description":"crude extracts of two fungal endophytes cultured in two different media was tested for antibacterial activity against few disease causing bacterias","fileCount":"52","fileSizeKB":"2160208","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alternaria destruens (NCBITaxon:230003);Alternaria burnsii (NCBITaxon:1187904)","instrument":"TSQ 9000","modification":"MS:1002864 - 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Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduced cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over the growth period compared with controls. Genome-resolved metatranscriptomic data from rhizosphere soils reveal lower ratios of gene activities for CH4 production versus consumption, decrease in activity of H2-producing genes, and increase in bacterial H2 oxidation pathways in the PSY genotypes. Metabolic modeling using metagenomic and metabolomic data predicts elevated levels of H2 oxidation and suppressed H2 production in the PSY rhizosphere. The H2- oxidizing bacteria have more genes for utilization of gluconeogenic acids than H2- producing counterparts, and their activities were likely stimulated by the observed enrichment of gluconeogenic acids (mostly amino acids) in PSY root exudates. Together these results suggest that decreased CH4 emission is due to the reduction of H2 available for hydrogenotrophic methanogenesis. The combination of rice phenotypic characterization, microbiome multi-omic analysis, and metabolic modeling described here provides a powerful strategy to discover the mechanisms by which specific plant genotypes can alter biogeochemical cycles to reduce CH4 emissions.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008481) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"206","fileSizeKB":"15458274","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Oryza sativa ssp. Japonica cultivar Kitaake","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"rice;roots;root exudates;DatasetType:Metabolomics","pi":[{"name":"Pam Ronald","email":"pcronald@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"34b6ce2ec6854d888c967aae75a41024","id":"958"}, {"dataset":"MSV000097724","datasetNum":"97724","title":"Elucidating the role of bacteriophage lifestyle strategy in Microbially-Mediated Perennial Rhizosphere Nitrogen Transformations","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527793000","created":"Apr. 24, 2025, 1:49 PM","description":"Illumination of the interplay between viral community lifestyle strategy (lytic vs. temperate) and the impact of these interactions on microbial population dynamics and metabolic functioning in soil is critical to our understanding of bioenergy crop productivity as well as carbon and nitrogen cycling more broadly. We will leverage an existing set of samples from switchgrass growing on marginal lands that were collected in a 2-week interval time-series over two years with comprehensive data on soil nitrogen pools, plant growth, and existing 16S-focused data on rhizosphere bacteria. We will investigate the role of phage in microbiome dynamics and nitrogen cycling in this system. Ecological and evolutionary trade-offs for bacteria and their bacteriophage are predicted to lead to shifts in viral lifestyle over the growing season and in response to shifts in nutrient availability. In particular, lytic phage are hypothesized to be more dominant during periods of rapid bacterial growth. Furthermore, temperate phage are hypothesized to be triggered into lysis by root exudates or microbial metabolites in soil. Lysis events are predicted to underlie variation in biogeochemical cycling, since the death of bacteria through viral lysis will liberate carbon and nitrogen compounds, contributing to the fluctuations in these compounds that our temporal dataset has documented.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001368) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"97","fileSizeKB":"7621276","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"soil microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"viral community;rhizosphere bacteria;nitrogen cycling;DatasetType:Metabolomics","pi":[{"name":"Rick White","email":"raw937@gmail.com","institution":"University of North Carolina Charlotte","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cd956e7a0e8a41a28a6cf96274ba31e7","id":"959"}, {"dataset":"MSV000097723","datasetNum":"97723","title":"Metabolomic analysis of stems of switchgrass lignin mutants under drought stress","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527792000","created":"Apr. 24, 2025, 1:49 PM","description":"This switchgrass project aims to identify metabolic consequences of lignin manipulation and impact on the responses to drought stress in switchgrass. Here we examine elongating internodes of six switchgrass lignin biosynthesis-altered transgenic and mutant and their isogenic wild-type negative segregant lines. Studies in the eudicot, Arabidopsis, have revealed metabolic and transcriptional differences in lignin biosynthesis mutants that appear to relate to feedback mechanisms for plants to compensate for lignin pathway disruption. Specifically, disruption of core lignin biosynthesis gene expression leads to increases in expression of cell wall-related pathways; whereas, disruption of downstream S- and G-lignin specific genes leads to down-regulation of lignin biosynthesis. This experiment allows us to test the generality of this observation in a bioenergy-relevant species. While we generally expect the same patterns, progress revealing differences in grass lignin biosynthesis pathways relative to eudicots suggests that we might also uncover differences.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000468) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"978","fileSizeKB":"81737424","spectra":"1757964","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Panicum virgatum","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"switchgrass;drought stress;lignin biosynthesis;DatasetType:Metabolomics","pi":[{"name":"Mariela Monteoliva","email":"monteoliva.mariela@inta.gob.ar","institution":"University of Oklahoma","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"284ef349ad89497d81b8a037afbd2766","id":"960"}, {"dataset":"MSV000097722","datasetNum":"97722","title":"GNPS - Tracking the degradation of fresh particulate organic matter in permeable riverbed sediments","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527776000","created":"Apr. 24, 2025, 1:49 PM","description":"This project builds upon a DOE Subsurface Biogeochemical Research (SBR) project on the transport and metabolism of fresh, photosynthetically-derived (mainly periphyton) particulate organic matter (POM) in near-surface riverbed sediments at the PNNL SFA Hanford 300 Area study site. We propose to utilize a combination of Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and polar metabolomics, together with metagenomic\/transcriptomic sequencing to track, in a substrate-explicit manner, the degradation of fresh POM in Hanford 300 Area riverbed sediments. The overarching hypothesis behind our proposed research is that there will be detectable chemical and (meta)genomic responses to the input of fresh POM. Many previous studies have demonstrated distinct metabolic and bulk geochemical responses to fresh POM input, and a few studies have directly examined the uptake and degradation of POM in permeable marine sediments. In addition, our recent studies at the Hanford 300 Area indicate that in situ input of fresh POM (likely dominated by periphyton detritus) to the near-surface riverbed is an important driver of both microbial community composition and activity in the vicinity of the Hanford 300 Area.\r\n\r\nThis research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:https:\/\/doi.org\/10.46936\/fics.proj.2021.60033\/60000394) and used resources at the DOE Joint Genome Institute (https:\/\/ror.org\/04xm1d337) and the Environmental Molecular Sciences Laboratory (https:\/\/ror.org\/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. 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The experiment exposed resistant (line H7996) and susceptible (line FL8000) tomatoes (Solanum lycopersicum) to the select agent soil pathogen Ralstonia solanacearum (RS5) which is responsible for Bacterial Wilt. R. solanacearum infects plants through root wounds and colonizes vascular tissues. The pathogen rapidly multiplies and clogs the xylem vessels causing the infected plant to quickly wilt and die. Exopolysaccharides from R. solanacearum activate salicylic acid (SA) pathways in the resistant plants, but not in susceptible plants (Mansfield et al., 2012; Milling et al., 2011). A recent study suggested the microbiome plays a role in host susceptibility (Kwak et al., 2018). The system is being used as a model for developing new techniques in modeling bacterial-fungal-plant interactions and developing statistical methods to engineer microbial consortia from these graphical models.\n\nThe work (proposal:httpas:\/\/doi.org\/10.46936\/10.25585\/60000455) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"232","fileSizeKB":"21070968","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"soil microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bacterial-fungal-plant interactions;polar metabolomics;DatasetType:Metabolomics","pi":[{"name":"Adam Rivers","email":"adam.rivers@ars.usda.gov","institution":"USDA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fac73deb9dd44144a86140d83c80ae35","id":"962"}, {"dataset":"MSV000097720","datasetNum":"97720","title":"GNPS - Metabolome analysis of sorghum in response to nutrient deficiency","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527739000","created":"Apr. 24, 2025, 1:48 PM","description":"Sorghum plants were grown in the hydroponic system in a growth chamber under 16h light\/8h dark, 28°C, 600 ?mol m?2 s?1 light condition. 4-week-old plants were treated, and the shoot and root were collected at 1d and 3d nitrogen-deficiency and potassium-deficiency treatment. Four biological replicates for each treatment at each time point were included.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008854) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"973","fileSizeKB":"87437522","spectra":"2085124","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sorghum bicolor","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sorghum;nitrogen use efficiency;DatasetType:Metabolomics","pi":[{"name":"Li-Qing Chen","email":"lqchen77@illinois.edu","institution":"University of Illinois Urbana-Champaign","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6056ab9ea9034f5cbf43489d3506ac6a","id":"963"}, {"dataset":"MSV000097719","datasetNum":"97719","title":"GNPS - Discover ectomycorrhizal fungi-triggered macro- and micronutrient reactions and movements: From cell to ecosystem function","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527738000","created":"Apr. 24, 2025, 1:48 PM","description":"The samples were collected from pine seedling bioassay, consisting of pine root wash-off water samples and washed pine root samples.\r\n\r\nThis research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:https:\/\/doi.org\/10.46936\/fics.proj.2019.50960\/60000126) and used resources at the DOE Joint Genome Institute (https:\/\/ror.org\/04xm1d337) and the Environmental Molecular Sciences Laboratory (https:\/\/ror.org\/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).","fileCount":"581","fileSizeKB":"47746855","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pinus taeda","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ectomycorrhizal fungi;soil;Pinus;Suillus;root;DatasetType:Metabolomics","pi":[{"name":"Hui-Ling (Sunny) Liao","email":"sunny.liao@ufl.edu","institution":"University of Florida","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6319044fc15d43c08b7056032ba40d32","id":"964"}, {"dataset":"MSV000097718","datasetNum":"97718","title":"GNPS - Root metabolome characteristics of different root functional types in response to water and N limitations","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527721000","created":"Apr. 24, 2025, 1:48 PM","description":"One upland and one lowland switchgrass genotypes were grown in native soil under a rainout shelter and for three years under well-watered and water limited conditions. Further, two N treatments, + 67.25 kg N\/ha and 0 fertilizer N application, were superimposed on the water availability treatments. Each of the 8 treatments (2 genotypes x 2 water availability x 2 N availability) was replicated three times with each experimental unit consisting of six plants in each of the treatments. Root and soil samples were collected at the end of the third year and roots were separated into transport and uptake roots to study how the metabolite profile in the two switchgrass ecotypes is influenced by water and N availability. This analysis will be coupled with a classification and identification of the root associated as well as rhizosphere microbiome.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001049) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"376","fileSizeKB":"28327186","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Panicum virgatum root, rhizosphere microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"switchgrass;drought tolerance;root metabolome;DatasetType:Metabolomics","pi":[{"name":"Thomas Juenger","email":"tjuenger@austin.utexas.edu","institution":"University of Texas at Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"556a0f182d17485e9e5143d6322386f1","id":"965"}, {"dataset":"MSV000097717","datasetNum":"97717","title":"Differential gene expression in Clostridium autoethanogenum due to sugar co-metabolism","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745527706000","created":"Apr. 24, 2025, 1:48 PM","description":"This experiment includes RNA-seq and metabolomics from a pure microbial strain to examine differential gene expression as a result of pre-adaptation and exposure to multiple carbon sources. This data will provide molecular insight into gene regulation and potential metabolic activity of Clostridium autoethanogenum, an important microbe for the bioenergy industry. C. autoethanogenum plays a unique role in lignocellulosic-based bioproduct synthesis due to its ability to consume single carbon gases as well as pentose and hexose sugars. Our preliminary research has demonstrated the organism\u2019s ability to co-metabolize the pentose and hexose sugars xylose and fructose. However, different responses were observed depending on pre-adaptation or culturing history - whether cultures were grown on either xylose or fructose prior to the dual-sugar experiment. Sugar consumption as well as ethanol and acetate production differed between cultures pre-adapted on xylose versus fructose prior to the xylose-fructose fermentation. Fructose pre-adaptation resulted in both a faster sugar consumption and greater total consumption of sugar. Fructose pre-adapted cultures also produced three times more ethanol and two times more acetate.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000475) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"559","fileSizeKB":"39364490","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Clostridium autoethanogenum","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"carbon metabolism;ethanol production;acetate production;DatasetType:Metabolomics","pi":[{"name":"Ashley Beck","email":"aebeck@ncsu.edu","institution":"North Carolina State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"66d714d76aa44093aaa1cd83e7157770","id":"966"}, {"dataset":"MSV000097716","datasetNum":"97716","title":"Biodiversity library of protein tri-methylation in bacteria","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745517507000","created":"Apr. 24, 2025, 10:58 AM","description":"Phyloproteomics analysis of tri-methylation sites across 49 bacterial strains from 48 species; 1~3 biological replicates. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"1373","fileSizeKB":"359564954","spectra":"0","psms":"9576733","peptides":"3804357","variants":"4871819","proteins":"362277","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis 638R (NCBITaxon:862962);Bacteroides thetaiotaomicron VPI-5482 (NCBITaxon:226186);Myxococcus xanthus DZ2 (NCBITaxon:1198133);Bacillus subtilis (NCBITaxon:1423);Rhodopseudomonas palustris (NCBITaxon:1076)","instrument":"Q Exactive Plus","modification":"UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"phyloproteomics;trimethylation;evolutionary conservation;DatasetType:Proteomics","pi":[{"name":"Ernesto S. Nakayasu","email":"ernesto.nakayasu@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD063294","task":"9a4febffd2d44d158c97b75f2a3cd3c3","id":"967"}, {"dataset":"MSV000097715","datasetNum":"97715","title":"Proliferative proteome induced by HPV 16E6 and NFX1-123 partnership in longitudinal keratinocyte cultures","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745505522000","created":"Apr. 24, 2025, 7:38 AM","description":"Human papillomaviruses (HPV) cause cervical, anogenital, and oropharyngeal cancers. Despite the availability of preventive HPV vaccines, their poor uptake leaves individuals at risk for these cancers, many of which remain common globally, and others that are increasing domestically. The HPV 16 E6 (16E6) protein plays a significant role in inducing and maintaining cellular transformation of its infected host cell; however, 16E6 itself has no enzymatic activity and executes its functions through partnerships with host proteins. Previously, we demonstrated that 16E6 binds to the host protein NFX1-123, and NFX1-123 expression is increased in HPV 16 positive cervical cancer cell lines and primary cancers compared to normal tissues. In this study, we quantify growth patterns of 16E6-expressing keratinocytes with endogenous or overexpressed NFX1-123 (16E6\/vec and 16E6\/FN123, respectively) levels and interrogate proteome expression changes early and late in longitudinal growth cultures. Early passage 16E6\/vec and 16E6\/FN123 cells showed similar growth rates; however, late passage 16E6\/FN123 cells had accelerated growth, greater population doublings, increased telomerase activity, and a dysplastic phenotype when compared to 16E6\/vec cells. Matching this, mass spectrometry revealed only 22 differentially expressed proteins at early passage; meanwhile, late passaged cells had 827 differentially expressed protein among 16E6\/FN123 and 16E6\/vec cells. In that, DNA maintenance and repair, proteins namely MCM2 and MCM4, were highly expressed in the 16E6\/FN123 compared to 16E6\/vec cells. These findings indicate that the 16E6 and NFX1-123 partnership, especially with sustained higher levels of NFX1-123, alters the longitudinal cellular environment in a manner that may initiate a preneoplastic phenotype.\n","fileCount":"16","fileSizeKB":"20775209","spectra":"0","psms":"192906","peptides":"43441","variants":"69656","proteins":"5781","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human papillomavirus (NCBITaxon:10566);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Human papillomavirus (HPV);E6;NFX1-123;cervical cancer;DatasetType:Proteomics","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"},{"name":"Rachel Katzenellenbogen","email":"rkatzene@iu.edu","institution":"Indiana University School of Medicine","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD063286","task":"651dfd74c8d54dffa66f49eb70c0de4a","id":"968"}, {"dataset":"MSV000097713","datasetNum":"97713","title":"LC-MS lipidomics analysis of monoclonal MDCK cells (C59 and C113) and purified influenza particles","user":"jmenard","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745499137000","created":"Apr. 24, 2025, 5:52 AM","description":"LC-MS lipidomics analysis of two MDCK monoclonal cell lines, C59 and C113, at 24, 48, and 72 hour post infection, including the purified influenza virus from each clone. \r\n","fileCount":"272","fileSizeKB":"44987409","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"MDCK cells, clone 59;MDCK cells, clone 113;influenza A\\\/Puerto Rico\\\/8\\\/1934","instrument":"Agilent 6546 Quadrupole Time-of-Flight LC-MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipids, lipidomics, virus, influenza, MDCK;DatasetType:Other (Lipidomics)","pi":[{"name":"Jeffrey C. Smith","email":"jeffcsmith@cunet.carleton.ca","institution":"Carleton University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1446680a54704a699853a299e1ed8ff4","id":"969"}, {"dataset":"MSV000097712","datasetNum":"97712","title":"GNPS GCMSMS Data of antibacterial activity of two fungal endophytes","user":"AbhiBeck_1914","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745496603000","created":"Apr. 24, 2025, 5:10 AM","description":"GCMSMS analysis was performed for the compounds around zone of inhibition shown in the antibacterial analysis of two fungal endophytes","fileCount":"53","fileSizeKB":"2664691","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alternaria destruens (NCBITaxon:230003);Alternaria burnsii (NCBITaxon:1187904)","instrument":"TSQ 9000","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Antibacterial;Zone of inhibition;DatasetType:Metabolomics","pi":[{"name":"S.J.Rehman","email":"cifresults@bitmesra.ac.in","institution":"Birla Institute of Technology, Mesra","country":"Ranchi"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"179d776c891e4466995dfffe8bbf089a","id":"970"}, {"dataset":"MSV000097710","datasetNum":"97710","title":"GNPS GCMSMS Data Deconvolution of antibacterial activity of crude extracts of two fungal endophytes","user":"AbhiBeck_1914","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745491913000","created":"Apr. 24, 2025, 3:51 AM","description":"Antibacterial activity of crude extracts of two fungal endophytes were done and compound identification around the zone of inhibition","fileCount":"53","fileSizeKB":"2664691","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alternaria destruens (NCBITaxon:230003);Alternaria burnsii (NCBITaxon:1187904)","instrument":"TSQ 9000","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Antibacterial;Zone of inhibition;DatasetType:Metabolomics","pi":[{"name":"S.J.Rehman","email":"cifresults@bitmesra.ac.in","institution":"Birla Institute of Technology, Mesra","country":"Ranchi"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b11395a29f284db49e2d38d7c671f4e4","id":"971"}, {"dataset":"MSV000097709","datasetNum":"97709","title":"GNPS GCMSMS Deconvolution of antibacterial analysis of two fungal isolates","user":"AbhiBeck_1914","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745487960000","created":"Apr. 24, 2025, 2:46 AM","description":"Compound identification around the zone of inhibition","fileCount":"53","fileSizeKB":"2381115","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alternaria destruens (NCBITaxon:230003);Alternaria burnsii (NCBITaxon:1187904)","instrument":"TSQ 9000","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Antibacterial Analysis;DatasetType:Metabolomics","pi":[{"name":"S.J.Rehman","email":"cifresults@bitmesra.ac.in","institution":"Birla Institute of Technology, Mesra","country":"Ranchi"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a1151640cffc414ca8ef260b5da3831a","id":"972"}, {"dataset":"MSV000097708","datasetNum":"97708","title":"GNPS - mice with antidepressants","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745480677000","created":"Apr. 24, 2025, 12:44 AM","description":"Multiple mice tissues with antidepressant exposures","fileCount":"1045","fileSizeKB":"102520233","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"NA","keywords":"antidepressant;mice;DatasetType:Metabolomics","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aed241c2202545b48c7933fa48b07f39","id":"973"}, {"dataset":"MSV000097706","datasetNum":"97706","title":"Biodiversity library of protein di-methylation in bacteria","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745476099000","created":"Apr. 23, 2025, 11:28 PM","description":"Phyloproteomics analysis of di-methylation sites across 49 bacterial strains from 48 species; 1~3 biological replicates. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"1373","fileSizeKB":"361344711","spectra":"0","psms":"10014064","peptides":"3828278","variants":"5349566","proteins":"361137","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis 638R (NCBITaxon:862962);Bacteroides thetaiotaomicron VPI-5482 (NCBITaxon:226186);Myxococcus xanthus DZ2 (NCBITaxon:1198133);Bacillus subtilis (NCBITaxon:1423);Rhodopseudomonas palustris (NCBITaxon:1076)","instrument":"Q Exactive Plus","modification":"UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"phyloproteomics;dimethylation;evolutionary conservation;DatasetType:Proteomics","pi":[{"name":"Ernesto S. Nakayasu","email":"ernesto.nakayasu@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD063267","task":"f0e35f655da14d2db53601a34bb94225","id":"974"}, {"dataset":"MSV000097705","datasetNum":"97705","title":"Biodiversity library of protein mono-methylation in bacteria","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745455043000","created":"Apr. 23, 2025, 5:37 PM","description":"Phyloproteomics analysis of mono-methylation sites across 49 bacterial strains from 48 species; 1~3 biological replicates. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"1583","fileSizeKB":"457887038","spectra":"8632506","psms":"10081283","peptides":"3837808","variants":"5411103","proteins":"361078","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis 638R (NCBITaxon:862962);Bacteroides thetaiotaomicron VPI-5482 (NCBITaxon:226186);Myxococcus xanthus DZ2 (NCBITaxon:1198133);Bacillus subtilis (NCBITaxon:1423);Rhodopseudomonas palustris (NCBITaxon:1076)","instrument":"Q Exactive Plus","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"phyloproteomics;mono-methylation;evolutionary conservation;DatasetType:Proteomics","pi":[{"name":"Ernesto S. Nakayasu","email":"ernesto.nakayasu@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD063254","task":"8f053bb6043d4021a9a57a61ce0b804e","id":"975"}, {"dataset":"MSV000097704","datasetNum":"97704","title":"Hierarchical small molecule inhibition of MYST acetyltransferases","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745434581000","created":"Apr. 23, 2025, 11:56 AM","description":"MYST lysine acetyltransferases (KATs) is a class of epigenetic enzymes critical for cellular function that constitute an emerging therapeutic target in cancer. Recently, several drug-like MYST inhibitors have been reported that show promise in a variety of preclinical models as well as in clinical trials of breast cancer. However, the comparative properties of these small molecules remain to be directly assessed. Here we apply an integrated profiling strategy to systematically define the potency and selectivity of drug-like MYST KAT inhibitors. First, we use optimized chemoproteomic profiling and histone acetylation biormarkers to study the industry-developed KAT inhibitor PF-9363. This revealed dose-dependent engagement of native KAT complexes, with hierarchical inhibition following the order KAT6A\/B > KAT7 >> KAT8 > KAT5. Next, we demonstrate how PF-9363s ability to disrupt capture of MYST complex members in chemoproteomic experiments can be leveraged identify new candidate members of these complexes, including the transcription factor FOXK2. Applying insights from these studies to WM-8014, WM-1119 and WM-3835, which have been extensively applied in the literature as MYST probes, highlights unexpected cross-inhibition and suggests a new framework for how these small molecules and biomarkers may be applied to differentiate KAT6A\/B and KAT7-dependent phenotypes. Finally, we benchmark the activity of PF-9363 in the NCI-60 cell line screen, providing evidence that its ability to inhibit the growth of cell lines that are resistant to other KAT inhibitors may derive from engagement of the essential KAT8 enzyme at high concentrations. Collectively, our studies indicate the potential for MYST KAT inhibitors to exhibit dose-dependent target engagement reminiscent of kinase inhibitors and specify assays and biomarkers for facile monitoring of selective and hierarchical effects.","fileCount":"27","fileSizeKB":"35868838","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse;Orbitrap Fusion Lumos","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Lysine acetyltransferases, MYST, drug-like MYST inhibitors, chemoproteomics, histone acetylation, PF-9363, WM-8014, WM-1119, WM-3835, FOXK2;DatasetType:Proteomics","pi":[{"name":"Jordan Meier","email":"jordan.meier@nih.gov","institution":"National Cancer Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"202464f6372d4f818b7ed1c2321d718b","id":"976"}, {"dataset":"MSV000097700","datasetNum":"97700","title":"Biodiversity library of protein phosphorylation in bacteria","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745428142000","created":"Apr. 23, 2025, 10:09 AM","description":"Phyloproteomics analysis of phosphorylation sites across 49 bacterial strains from 48 species; 1~3 biological replicates. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"1372","fileSizeKB":"364661400","spectra":"0","psms":"10703349","peptides":"4308340","variants":"6133235","proteins":"376905","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis 638R (NCBITaxon:862962);Bacteroides thetaiotaomicron VPI-5482 (NCBITaxon:226186);Myxococcus xanthus DZ2 (NCBITaxon:1198133);Bacillus subtilis (NCBITaxon:1423);Rhodopseudomonas palustris (NCBITaxon:1076)","instrument":"Q Exactive Plus","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phyloproteomics;phosphorylation;evolutionary conservation;DatasetType:Proteomics","pi":[{"name":"Ernesto S. 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The cell pellets were collected after 12 or 24 hours of incubation and the proteome was extracted.","fileCount":"56","fileSizeKB":"30249694","spectra":"0","psms":"167517","peptides":"17097","variants":"22134","proteins":"2284","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Serotonin;5-HT;Pseudomonas fluorescens;untargeted proteomics;DatasetType:Proteomics","pi":[{"name":"Gilles van Wezel","email":"g.wezel@biology.leidenuniv.nl","institution":"Institute of Biology, Leiden University","country":"The Netherlands"},{"name":"Sahar El Aidy","email":"s.elaidy@uva.nl","institution":"Swammerdam Institute for Life Sciences (SILS), University of Amsterdam","country":"The Netherlands"}],"complete":"true","quant_analysis":"Quantification Results;Study Design","status":"Complete","private":"false","hash":"","px":"","task":"6bfdcb062ce0497585c222ccffa0bbe9","id":"978"}, {"dataset":"MSV000097693","datasetNum":"97693","title":"Validation of antibodies suitable for flow cytometric analysis and immunopeptidomics of peptide-MHC complexes in the outbred Swiss albino mouse strain","user":"abraun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745379816000","created":"Apr. 22, 2025, 8:43 PM","description":"Antigen presentation on major histocompatibility complex (MHC) molecules is central to the ini-tiation of immune responses and a lot of our understanding about the antigen processing and presentation pathway has been gained through studies in mice. MHC molecules are the most genetically diverse genes, consequently mouse strains differ substantially in their MHC make up and resulting antigen presentation. Swiss mice are commonly used in pharmacological research, yet our understanding of antigen presentation in this strain is surprisingly limited. Here, we have tested a range of anti-MHC antibodies and present a range of clones suitable to analyse MHC class I and II molecules in Swiss mice who have the H2-q MHC haplotype. Moreover, we demonstrate using immunopeptidomics that clones 28-12-8, 34-1-2, MKD6 and N22 are also suited to isolate MHC class I and class II ligands in this mouse strain. Thus, this work also establishes a first experimental account of the H2-q derived thymus and spleen immunopeptidome in Swiss mice which bears strong resemblance with ligands isolated from the H2-d MHC haplotype of Balb\/C mice.","fileCount":"294","fileSizeKB":"80796755","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Pro 2","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Swiss mice;Immunopeptidome;immunopeptidomics;MHC;antigen presentation;thymus;spleen;DatasetType:Proteomics;DatasetType:Other (Immunopeptidomics)","pi":[{"name":"Asolina Braun","email":"asolina.braun@monash.edu","institution":"Monash University","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD063210","task":"f68a2f8ac8f54ab8842e98aad39e5b39","id":"979"}, {"dataset":"MSV000097692","datasetNum":"97692","title":"Biodiversity library of protein acetylation in bacteria","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745370813000","created":"Apr. 22, 2025, 6:13 PM","description":"Phyloproteomics analysis of acetylation sites across 49 bacterial strains from 48 species; 1~3 biological replicates. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"1372","fileSizeKB":"359634600","spectra":"0","psms":"9626123","peptides":"4312428","variants":"5289182","proteins":"368597","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis 638R (NCBITaxon:862962);Bacteroides thetaiotaomicron VPI-5482 (NCBITaxon:226186);Myxococcus xanthus DZ2 (NCBITaxon:1198133);Bacillus subtilis (NCBITaxon:1423);Rhodopseudomonas palustris (NCBITaxon:1076)","instrument":"Q Exactive Plus","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"phyloproteomics;acetylation;evolutionary conservation;DatasetType:Proteomics","pi":[{"name":"Ernesto S. 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Basal M9 media with no trace metal supplementation served as the metal deplete condition. Basal M9 supplemented with both Zinc and Iron were used for metal replete conditions.","fileCount":"111","fileSizeKB":"5222541","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Providencia stuartii (NCBITaxon:588)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Providencia stuartii;metallophore;minimal media;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"fa7df0c3a8b34a08b52e6eee39f695db","id":"982"}, {"dataset":"MSV000097686","datasetNum":"97686","title":"TIE-UP-SIN: A Novel Method for Enhanced Identification of Protein-Protein Interactions","user":"stemicha","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745336946000","created":"Apr. 22, 2025, 8:49 AM","description":"Proteins are indispensable biomolecules playing vital roles in nearly every aspect of cellular function. They participate in processes such as enzymatic catalysis, signaling pathways, cell responses, pathogenicity as well as structural components of cells. Their structural and functional diversity are the foundation of biological complexity and adaptability. As many proteins function collaboratively through interactions with others, identifying protein-protein interactions (PPIs) is fundamental to understanding the complicated networks and pathways governing cellular activities. Numerous methods exist to study PPIs, including two-hybrid screening, co-immunoprecipitation, mass spectrometry (MS), and computational approaches. While each technique has its strengths, limitations such as high false-positive rates, technical complexity, and low efficiency can hinder precise identification of specific interaction partners. We present TIE-UP-SIN (Targeted Interactome Experiment for Unknown Proteins by Stable Isotope Normalization), a novel simple and straight forward approach for in vivo PPI identification. It combines stable isotope labeling, reversible crosslinking, and affinity purification with highly sensitive mass spectrometry analysis. Stable isotope labeling improves MS data by enhancing quantification accuracy and reproducibility while reducing the number of false discoveries. Rapid, cost-effective reversible crosslinking captures transient interactions for stringent purification, ensuring maximum specificity. The effectiveness of TIE-UP-SIN is showcased by identifying key interaction partners of the essential Bacillus subtilis sigma factor RpoD (SigA) under control and ethanol stress conditions, highlighting its reliability and affordability for in vivo protein-protein interaction studies.","fileCount":"68","fileSizeKB":"41620455","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis (NCBITaxon:1423)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:994 - \\\"15N(1).\\\";UNIMOD:995 - \\\"15N(2).\\\";UNIMOD:996 - \\\"15N(3).\\\";UNIMOD:897 - \\\"SILAC 15N(4).\\\"","keywords":"TIE-UP-SIN;XL-MS;Protein-Protein-Interaction;Formaldehyde cross linking;in vivo;DatasetType:Proteomics","pi":[{"name":"Alexander Reder","email":"redera@uni-greifswald.de","institution":"University Medicine Greifswald","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f9b7997f26144b859c5c4c3a9add3d7f","id":"983"}, {"dataset":"MSV000097684","datasetNum":"97684","title":"GNPS - Untargeted metabolome using LCMS and GCMS","user":"shangshengping","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745307999000","created":"Apr. 22, 2025, 12:46 AM","description":"Detection of the metabolites in the transgenic wheat plants using untargeted metabolics.","fileCount":"57","fileSizeKB":"4208253","spectra":"117043","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565)","instrument":"Waters ACQUITY UPLC I-Class plus\\\/Thermo QE; Agilent 8890-5977B","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"untargeted metabolome LCMS GCMS;DatasetType:Metabolomics","pi":[{"name":"shangshengping","email":"1055625610@qq.com","institution":"caas","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a76e498af0124060a13684428c39f8d4","id":"984"}, {"dataset":"MSV000097681","datasetNum":"97681","title":"GNPS - Targeted amino acid metabolome","user":"shangshengping","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745293139000","created":"Apr. 21, 2025, 8:38 PM","description":"Detection of the amino acid contents in the transgenic wheat plants.","fileCount":"33","fileSizeKB":"28890","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565)","instrument":"AB Sciex Qtrap 5500\\\/Nexera UHPLC LC-30A","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"amino acid;DatasetType:Metabolomics","pi":[{"name":"shangshengping","email":"1055625610@qq.com","institution":"caas","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1c7b1a3bc8004fa1882263665afad1aa","id":"985"}, {"dataset":"MSV000097672","datasetNum":"97672","title":"To Study effect of Bisphenol A mitochondrial proteins through LCMS","user":"Sonal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745227311000","created":"Apr. 21, 2025, 2:21 AM","description":"HepG2 cells were maintained in DMEM media with 10 percent FBS under standard conditions of 37 degree Celsius, 5 percent CO2. Cells were then treated with Bisphenol A at various concentrations (1, 10, 100 micromolar) for 48 hrs. Mitochondrial proteins were isolated following differential centrifugation method (bioprotocol.org\/e1809). Quantification of the mitochondrial proteins was done using the BCA reagent. Isolated proteins (100microgram), trypsin digested were then proceeded for LCMS analysis as detailed earlier (PMID 39216816). Label free quantification is done without any PTMs.\nThe study protocol is approved by the competent authority of the institute (vide number: IN_IEC_SPL_75). The team acknowledges PGIMER Chandigarh for providing financial assistance (IM213_0_28-08-23_1123, Structure activity relationship of Bisphenol A on lysosomal Enzymes- A step towards understanding plastic induced Nonalcoholic fatty liver disease).\n","fileCount":"13","fileSizeKB":"6967101","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bisphenol A;LCMS;HepG2;mitochondrial proteins;DatasetType:Proteomics","pi":[{"name":"Prof DIBYAJYOTI BANERJEE","email":"dibyajyoti5200@yahoo.co.in","institution":"PGIMER, Chandigarh","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d9b5a95ec43a46258e0ed33410aea9fe","id":"986"}, {"dataset":"MSV000097665","datasetNum":"97665","title":"GNPS - Bile Salt Hydrolase Screening with bile acid and amines","user":"Dpattynama1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1745008866000","created":"Apr. 18, 2025, 1:41 PM","description":"120 Bile Salt Hydrolases (BSH) and Penicillin V Acylase (PVA) enzymes from various microbial strains were overexpressed in E. coli and purified using nickel affinity chromatography. Enzyme assays were performed by incubating the purified enzymes with 18 bile acids and 49 amines. Following incubation, the reactions were quenched, and the extracts were dried and reconstituted in 80% methanol containing an internal standard. MS\/MS data acquisition was carried out on Thermo Exploris 240 mass spectrometer in positive ionization mode, with chromatographic separation achieved using a Phenomenex Polar C18 column.","fileCount":"1629","fileSizeKB":"122843950","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"N\\\/A","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"BSH;Bile Salt Hydrolase;DatasetType:Metabolomics","pi":[{"name":"Pieter C. 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Each strain is replicated on the plate (n=6)","fileCount":"10","fileSizeKB":"65191","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Botrytis cinerea (NCBITaxon:40559);Chaetomium globosum (NCBITaxon:38033);Coprinellus disseminatus (NCBITaxon:71703);Fusarium circinatum (NCBITaxon:48490);Fusarium culmorum (NCBITaxon:5516);Fusarium thapsinum (NCBITaxon:120644);Fusarium graminearum (NCBITaxon:5518);Fusarium equiseti (NCBITaxon:61235);Fusarium poae (NCBITaxon:36050);Fusarium nygamai (NCBITaxon:42673);Fusarium lateritium (NCBITaxon:5523);Trichoderma atroviride (NCBITaxon:63577)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Comparative study;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"19e57c19515744f4afc37ad49316c577","id":"990"}, {"dataset":"MSV000097655","datasetNum":"97655","title":"Characterization of the cyclic dipeptide cyclo(His-Pro) in Arabidopsis","user":"lolacamalle","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744914368000","created":"Apr. 17, 2025, 11:26 AM","description":"The iTSA experiment was designed to map putative protein targets of cyclic dipeptides in Arabidopsis. ","fileCount":"12","fileSizeKB":"20532013","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DatasetType:Proteomics;isothermal shift assay, Arabidopsis, seedling, DKPs","pi":[{"name":"Aleksandra Skirycz","email":"skirycza@msu.edu","institution":"Michigan State University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"be47b02f687d4a6891733c356b812f1c","id":"991"}, {"dataset":"MSV000097653","datasetNum":"97653","title":"Exosome from Human Mesenchymal Stem Cell","user":"ratnapuspita","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744900931000","created":"Apr. 17, 2025, 7:42 AM","description":"Exosomes-derived from Mesenchymal Stem Cells Preconditioned with Biliary Atresia Serum","fileCount":"78","fileSizeKB":"2887652","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TSQ Quantum Ultra","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Exosome;Umbilical Cord;DatasetType:Metabolomics","pi":[{"name":"Ratna Puspita","email":"ratnapuspita@upnvj.ac.id","institution":"UPN Veteran Jakarta","country":"Indonesia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"638f64ebec2249c7a468f133c980729d","id":"992"}, {"dataset":"MSV000097644","datasetNum":"97644","title":"UBE3A reinstatement restores behavior and proteome in an Angelman Syndrome mouse model of Imprinting Defects","user":"manueltz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744819744000","created":"Apr. 16, 2025, 9:09 AM","description":"Abstract Background: Angelman Syndrome (AS) is a severe neurodevelopmental disorder with only symptomatic treatment currently available. The primary cause of AS is loss of functional UBE3A protein. This can be caused by deletions in the maternal 15q11-q13 region, maternal AS-imprinting center defects (mICD), paternal uniparental distomy of chromosome 15 (UPD) or mutations within the UBE3A gene. Current mouse models are Ube3a-centric and do not address expression changes of other genes in the 15q11-q13 locus on the pathophysiology of AS. This limits the ability to discern differences in therapeutic responses to current UBE3A-targeting strategies and hampers the identification of novel therapeutics\/co-therapeutics. Methods: Using a mouse line that harbors a mutation affecting the AS-PWS imprinting center (mICD mice), we studied the impact of the mICD or UPD AS subtype on behavior and proteome. Additionally, by using mice overexpressing two copies of Ube3a or antisense oligonucleotide (ASO) targeting Ube3a-ATS, we analyzed the impact of bi-allelic Ube3a activation on behavior and proteome. Results: mICD mice showed a 80% reduction in UBE3A protein, bi-allelic expression of Ube3a-ATS and Mkrn3-Snord115 gene cluster, leading to robust AS behavioral deficits and proteome alterations similar to Ube3aKO mice. Genetic UBE3A overexpression in mICD mice, mimicking therapeutic strategies that effectively activate the biallelic silenced Ube3a gene, resulted in a complete rescue of all behavioral and proteome alterations. Subsequently, treatment with an antisense oligonucleotide (ASO) to directly activate the biallelic silenced Ube3a gene in mICD mice also resulted in efficient reinstatement of UBE3A, 30% higher relative to WT, alongside a partial rescue of behavioral phenotypes. Limitations: Despite using a highly robust AS specific behavioral battery, we did not employ readouts such as neuronal activity, audiogenic seizures and sleep, which might be different in the mICD mice compared to Ube3aKO mice. Conclusions: Taken together, these findings demonstrate that the loss of UBE3A protein is the primary factor underlying AS phenotypes in this mICD\/UPD mouse model of AS, while the biallelic expressed genes in this locus play either a marginal, or yet unidentified role. These findings also corroborate UBE3A reinstatement as an attractive therapeutic strategy for AS individuals carrying a mICD or UPD mutation.","fileCount":"64","fileSizeKB":"245402570","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Angelman Syndrome;imprinting defects;mouse model;antisense oligonucleotide;behavior;proteome;DatasetType:Proteomics","pi":[{"name":"Manuel Tzouros","email":"manuel.tzouros@roche.com","institution":"Hoffmann-La Roche Ltd","country":"Switzerland"},{"name":"Ramanathan Narayanan","email":"ramneuro13@gmail.com","institution":"Hoffmann-La Roche Ltd","country":"Switzerland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"20fb525f0f554b46ab37de2cdb07635b","id":"993"}, {"dataset":"MSV000097643","datasetNum":"97643","title":"Manihotesculenta_cassava_ethanolicextract","user":"Micahfajardo16","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744818990000","created":"Apr. 16, 2025, 8:56 AM","description":"lcms of crude ethanolic extract of Manihot esculenta (cassava)","fileCount":"15","fileSizeKB":"646030","spectra":"5362","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Manihot esculenta (NCBITaxon:3983)","instrument":"6530A Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cassava;Philippines;DatasetType:Metabolomics","pi":[{"name":"Ayah Lim","email":"princessaliyah.lim.pharma@ust.edu.ph","institution":"University of Santo Tomas","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3c90ec04761d498db014fb570fe96244","id":"994"}, {"dataset":"MSV000097641","datasetNum":"97641","title":"GNPS - Endozoicomonas provides corals with steroid hormones during thermal stress","user":"aminlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744805392000","created":"Apr. 16, 2025, 5:09 AM","description":"LC-MS metabolic profiling of Endozoicomonas incubated with testosterone or cholesterol","fileCount":"102","fileSizeKB":"20403908","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Endozoicomonas (NCBITaxon:305899)","instrument":"Orbitrap Fusion Lumos","modification":"No modifications","keywords":"coral symbiosis;Endozoicomonas;steroids;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Shady Amin","email":"SAmin@nyu.edu","institution":"New York University Abu Dhabi","country":"United Arab Emirates"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"191b0ef929c74de28c28f15ae3a652e2","id":"995"}, {"dataset":"MSV000097640","datasetNum":"97640","title":"nudibranchs associated streptomyces metabolome","user":"samarabdelrahman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744790225000","created":"Apr. 16, 2025, 12:57 AM","description":"Streptomyces species are recognized as a major source of a wide variety of natural compounds due to their complex and effective secondary metabolic processes.","fileCount":"13","fileSizeKB":"58076","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces tunisiensis ","instrument":"Qq-TOF ","modification":"not applicable","keywords":"streptomyces isolated from Red Sea, Egypt;DatasetType:Metabolomics","pi":[{"name":"Nicole Lopanik","email":"nicole.lopanik@cancer.org","institution":"American cancer society","country":"Egypt"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"598b0ff5ebff484893356f22e3a26bd6","id":"996"}, {"dataset":"MSV000097637","datasetNum":"97637","title":"GNPS - Computationally unmasking each fatty acyl C=C position in complex lipids by routine LC-MS\/MS lipidomics","user":"Leonida","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744779863000","created":"Apr. 15, 2025, 10:04 PM","description":"Identifying carbon-carbon double bond (C=C) positions in complex lipids is essential for elucidating physiological and pathological processes. Currently, this is impossible in high-throughput analyses of native lipids without specialized instrumentation that compromises ion yields. Here, we demonstrate automated, chain-specific identification of C=C positions in complex lipids based on the retention time derived from routine reverse-phase chromatography tandem mass spectrometry (RPLC-MS\/MS). We introduce LC=CL, a computational solution that utilizes a comprehensive database capturing the elution profile of more than 2,400 complex lipid species identified in RAW264.7 macrophages, including 1,145 newly reported compounds. Using machine learning, LC=CL provides precise and automated C=C position assignments, adaptable to any suitable chromatographic condition. To illustrate the power of LC=CL, we re-evaluated previously published data and discovered new C=C position-dependent specificity of cytosolic phospholipase A2 (cPLA2). Accordingly, C=C position information is now readily accessible for large-scale high-throughput studies with any MS\/MS instrumentation and ion activation method.","fileCount":"3055","fileSizeKB":"254395983","spectra":"4487133","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;ZenoTOF 7600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RPLC;lipidomics;cPLA2;phospholipids;double bond positions;LC=CL;EAD;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Edward A Dennis","email":"edennis@ucsd.edu","institution":"University of California, San Diego","country":"USA"},{"name":"Juergen Hartler","email":"juergen.hartler@uni-graz.at","institution":"University of Graz","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a69526cc26f04f098cb86d7804c686db","id":"997"}, {"dataset":"MSV000097636","datasetNum":"97636","title":"Relationships Between Feed Efficiency and Meat Quality in Feedlot-Finished Nelore Cattle and Associations With the Muscle Tissue Proteome","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744779637000","created":"Apr. 15, 2025, 10:00 PM","description":"Residual feed intake (RFI) as a measure of feed efficiency (FE) is an index that can help producers reduce costs by enabling the selection of more efficient and profitable cattle. However, the meat quality of these animals may be negatively impacted due to the lower subcutaneous fat deposition commonly observed in more efficient (low RFI) cattle. Traits such as tenderness, color, and juiciness may be affected by the reduced fat deposition, influencing consumers' purchasing decisions. Although low RFI cattle exhibit better FE in feedlot systems, few studies have described the molecular mechanisms regulating meat quality traits in these animals. Therefore, the objective of this project is to compare low RFI (efficient) and high RFI (inefficient) cattle finished in feedlots and to evaluate their meat quality in both physicochemical and molecular contexts. Comparing efficient and inefficient feedlot-finished cattle in terms of meat quality traits and identifying associations with the proteome of muscle tissue may contribute to a better understanding of the metabolic pathways that influence economically important characteristics in these animals.","fileCount":"123","fileSizeKB":"30204882","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos indicus x Bos taurus (NCBITaxon:30522)","instrument":"Q-Exactive (Thermo Fisher)","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Residual feed intake (RFI);cattle;Muscle Tissue;DatasetType:Proteomics","pi":[{"name":"Daniela Alvarado Vesga","email":"daniela.alvarado@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Rafaela Cristina Rodrigues","email":"rafaela.c.rodrigues@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Welder Angelo Baldassini","email":"w.baldassini@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"254b3f181c2e420eac11f02170812d60","id":"998"}, {"dataset":"MSV000097631","datasetNum":"97631","title":"Proteomic Analysis of Mus musculus Heart Tissues WT and MDX treated (and not) with human CSPG4 CAR T","user":"raffaellovigano","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744731374000","created":"Apr. 15, 2025, 8:36 AM","description":"Mouse hearts were thawed and weighed into conical bottom glass vials; 2.5 ul of Universal Nuclease (ThermoFisher Scientific, Waltham, MA, USA) and 1 ml of Lysis Solution (ThermoFisher Scientific, Waltham, MA, USA) were added to each sample. Hearth samples were all mechanically homogenized in order to disrupt tissue; homogenized tissues were then centrifuged at 13.000 rpm for 10 minutes. Each supernatant was recovered, and the protein content was evaluated by using the Qubit protein assay performed with Qubit4 fluorimeter (Invitrogen, part of ThermoFisher Scientific, Waltham, MA, USA). 100 ug of proteins for each sample were reduced, alkylated, digested with Tryp\/LysC enzymes and, finally, cleaned up according to the protocol of the EasyPep Mini MS sample preparation kit (ThermoFisher Scientific, Waltham, MA, USA). Each digested sample was dried after clean-up procedure and reconstituted in 0.1% formic acid (Sigma-Aldrich Inc., St. Louis, MO, USA) at a concentration of 1 ug\/ul; samples were then diluted at 0.1 ug\/ul before the nLC hrMS\/MS analyses.\nDigested samples were separated using the Vanquish Neo UHPLC System (ThermoFisher Scientific, San Jose, CA, USA); this chromatographical system was implemented with PepMap Neo trap column (300 um X 5 mm, Thermo Scientific) and EASY Spray PepMap Neo Column (75 um I.D, 5 um, 15 cm; ThermoFisher Scientific, San Jose, CA, USA) for peptide separation, working in trap-and-elute mode (Flush Direction of trap column: forward). The Vanquish autosampler parameters were: temperature set at 7 C, loading volume of 4 ul; loading flow rate of 50 ul\/min. \nFor HPLC, following solvents were used: eluent A, H2O with 0.1% FA and eluent B, 80\/20 ACN\/H2O (%, v\/v) with 0.1% FA. A 90-minute gradient (excluding ca. 1.4 min. of sample pickup and sample loading) was used for separation phase set as follows: 4% to 5% B in 1 min., 5% to 29% B in 54 min., 29% to 50% B in 34 min. and 50 to 70% B in 1 min. The column wash phase was from 90 to 96 min. at 99% B. The flow rate during the gradient was set at 300 nL\/min. \nMass spectra of heart samples were acquired in two technical replicates using a ThermoFisher Scientific Orbitrap Exploris 240 Mass Spectrometer for high-throughput bottom up proteomic profiling. The Orbitrap Exploris 240 mass spectrometer was equipped with the NSI Easy Spray source (Thermo Fisher Scientific, San Jose, CA, USA) working in a positive ion mode (positive ion spray voltage static at 1900V, ion transfer tube temperature 280 C, 35 C). \n","fileCount":"26","fileSizeKB":"26155959","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Duchenne;CAR-T Cells;Cardiac Tissue;DatasetType:Proteomics","pi":[{"name":"Dario Di Silvestre","email":"dario.disilvestre@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Francesca Brambilla","email":"francesca.brambilla@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Raffaello Vigano","email":"raffaello.vigano@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"cc49ca7f5c194e6fb1e1f6bcb0925217","id":"999"}, {"dataset":"MSV000097630","datasetNum":"97630","title":"The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744721388000","created":"Apr. 15, 2025, 5:49 AM","description":"Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1. \nWe identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both, transcriptional regulation of Pantr1 by FOXG1 and association of both partners, build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1\/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1\/Pantr1 regulative network.","fileCount":"61","fileSizeKB":"2307060","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hippocampus, Rett, transcription, neuron, neurite outgrowth;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Tanja Vogel","email":"tanja.vogel@anat.uni-freiburg.de","institution":"Institute for Anatomy and Cell Biology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062981","task":"427407db0da148479cb81df969a8e328","id":"1000"}, {"dataset":"MSV000097629","datasetNum":"97629","title":"The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744719394000","created":"Apr. 15, 2025, 5:16 AM","description":"Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1. \nWe identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both, transcriptional regulation of Pantr1 by FOXG1 and association of both partners, build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1\/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1\/Pantr1 regulative network.\n","fileCount":"71","fileSizeKB":"769401","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hippocampus, Rett, transcription, neuron, neurite outgrowth, FOXG1;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Tanja Vogel","email":"tanja.vogel@anat.uni-freiburg.de","institution":"Institute for Anatomy and Cell Biology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062978","task":"7cd4c439715c4f20a302c1719cde6734","id":"1001"}, {"dataset":"MSV000097625","datasetNum":"97625","title":"REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes","user":"JSha","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744670874000","created":"Apr. 14, 2025, 3:47 PM","description":"In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific genomic loci is largely unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes. This targeted recruitment leads to the production of 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific genomic sites in plant female reproductive tissues. In the absence of GDE1, Pol IV transcription complexes are directed to loci bound by an alternative transcription factor, REM8, highlighting the role of REM transcription factors and GDE1 proteins as positional cues for epigenetic modulation. 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Participants were recruited at Vanderbilt University Medical Center (VUMC). Untargeted LC-MS\/MS acquisition was performed on a Vanquish ultra-high-performance liquid chromatography (UHPLC) system coupled to a QExactive quadrupole orbitrap (Thermo Scientific) mass spectrometer.","fileCount":"238","fileSizeKB":"9974435","spectra":"171049","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"feces;pediatrics;IBD;microbiome;DatasetType:Metabolomics","pi":[{"name":"Pieter C. 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Here we demonstrate the qualitative and quantitative performance gain of the timsTOF HT over the timsTOF Pro 2 mass spectrometer in the analysis of neat (unfractionated) and Proteograph? (PG)-processed plasma across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV<20%) with timsTOF HT compared to timsTOF Pro 2. In an exploratory study of 20 late-stage cancer and 20 control sampleswe observed a ~50% increase in total and statistically significant plasma peptide precursors (q<0.05) with timsTOF HT compared to Pro 2. Our data demonstrated the superior performance of timsTOF HT in identifying and quantifying differences between biologically diverse samples, which can improve disease biomarker discovery in large cohort studies. Moreover, researchers can leverage datasets from this study to optimize their LCMS workflows for plasma protein profiling and biomarker discovery. See the details in a paper, entitled \"timsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery\".","fileCount":"412","fileSizeKB":"1232605180","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF;timsTOF Pro 2","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Plasma;Liquid chromatography;Mass spectrometry;Timstof;Proteomics;Biomarkers;DatasetType:Proteomics","pi":[{"name":"Bruce Wilcox","email":"bruce.wilcox@prognomiq.com","institution":"PrognomiQ Inc.","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047839","task":"94a26a8e53294fb3a843bbb3e47ba88f","id":"1008"}, {"dataset":"MSV000097606","datasetNum":"97606","title":"KOLF2 neuronal and cardiomyocyte differentiation SEC-MS CM4AI","user":"aforget","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744398719000","created":"Apr. 11, 2025, 12:11 PM","description":"This projects aims at mapping protein complexes involved in neuronal and cardiac differentiation using KOLF2 IPSCs using size exclusion chromatography coupled to mass spectrometry (SEC-MS). 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This project covers raw files from data-dependent acquisition (DDA) \u2013 parallel accumulation-serial fragmentation (PASEF) measurements of 12 hydrophilic chromatography (HILIC) fractions of aliquot pool from complete set of 105 samples measured on timsTOF Pro; raw files of 16 individual samples measured in data-independent acquisition (DIA) \u2013 PASEF mode and used for hybrid library generation and for demonstrative quantitative DIA data extraction; Pulsar archive generated in Spectronaut 16.0 from 12 DDA-PASEF measurements of HILIC fractions and from 16 data-independent acquisition DIA-PASEF measurements of individual samples. \nThe 16 DIA-PASEF runs of individual samples used for library generation were analyzed using newest versions of Spectronaut (version 18.5) and DIA-NN (version 1.8.1) software tools in library-based setting using the newly generated library as well as in library-free setting showing library-based method to outperform the use of predicted libraries in the terms of identification numbers. 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Various breeding initiatives have yielded lettuce varieties such as romaine or cos lettuce (Lactuca sativa var. longifolia), characterized by pigmented germplasm and enhanced tolerance to elevated temperatures. Despite its significance, a notable need exists for targeted study investigations into its chemical composition. Thus, this study aims to define the volatile and non-volatile components of the red romaine Thurinus RZ lettuce cultivar using LC-MS and GC-MS analysis. For LC-MS analysis, a C18 column will be accompanied by gradient elution using (A) water and (B) acetonitrile, each containing 0.1% formic acid as the mobile phase. For GC-MS analysis, the HP-5 column will be accompanied by Helium as the carrier gas. The molecules determined will then be ionized, and fragments will be interpreted and annotated using the mass-to-charge (m\/z) ratio, which will further be tabulated.","fileCount":"3","fileSizeKB":"68246","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Red Romaine Lettuce","instrument":"GCMS","modification":"PRIDE:0000398","keywords":"Lettuce, Cultivar;DatasetType:Metabolomics","pi":[{"name":"Cj Clanyns De Jesus","email":"dejesuscjclanyns@gmail.com","institution":"PUP","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7a9987dcc8874c6f9e1246bee18d4727","id":"1012"}, {"dataset":"MSV000097598","datasetNum":"97598","title":"GNPS - Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry.","user":"mateuszwagner","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744317416000","created":"Apr. 10, 2025, 1:36 PM","description":"Metabolomics data of samples acquired from IEX and SEC cofractionation-mass spectrometry.","fileCount":"303","fileSizeKB":"145105968","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive","modification":"Metabolomics dataset","keywords":"dipeptides;CF-MS;protein-metabolite interactions;DatasetType:Metabolomics","pi":[{"name":"Aleksandra Skirycz","email":"skirycza@msu.edu","institution":"Michigan State University","country":"United States of America"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"9662e810cd53404582f88050c2e33ef2","id":"1013"}, {"dataset":"MSV000097597","datasetNum":"97597","title":"Dietary intake of a milk sphingolipid-rich MFGM\/EV concentrate ameliorates age-related metabolic dysfunction | Kidney | Sprenger et al. 2025","user":"ChristerEjsing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744314173000","created":"Apr. 10, 2025, 12:42 PM","description":"Lipidomic analysis of kidney samples from aged rats with and without dietary intervention with an MFGM\/EV-rich concentrate. 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A detailed description of the analysis is provided in the publication with the title: Dietary intake of a milk sphingolipid-rich MFGM\/EV concentrate ameliorates age-related metabolic dysfunction.","fileCount":"77","fileSizeKB":"1767882","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics;High-resolution shotgun lipidomics;MSaLL analysis;DatasetType:Other (Lipidomics)","pi":[{"name":"Christer Ejsing","email":"cse@bmb.sdu.dk","institution":"University of Southern Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4bbf5f0d86574ce789f0471f17f4d2c3","id":"1018"}, {"dataset":"MSV000097590","datasetNum":"97590","title":"Omics Insights into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology","user":"moravcor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744310299000","created":"Apr. 10, 2025, 11:38 AM","description":"Honey bees (Apis mellifera) are essential pollinators in agricultural systems, particularly in fruit-producing agroecosystems such as highbush blueberry and cranberry. However, their health is increasingly compromised by multiple interacting stressors, including pesticide exposure, pathogen infections, and changing nutritional landscapes. To test the hypothesis that distinct agricultural ecosystems, with different combinations of agrochemical exposure, pathogen loads, and floral resources, elicit ecosystem specific, tissue level molecular responses in honey bees, we conducted an integrated multiomics analysis.\nWe combined RNA sequencing, quantitative proteomics, and gut microbiome profiling across three key tissues: head, abdomen, and gut collected from bees in blueberry and cranberry agroecosystems over two field seasons. In parallel, we quantified pesticide residues and pathogen and parasite loads (e.g., Nosema spp., Varroa destructor, and several viruses). Notably, our weighted gene co-expression network analysis (WGCNA) revealed tissue specific coregulated protein modules with ecosystem associated patterns. Bees from blueberry agroecosystems exhibited elevated expression of modules in oxidative phosphorylation, and translation, while those from cranberry agroecosystems showed increased activity in immune pathways and endoplasmic reticulum associated protein processing, indicating potential as robust markers for ecosystem induced physiological adaptation. To further explore the molecular mechanisms underlying different ecosystems, we also conducted the integrative analysis of proteomics, transcriptomics and gut microbiome metagenomics. Gut microbiota composition also differed significantly, with key genera (e.g., Gilliamella, Snodgrassella, Bartonella) correlating with host metabolic and immune modules.\nThese findings underscore the complex, environment-dependent impacts of agroecosystem conditions on bee health. Our study provides a systems level understanding of how combined pesticide, pathogen, and parasitic stressors, mediated by diet and microbiome, shape molecular phenotypes in honey bees, informing strategies for pollinator protection in managed landscapes.","fileCount":"13221","fileSizeKB":"905991693","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Apis Mellifera;co-expression networks;microbiome;proteomics;transcriptomics;DatasetType:Proteomics","pi":[{"name":"Leonard J. 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Using proteomic data from 300 patient samples, we identified differentially abundant proteins (DAPs) such as SNCG, S100A1, VWA2, AGR2, CTH, and SPINK1 and biomarker panels to stratify the tissues. Enrichment of biological processes profiled histotypes and involvement of DAPs. Survival analysis identified candidate biomarkers predicting overall- and disease-specific survival with histotype-specificity. Of these, GLYR1, RPL12, GDPGP1, and POLR2M were associated with favorable outcomes, while SDF4, PPP3CC, EIF2AK2, and STX6 were linked to unfavorable outcomes. Collectively, these findings provide attributes spefici for histotypes for known and novel EOC biomarkers that may serve as new clinical tools for EOC treatment decisions and diagnosis.","fileCount":"12393","fileSizeKB":"1424679050","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF HT","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"epithelial ovarian cancer;histotype;ovarian borderline;ovarian benign;proteomics;disease stratification;differential abundance analysis;biomarkers;biomarker panels;enrichment analysis;survival analysis;fresh-frozen tissue;novel biomarkers;biomarker discovery;DatasetType:Proteomics","pi":[{"name":"Khalil Helou","email":"khalil.helou@oncology.gu.se","institution":"University of Gothenburg, Institute of Clinical Sciences, Department of Oncology","country":"Sweden"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD062815","task":"d49017f42a1e482299a6d9d0f9557b15","id":"1020"}, {"dataset":"MSV000097587","datasetNum":"97587","title":"Rapid Multi-Omics for Bacteria Identifications using Flow Injection-Ion Mobility-Mass Spectrometry","user":"kmhines5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744304492000","created":"Apr. 10, 2025, 10:01 AM","description":"The implementation of mass spectrometry (MS) in clinical microbiology has made significant improvement in the turnaround time from positive culture to identification, but current protein-based approaches can struggle with species level identifications because of the high degree of homology within a genus. However, other MS-based strategies for bacteria identifications that are based on lipids and small molecules have shown promise towards species-level identifications and detection of specific phenotypes, including those related to antibiotic resistance. While the concept of using multi-omics in diagnostic situations is not new, the issues of time and efficiency remain major hurdles to implementing multi-omics into situations that demand rapid and high-throughput analyses like clinical microbiology. We are addressing this gap by leveraging rapid, gas-phase ion mobility (IM) separations coupled to MS to simultaneously detect the lipids and metabolites in bacterial pathogens. Using flow-injection (FI) rather than liquid chromatography (LC), we instead rely more directly on the structural separations of the IM dimension to resolve features from different biochemical classes and aid in identifications. A head-to-head comparison demonstrates that the FI-IM-MS multi-omic strategy performs similarly to LC-IM-MS in its ability to distinguish 24 strains of the high-concern ESKAPE pathogens, while shortening overall analysis time from 17 min to 1 min per injection. We demonstrate that the IM dimension has excellent stability and reproducibility, which enables extracted IM peak areas to be used in lieu of chromatographic peak areas. Although the total number of features detected in the FI-IM-MS dataset is lower than the HILIC-IM-MS dataset, the overlap between the two datasets includes the features that are most heavily weighted in the PCA separation of the 24 strains. These results showcase the capabilities of mobility-enabled rapid multi-omics and open the possibility to detect subtle strain-level differences and resistance phenotypes in bacteria pathogens by including additional classes of biomolecules.","fileCount":"12162","fileSizeKB":"215196278","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Synapt XS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ion mobility;lipidomics;metabolomics;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Kelly M. 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Dataset was used for MassCube software benchmarking.","fileCount":"1272","fileSizeKB":"59381054","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Alzheimer's disease;DatasetType:Metabolomics","pi":[{"name":"Oliver Fiehn","email":"ofiehn@ucdavis.edu","institution":"University of California, Davis","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"100416b91eb24735a53eb2eecf2fd3d6","id":"1024"}, {"dataset":"MSV000097580","datasetNum":"97580","title":"Proteomic profiling of optogenetically activated mouse S1 microglia","user":"minheeyi426","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744252200000","created":"Apr. 9, 2025, 7:30 PM","description":"Proteomic profiling of optogenetically activated mouse S1 microglia","fileCount":"33","fileSizeKB":"41842553","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Proteomics;Optogenetics;S1 microglia;Pain;Neuroinflammation;DatasetType:Proteomics","pi":[{"name":"Min-Hee Yi","email":"minheeyi426@jnu.ac.kr","institution":"Department of Microbiology and Immunology, Chonnam National University Medical School","country":"Republic of Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062790","task":"ffbed534694d401a9b40f524384a5ff6","id":"1025"}, {"dataset":"MSV000097577","datasetNum":"97577","title":"De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting in pancreatic cancer","user":"SantanaCodina","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1744222059000","created":"Apr. 9, 2025, 11:07 AM","description":"Oncogenic KRAS induces metabolic rewiring in pancreatic adenocarcinoma (PDAC) characterized, in part, by dependency on de novo pyrimidine biosynthesis. Pharmacologic inhibition of dihydroorotate dehydrogenase (DHODH), an enzyme in the de novo pyrimidine synthesis pathway, delays pancreatic tumor growth; however, limited monotherapy efficacy suggests that compensatory pathways may drive resistance. Here, we use an integrated metabolomic, proteomic and in vitro and in vivo DHODH inhibitor-anchored genetic screening approach to identify compensatory pathways to DHODH inhibition (DHODHi) and targets for combination therapy strategies. We demonstrate that DHODHi alters the apoptotic regulatory proteome thereby enhancing sensitivity to inhibitors of the anti-apoptotic BCL2L1 (BCL-XL) protein. Co-targeting DHODH and BCL-XL synergistically induces apoptosis in PDAC cells and patient-derived organoids. The combination of DHODH inhibition with Brequinar and BCL-XL degradation by DT2216, a proteolysis targeting chimera (PROTAC), significantly inhibits PDAC tumor growth. These data define mechanisms of adaptation to DHODHi and support combination therapy targeting BCL-XL in PDAC.","fileCount":"38","fileSizeKB":"35715","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QTRAP 5500","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PDAC;DHODH inhibition;DatasetType:Metabolomics","pi":[{"name":"Joseph D. 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Iron deficiency affects >1 billion people and decreased iron availability impairs immunity. Nevertheless, how iron deprivation impacts immune cell function remains poorly characterised. We interrogated how physiologically low iron availability affected CD8+ T cell metabolism and function, using multi-omic and metabolic labelling approaches. Iron limitation did not substantially alter initial post-activation increases in cell size and CD25 upregulation. However, low iron profoundly stalled proliferation (without influencing cell viability), altered histone methylation status, gene expression, and disrupted mitochondrial membrane potential. Glucose and glutamine metabolism in the TCA cycle was limited and partially reversed to a reductive trajectory. Previous studies identified mitochondria-derived aspartate as crucial for proliferation of transformed cells. Surprisingly and despite aberrant TCA cycling, aspartate was increased in stalled iron deficient CD8+ T-cells but was not utilised for nucleotide synthesis, likely due to trapping within depolarised mitochondria. Exogenous aspartate markedly rescued expansion and some functions of severely iron-deficient CD8+ T-cells. Overall, iron scarcity creates a mitochondrial-located metabolic bottleneck, which is bypassed by supplying inhibited biochemical processes with aspartate. These findings reveal molecular consequences of iron deficiency for CD8+ T cell function, providing mechanistic insight into the basis for immune impairment during iron deficiency.\n","fileCount":"18","fileSizeKB":"330145","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Agilent GCMS 7890B 5977A","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Iron, T Cell, metabolism, 13C-Glucose;DatasetType:Metabolomics","pi":[{"name":"Alexander Drakesmith","email":"Alexander.drakesmith@ndm.ox.ac.uk","institution":"University of Oxford","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ec2369d9e92b40acabce8f292df2cc2c","id":"1045"}, {"dataset":"MSV000097524","datasetNum":"97524","title":"O-mannose glycosylations influence E-cadherin protein interactions","user":"shaoshuai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743759643000","created":"Apr. 4, 2025, 2:40 AM","description":"Cadherins are plasma membrane adhesion molecules that play critical roles in maintaining cell-cell adhesion and modulating cell signaling during development. Their functions are mediated by extracellular cadherin (EC) domains, which facilitate adhesive interactions and enable the formation of cis- and trans assemblies at adherens junctions and desmosomes. The EC domains adopt a characteristic immunoglobulin-like fold composed of seven beta-strands (A-G), and are further modified by N-linked and O-linked glycosylation, including alpha-linked mannose monosaccharides (O-Man) on conserved serine and threonine residues of B- and G-strands. EC domain O-Man glycosylation is catalyzed by TMTC enzymes: TMTC3 catalyzes modifications to the G-strands, whereas TMTC2 targets the B-strands. Given the site-specific deposition of O-Man glycans by dedicated enzymes and the central role of EC domains in cadherins functions, we hypothesized that these PTMs may fine-tune cellular adhesion strength and otherwise contribute to diverse physical interactions that involve cadherins. To test these hypotheses, we assayed for changes in protein-protein interactions formed with epithelial (E)-cadherin in model cells where O-Man PTMs were genetically ablated. Herein, we report O-Man-dependent, E-cadherin (CDH1) protein interactions, revealed by affinity proteomics; we orthogonally validate an altered association between CDH1 and CDH3 (P-cadherin), and demonstrate loss-of-function consequences of O-Man ablation on specific positions, highlighting the importance of these PTMs in cadherin-mediated adhesion. These findings provide new insights into how post-translational modifications regulate cadherin-dependent adhesion complexes.","fileCount":"218","fileSizeKB":"130691895","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1004 - \\\"Monomethylated Arg13C(6) 15N(4).\\\";UNIMOD:836 - \\\"Acetyl_13C(6) 15N(2) Silac label.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\";MOD:00110 - \\\"A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide.\\\"","keywords":"E-cadherin interactome;IP screening;O-Man glycosyaltion;DatasetType:Proteomics","pi":[{"name":"John LaCava","email":"jlacava@rockefeller.edu","institution":"Laboratory of Cellular and Structural Biology, The Rockefeller University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD062594","task":"48d2cc14e15144e1a43c0163139d88e2","id":"1046"}, {"dataset":"MSV000097523","datasetNum":"97523","title":"Improving cellular fitness of human stem cell-derived islets under hypoxia","user":"sbrielle","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743749972000","created":"Apr. 3, 2025, 11:59 PM","description":"Stem cell-derived islet cell therapy can effectively treat type 1 diabetes, but its efficacy is hindered by low oxygen supply post-transplantation, particularly in subcutaneous spaces and encapsulation devices, leading to cell dysfunction. The response to hypoxia and effective strategies to alleviate its detrimental effects remain poorly understood. Here, we show that beta cells within stem cell-derived islets gradually undergo a decline in cell identity and metabolic function in hypoxia. This is linked to reduced expression of immediate early genes (EGR1, FOS, and JUN), which downregulates key beta cell transcription factors. We further identified genes important for maintaining beta cell fitness in hypoxia, with EDN3 as a potent player. Elevated EDN3 expression preserves beta cell identity and function in hypoxia by modulating genes involved in beta cell maturation, glucose sensing and regulation. These insights improve the understanding of hypoxias impact on stem cell-derived islets, offering a potential intervention for clinical applications.","fileCount":"166","fileSizeKB":"75300408","spectra":"945180","psms":"166035","peptides":"10889","variants":"17806","proteins":"4647","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"hypoxia beta cells pancreas sc-islets;DatasetType:Proteomics","pi":[{"name":"Doug Melton","email":"dmelton@harvard.edu","institution":"Harvard University","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD062589","task":"b7894f5bb07847a093617a07c7026d35","id":"1047"}, {"dataset":"MSV000097501","datasetNum":"97501","title":"Replication stress impairs CENP-A nucleosome stability in S phase","user":"leeal0011","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743655745000","created":"Apr. 2, 2025, 9:49 PM","description":"MS .raw files for manuscript, \"DNA Replication Stress Impairs Proper Centromere Inheritance.\"","fileCount":"188","fileSizeKB":"100712613","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Orbitrap Exploris 240","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:329 - \\\"Monomethylated arginine.\\\"","keywords":"TurboID;Proximity labeling;Bottom-Up Proteomics;Histones;Replication stress;DatasetType:Proteomics","pi":[{"name":"Daniel R Foltz","email":"dfoltz@northwestern.edu","institution":"Northwestern University","country":"United States"},{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ba99ecfa221143aeac1e1f469028e100","id":"1048"}, {"dataset":"MSV000097500","datasetNum":"97500","title":"Worker honey bee heat stress proteomics","user":"amcafee","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743628927000","created":"Apr. 2, 2025, 2:22 PM","description":"Worker honey bees were held in cages and subject to chronic heat stress or control conditions (see publication for experimental details). At the end of the experiment, hemolymph was collected by severing one antenna and retrieving the exuding liquid. Final sample sizes are 10 per cage and 30 per group.","fileCount":"5","fileSizeKB":"214894902","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"timsTOF Pro 2","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"Hemolymph;Heat stress;DIA;DatasetType:Proteomics","pi":[{"name":"Leonard Foster","email":"foster@msl.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD062537","task":"e8df3940a67f4310a91163367eaaeff1","id":"1049"}, {"dataset":"MSV000097497","datasetNum":"97497","title":"Proteomic analysis of bone marrow CD138+ cells to identify proteins associated with the response of multiple myeloma patients to commonly used therapeutic regimens.","user":"mmakrid","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743610643000","created":"Apr. 2, 2025, 9:17 AM","description":"Multiple Myeloma (MM) remains incurable; gaps in our understanding of MM molecular pathogenesis and drugs resistance mechanisms are involved in the failure of therapies to eradicate the disease. This study aims to identify proteins significantly impacting MM patients' response to commonly used therapeutic regimens. Bone marrow CD138+ selected plasma cells were isolated from patients that had achieved Response (Responders, R) and those who were Non-Responders (NR) to their primary MM therapy. We used LC-MS\/MS to investigate the proteomic profile of MM samples, followed by statistical and bioinformatics analysis. Collectively, proteomics data obtained from R and NR to MM therapy displayed significant changes in the immune system and protein synthesis regulation, supporting their potential role in progression and therapeutic response of MM.","fileCount":"97","fileSizeKB":"89349481","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Biomarkers, Cancer, Multiple Myeloma, Proteomics, Therapy;DatasetType:Proteomics","pi":[{"name":"Jerome Zoidakis","email":"izoidakis@bioacademy.gr","institution":"BRFAA","country":"Greece"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062530","task":"a64b4f88e6a84e9ebc7cedd0c16f6795","id":"1050"}, {"dataset":"MSV000097485","datasetNum":"97485","title":"GNPS - Germ-free and mono colonized mice","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743545489000","created":"Apr. 1, 2025, 3:11 PM","description":"Several organs from mice (germ-free vs mono colonized) run on micro flow Exploris. Reversed-phase, ESI positive, EVO C18 column (1.7 um particle size, 1 mm x 150 mm Phenomenex, Kinetex).\n","fileCount":"287","fileSizeKB":"26328716","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mice, germ-free, mono colonized mice, bacteria, untargeted metabolomics,;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4deef586c787489c91fe8c91dc26a98f","id":"1051"}, {"dataset":"MSV000097484","datasetNum":"97484","title":"GNPS - Hepatocellular Metabolic Profile: Understanding Post-Thawing Metabolic Shift in Primary Hepatocytes in vitro","user":"spalmisano","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743541671000","created":"Apr. 1, 2025, 2:07 PM","description":"Positive and negative-mode metabolomics data from a time-course experiment for unexposed cells during a 24-hour time course, investigating the changes in metabolism of primary human hepatocytes in vitro post-thawing.\r\n","fileCount":"163","fileSizeKB":"66643940","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Primary human hepatocytes (PHHs);liver metabolism;LC-MS\/MS metabolomics;metabolic profiling;in vitro liver models;post-thawing hepatocyte stability;DatasetType:Metabolomics","pi":[{"name":"Emilio S. Rivera","email":"esrivera@lanl.gov","institution":"Los Alamos National Laboratory","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"16821e08ecc94d91b75703eecf95738b","id":"1052"}, {"dataset":"MSV000097480","datasetNum":"97480","title":"Metabolomics data from Inverse stable isotope probing\u2013metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community","user":"robesjm25","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743538095000","created":"Apr. 1, 2025, 1:08 PM","description":"Raw LC-MS\/MS data of methane-oxidizing community from Lake Washington sediment enrichment (collected from 47.63 N, 122.25 W on July 15, 2013) grown in low-iron nitrate mineral salts (0.1uM FeCl3). Included are .mzml and .raw files for the enrichment grown in 12C-methane, 13C-methane, and 13C-methane plus 12C-DHB.","fileCount":"7","fileSizeKB":"610130","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Methane oxidizing bacterial community","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Methane-oxidizing bacterial community;Siderophore;Inverse Stable Isotopic Labeling;Metabolomics-SIP;DatasetType:Metabolomics","pi":[{"name":"Aaron Puri","email":"a.puri@utah.edu","institution":"University of Utah","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3bb2be78d2c540bfa175324aa9fed6b2","id":"1053"}, {"dataset":"MSV000097479","datasetNum":"97479","title":"GNPS unttargeted metabolomic analysis of: Coffea canephora methanolic extract from Cordoba, Veracruz, Mexico","user":"shaulacast","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743534089000","created":"Apr. 1, 2025, 12:01 PM","description":"We analyzed unroasted coffee beans extract of the species Coffea canephora (San Felipe coffee company, Mexico) grown and harvested in Cordoba, Veracruz, Mexico. The unroasted coffee beans were ground using a burr mill. Ground coffee was added to absolute methanol at 1:10 ratio. The mixture was subjected to magnetic stirring at 1000 rpm for 1 h at room temperature. Following this, the mixture was filtered with a 0.20 uM syringe filter and concentrated in a vacuum evaporator Rocket Synergy (Genevac, UK) at 50 celsius and <30 mBar for 2 h. The resulting solid was stored protected from light at -20 celsius for further UPLC-MS\/MS analysis.\n\nMass spectrometry was conducted using a QTRAP 6500+ system (Sciex, Canada) equipped with an ESI Turbo ion spray interface operating in both positive and negative ion modes. The source temperature was 550 celsius, and the ion spray voltage was 5500 V (positive mode) or -4500 V (negative mode). CUR, GSI, and GSII were maintained at 25, 50, and 60 psi, respectively. Collision-induced dissociation was set to high, and metabolite detection was performed in MRM mode using nitrogen as the collision gas. Data acquisition was managed with Analyst 1.6.3 software (Sciex, Canada), monitoring MRM ion pairs according to the metabolites' elution times.\n","fileCount":"13","fileSizeKB":"36488","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Coffea canephora (NCBITaxon:49390)","instrument":"QTRAP 6500+","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coffea canephora extract Mexico;DatasetType:Metabolomics","pi":[{"name":"Aldo Moreno Ulloa","email":"amoreno@cicese.mx","institution":"Centro de Investigacion Cientifica y de Educacion Superior de Ensenada ","country":"Mexico"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f3efb5e8d8224c599c11d0f627da5484","id":"1054"}, {"dataset":"MSV000097478","datasetNum":"97478","title":"Effects of Bortezomib and hydroxychloroquine Treatment on Protein Dynamics in Multiple Myeloma using label free","user":"fahlmanlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743533990000","created":"Apr. 1, 2025, 11:59 AM","description":"Label free proteomics for multiple myeloma samples treated with four conditions; Bortezomib, Hydroxychloroquine, combination of the two drugs and control treated with DMSO. the labeled tubes as follow :\nTreatment\tTube Number\n\nBortezomib\t1\n\t2\n\t3\n\t4\n\nHydroxyquinone\t7\n\t8\n\t9\n\t12\n\nCombination\t13\n\t16\n\t17\n\t18\n\nControl\t19\n\t20\n\t23\n\t24\n\n","fileCount":"14","fileSizeKB":"42098963","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"multiple myeloma, label free, hydroxychloroquine, Bortezomib, RPMI;DatasetType:Proteomics","pi":[{"name":"Richard Fahlman","email":"rfahlman@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8ea81c16fe3f4362bff4189ad3fcf60a","id":"1055"}, {"dataset":"MSV000097475","datasetNum":"97475","title":"GNPS - Alzheimer's Mouse Brain Tissue HILIC Metabolomics","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743527342000","created":"Apr. 1, 2025, 10:09 AM","description":"Healthy and Alzheimer's diseased mice were treated with\/without Bacteroides fragilis gut bacteria. Frontal cortex and hippocampus brain tissue were analyzed for metabolites using untargeted LC-MS.","fileCount":"205","fileSizeKB":"3089059","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088);Bacteroides fragilis (NCBITaxon:817)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bacteroides;fragilis;alzheimers;gut;brain;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"218f482238104d9a9078f2f7e1f73042","id":"1056"}, {"dataset":"MSV000097474","datasetNum":"97474","title":"H3.1K27M-induced misregulation of the TSK\/TONSL-H3.1 pathway causes genomic instability","user":"YJacob","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743521150000","created":"Apr. 1, 2025, 8:25 AM","description":"The oncomutation lysine 27-to-methionine in histone H3 (H3K27M) is frequently identified in tumors of patients with diffuse midline glioma-H3K27 altered (DMG-H3K27a). H3K27M inhibits the deposition of the histone mark H3K27me3, which affects the maintenance of transcriptional programs and cell identity. Cells expressing H3K27M are also characterized by defects in genome integrity, but the mechanisms linking expression of the oncohistone to DNA damage remain mostly unknown. In this study, we demonstrate that expression of H3.1K27M in the model plant Arabidopsis thaliana interferes with post-replicative chromatin maturation mediated by the H3.1K27 methyltransferases ATXR5 and ATXR6. As a result, H3.1 variants on nascent chromatin remain unmethylated at K27 (H3.1K27me0), leading to ectopic activity of TONSOKU (TSK), which induces DNA damage and genomic alterations. Elimination of TSK activity suppresses the genome stability defects associated with H3.1K27M expression, while inactivation of specific DNA repair pathways prevents survival of H3.1K27M-expressing plants. Overall, our results suggest that H3.1K27M disrupts the chromatin-based mechanisms regulating TSK\/TONSL activity, which causes genomic instability and may contribute to the etiology of DMG-H3K27a.","fileCount":"14","fileSizeKB":"16310080","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:58 - \\\"Propionate labeling reagent light form (N-term & K).\\\"","keywords":"Genome stability;H3K27M;replication stress;chromatin;DNA repair;DatasetType:Proteomics","pi":[{"name":"Yannik Jacob","email":"yannick.jacob@yale.edu","institution":"Yale University","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062467","task":"e44e092742d44fdf88b0da7fa384f0de","id":"1057"}, {"dataset":"MSV000097473","datasetNum":"97473","title":"GNPS - Metabolic adaptations of micrometastases alter EV production to generate invasive microenvironments","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743518860000","created":"Apr. 1, 2025, 7:47 AM","description":"Altered cellular metabolism has been associated with acquisition of invasive\r\nphenotypes during metastasis. To study this, we combined a genetically engineered\r\nmouse model of mammary carcinoma with syngeneic transplantation and primary\r\ntumour resection to generate isogenic cells from primary tumours and their\r\ncorresponding lung micrometastases. Metabolic analyses indicated that\r\nmicrometastatic cells increase proline production at the expense of glutathione\r\nsynthesis leading to a reduction in total glutathione levels. Micrometastatic cells also\r\nhave altered sphingomyelin metabolism leading to increased intracellular levels of\r\nspecific ceramides. The combination of these two metabolic adaptations alters small\r\nextracellular vesicle (sEV) production to drive generation of an invasive\r\nmicroenvironment. Indeed, micrometastatic cells shut-down Rab27-dependent\r\nproduction of sEVs and, instead, switch-on neutral sphingomyelinase-2 (nSM2)-\r\ndependent sEV release. sEVs released in a nSM2-dependent manner from\r\nmicrometastatic cells, in turn, influence the ability of fibroblasts to deposit extracellular\r\nmatrix which promotes cancer cell invasiveness. These data provide evidence that\r\nmetabolic rewiring drives invasive processes in metastasis by influencing sEV release","fileCount":"753","fileSizeKB":"84076941","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolism;extracellular vesicles (EVs);invasiveness;micrometastases;mammary cancer;DatasetType:Metabolomics","pi":[{"name":"Cassie Clarke","email":"c.clarke@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Institute","country":"United Kingdom"},{"name":"David Sumpton","email":"d.sumpton@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Jim Norman","email":"j.norman@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Institute","country":"United Kingdom"},{"name":"Michalis Gounis","email":"michail.gounis@utu.fi","institution":"Turku Centre for Biotechnology","country":"Finland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0078c09d79764a7499516344ae75954d","id":"1058"}, {"dataset":"MSV000097470","datasetNum":"97470","title":"CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase during Spermatogenesis and T Cell Activation","user":"Lukascermak","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743512997000","created":"Apr. 1, 2025, 6:09 AM","description":"HEK293T cells were co-transfected with StrepII-FLAG-tagged DCAF12 and HA-tagged CUL4A, grown for 48 h, harvested, and lysed as described above. In the first step, Strep-TactinXT Superflow resin (IBA Lifesciences, Gottingen, Germany) was used to purify proteins associated with StrepII-FLAG-tagged subsrtrate receptors. In the second step, eluates from the previous step were used for immunoprecipitation of HA-CUL1\/4A-associated proteins. Eluates from both steps were analyzed by LC-MS\/MS at the Proteomics facility of Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University (BIOCEV) in Vestec, Czech Republic. Further details are provided in Supplementary methods.","fileCount":"25","fileSizeKB":"24803817","spectra":"576243","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ubiquitin, proteasome;DatasetType:Proteomics","pi":[{"name":"Lukas Cermak","email":"lukas.cermak@img.cas.cz","institution":"Institute of Molecular Genetics of the ASCR, v. v. i.","country":"Czech republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD067954","task":"bfce591fe8cb4c19ba57989060407146","id":"1059"}, {"dataset":"MSV000097469","datasetNum":"97469","title":"CRL4-DCAF12 regulation of MCMBP ensures optimal licensing of DNA replication","user":"Lukascermak","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743510387000","created":"Apr. 1, 2025, 5:26 AM","description":"HEK293T cells were transfected with StrepII-FLAG-tagged DCAF12 and, where indicated, treated with the proteasome inhibitor MG-132 for 6 hours. Following treatment, cells were harvested and lysed. Protein complexes associated with StrepII-FLAG-tagged DCAF12 were purified using Strep-TactinXT Superflow resin (IBA Lifesciences, Gottingen, Germany) and eluted with desthiobiotin. Eluted samples were subjected to liquid chromatography-tandem mass spectrometry (LC-MS\/MS) analysis at the Proteomics Facility of the Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University (BIOCEV) in Vestec, Czech Republic.","fileCount":"4","fileSizeKB":"4238694","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ubiqutin, protein degradation, replication;DatasetType:Proteomics","pi":[{"name":"Lukas Cermak","email":"lukas.cermak@img.cas.cz","institution":"Institute of Molecular Genetics of the ASCR, v. v. i.","country":"Czech republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055947","task":"82140b3bc5854ba7b1c7a126b1429b51","id":"1060"}, {"dataset":"MSV000097468","datasetNum":"97468","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Chlorpyrifos using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743508445000","created":"Apr. 1, 2025, 4:54 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Chlorpyrifos using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Chlorpyrifos (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Chlorpyrifos is Human serum albumin treated with Chlorpyrifos and HSA_Chlorpyrifos _2NA is Human serum Albumin treated with Chlorpyrifos and then substrate (2NA) was added.","fileCount":"8","fileSizeKB":"6669246","spectra":"55410","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Organophosphorous;Pseudoesterase;Albumin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"75d894fb42004776a64a9648c373c9d3","id":"1061"}, {"dataset":"MSV000097466","datasetNum":"97466","title":"GNPS - Stable-isotope-assisted metabolomics: Deoxynivalenol-stress-related Tyrosine and Phenylalanine metabolism in wheat","user":"tomas_rypar","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743506419000","created":"Apr. 1, 2025, 4:20 AM","description":"Part of xx paper will be finished and changed after submission","fileCount":"192","fileSizeKB":"2789275","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"aromatic amino acids, polyphenols, specialized metabolites, Fusarium head blight (FHB), mycotoxins, plant defense, untargeted metabolomics;DatasetType:Metabolomics","pi":[{"name":"Rainer Schuhmacher","email":"rainer.schuhmacher@boku.ac.at","institution":"University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics","country":"Austria"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"2f93162140614f69a3d05df48a1f3081","id":"1062"}, {"dataset":"MSV000097465","datasetNum":"97465","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Rivastigmine using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743501460000","created":"Apr. 1, 2025, 2:57 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Rivastigmine using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Rivastigmine (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Rivastigmine is Human serum albumin treated with Rivastigmine and HSA_Rivastigmine _2NA is Human serum Albumin treated with Rivastigmine and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"4961148","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Albumin;Organocarbamate;Pseudoesterase;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"489ddb17609c4f76bac97aa5a6a95949","id":"1063"}, {"dataset":"MSV000097464","datasetNum":"97464","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Pyridostigmine_Bromide using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743499849000","created":"Apr. 1, 2025, 2:30 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Pyridostigmine_Bromide using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Pyridostigmine_Bromide (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_ Pyridostigmine_Bromide is Human serum albumin treated with Pyridostigmine_Bromide and HSA_ Pyridostigmine_Bromide _2NA is Human serum Albumin treated with Pyridostigmine_Bromide and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"4510079","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Pseuodesterase;Organocarbamate;Albumin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cd0a8e4ea7b74c7ea75cb31b4a14741f","id":"1064"}, {"dataset":"MSV000097463","datasetNum":"97463","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Physostigmine using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743498662000","created":"Apr. 1, 2025, 2:11 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Physostigmine using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Physostigmine (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Physostigmine is Human serum albumin treated with Physostigmine and HSA_Physostigmine _2NA is Human serum Albumin treated with Physostigmine and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"6888238","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Organocarbamate;Albumin;Pseudoesterase;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"316dba2a1c2f4e19afe38836ee82a317","id":"1065"}, {"dataset":"MSV000097462","datasetNum":"97462","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Paraoxon using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743496193000","created":"Apr. 1, 2025, 1:29 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Paraoxon using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Paraoxon (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Paraoxon is Human serum albumin treated with Paraoxon and HSA_Paraoxon _2NA is Human serum Albumin treated with Paraoxon and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"6298120","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Organophosphorous;Albumin;Pseudoesterase;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"33ebb76657b04ca6975f4f82fb7f354b","id":"1066"}, {"dataset":"MSV000097461","datasetNum":"97461","title":"Ferroptotic Cell Death upon BCL2 Inhibition","user":"akoulman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743495994000","created":"Apr. 1, 2025, 1:26 AM","description":"B-cell acute lymphoblastic leukemia (B-ALL) is a leading cause of death in childhood and outcomes in adults remain dismal. There is therefore an urgent clinical need for therapies that target the highest risk cases. Mutations in the histone acetyltransferase CREBBP confer high-risk and increased chemoresistance in ALL. Performing a targeted drug-screen in isogenic human cell lines, we identified a number of small molecules that specifically targeted CREBBP-mutated B-ALL, with the most potent the BCL2-inhibitor Venetoclax. Of note, this acted through a non-canonical mechanism resulting in ferroptotic rather than apoptotic cell death. CREBBP-mutated cell lines showed differences in cell-cycle, metabolism, lipid composition and response to oxidative stress, predisposing them to \nferroptosis, which were further dysregulated upon acquisition of Venetoclax resistance. Lastly, small-molecule inhibition of CREBBP pharmacocopies CREBBP-mutation, sensitizing B-ALL cells, regardless of genotype, to Venetoclax-induced ferroptosis in-vitro and in-vivo, providing a potential novel drug combination for broader clinical translation in B-ALL.","fileCount":"406","fileSizeKB":"17339134","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"B-cell acute lymphoblastic leukemia (B-ALL);lipidomics, ferroptosis;DatasetType:Metabolomics","pi":[{"name":"Albert Koulman","email":"ak675@cam.ac.uk","institution":"University of Cambridge","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6746d9c3cb2d4c4e957cde41bd03aa08","id":"1067"}, {"dataset":"MSV000097460","datasetNum":"97460","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Neostigmine using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743494809000","created":"Apr. 1, 2025, 1:06 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Neostigmine using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Neostigmine (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_NMS is Human serum albumin treated with Neostigmine and HSA_NMS _2NA is Human serum Albumin treated with Neostigmine and then substrate (2NA) was added.","fileCount":"9","fileSizeKB":"7326754","spectra":"107233","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Albumin;Pseudoesterase;Organocarbamate;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e00f0aa3dada4042a7de292124124a71","id":"1068"}, {"dataset":"MSV000097459","datasetNum":"97459","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Malaoxon using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743493340000","created":"Apr. 1, 2025, 12:42 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Malaoxon using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Malaoxon (in Acetonitrile)(working concentration of 5 microMolar for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Malaoxon is Human serum albumin treated with Malaoxon and HSA_Malaoxon _2NA is Human serum Albumin treated with Malaoxon and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"5248179","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Albumin;pesticide;Pseudoesterase;Organophosphorous;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"44d73b05a7a14191a89fe241b14384b9","id":"1069"}, {"dataset":"MSV000097457","datasetNum":"97457","title":"Optimization of 13C stable isotope labeling for the study of tricarboxylic cycle intermediates in mouse models","user":"jarrodroach","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1743484225000","created":"Mar. 31, 2025, 10:10 PM","description":"Data for \"Optimization of 13C stable isotope labeling for the study of tricarboxylic cycle intermediates in infected mouse models\"","fileCount":"1750","fileSizeKB":"238607122","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"C13;Stable Isotope;TCA;DatasetType:Metabolomics","pi":[{"name":"Laura-Isobel McCall ","email":"lmccall@sdsu.edu","institution":"SDSU","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d1416d322439452dbfdac5faa08bafb1","id":"1070"}, {"dataset":"MSV000097453","datasetNum":"97453","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Glyphosate using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742973566000","created":"Mar. 26, 2025, 12:19 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Glyphosate using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Glyphosate (in Acetonitrile)(working concentration of 5 microMolar (Organophosphorous) for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Glyphosate is Human serum albumin treated with Glyphosate and HSA_Glyphosate _2NA is Human serum Albumin treated with Glyphosate and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"4064546","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Organophosphorous;Pseudoesterase;Albumin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"92b997a6689b4143ac9356aa9e71ded1","id":"1071"}, {"dataset":"MSV000097452","datasetNum":"97452","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Dichlorvos using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742972746000","created":"Mar. 26, 2025, 12:05 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Dichlorvos using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Dichlorvos (in Acetonitrile)(working concentration of 5 microMolar (Organophosphorous) for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Dichlorvos is Human serum albumin treated with Dichlorvos and HSA_Dichlorvos _2NA is Human serum Albumin treated with Dichlorvos and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"4362298","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Organophosphorous;Pseudoesterase;Albumin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"41d57aba3e054944b95055e39cc5abed","id":"1072"}, {"dataset":"MSV000097451","datasetNum":"97451","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Chlorpyrifos_oxon using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742964653000","created":"Mar. 25, 2025, 9:50 PM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Chlorpyrifos_oxon using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Chlorpyrifos_oxon (in Acetonitrile)(working concentration of 5 microMolar (Organophosphorous) for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Chlorpyrifos_oxon is Human serum albumin treated with Chlorpyrifos_oxon and HSA_Chlorpyrifos_oxon_2NA is Human serum Albumin treated with Chlorpyrifos_oxon and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"4598326","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"pesticide;Organophosphorous;Pseudoesterase;Albumin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"73a99fcda82848d38ab815dd8a98f44b","id":"1073"}, {"dataset":"MSV000097449","datasetNum":"97449","title":"GNPS - Blood-brain barrier role in metabolite regulation via excitatory amino acid transporter 3","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742955164000","created":"Mar. 25, 2025, 7:12 PM","description":"Blood-brain barrier role in metabolite regulation via excitatory amino acid transporter 3. The questions we would like to address are: What are the metabolomic changes in whole brain regions and blood-brain barrier compartments with and without endothelial cell-specific slc1a1 glutamate transporter? Are these differences pulled out or exacerbated by mimicking an excess extracellular glutamate state using a subseizure dose of Kainic Acid? Cortex, hypothalamus, and cerebellum were isolated as well as whole brain, enriched microvessels, and plasma fractions from slc1a1 (EAAT3) endothelial cell-specific conditional knockout mice. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA). LC-MS\/MS data acquired in positive mode.","fileCount":"561","fileSizeKB":"27467732","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;MSCollaboratory;slc1a1;Glutamate;DatasetType:Metabolomics","pi":[{"name":"Richard Daneman","email":"rdaneman@ucsd.edu","institution":"University of California - San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"274c356a920243489743ec8e286464d4","id":"1074"}, {"dataset":"MSV000097448","datasetNum":"97448","title":"GNPS - REGIONAL MICROBIOTA MISMATCHES FROM FECAL MICROBIOTA TRANSPLANTS DRIVE PERSISTENT, OFF-TARGET CONSEQUENCES TO THE HOST","user":"amsidebottom","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742954802000","created":"Mar. 25, 2025, 7:06 PM","description":"REGIONAL MICROBIOTA MISMATCHES FROM FECAL MICROBIOTA TRANSPLANTS DRIVE PERSISTENT, OFF-TARGET CONSEQUENCES TO THE HOST","fileCount":"271","fileSizeKB":"869728986","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Microbiome","instrument":"6470A Triple Quadrupole LC\\\/MS;6540 Q-TOF LC\\\/MS;Agilent 5975 GC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Microbiome;Metabolites;Fecal microbiota transplant;DatasetType:Metabolomics","pi":[{"name":"Orlando DeLeon","email":"odeleon@uchicagomedicine.org","institution":"University of Chicago","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"de800eedf2fa44e594b5f429f1c481b1","id":"1075"}, {"dataset":"MSV000097446","datasetNum":"97446","title":"GNPS - E. meliloti USDA 1021 and USDA 1157 in Succinate Minimal Media (Copper Infusion)","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742924553000","created":"Mar. 25, 2025, 10:42 AM","description":"Ensifer meliloti strains USDA 1021 and USDA 1157 were cultured in succinate minimal media and then analyzed for metabolites using untargeted LC-MS with a copper infusion.","fileCount":"21","fileSizeKB":"900155","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sinorhizobium meliloti (NCBITaxon:382);Sinorhizobium meliloti USDA 1021 (NCBITaxon:1230617)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Ensifer;meliloti;succinate minimal;copper;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f0e7a1247b6343c9a06658684dab4fe5","id":"1076"}, {"dataset":"MSV000097445","datasetNum":"97445","title":"GNPS - P. fluorescens in CAA (Normal v Low Fe)","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742923688000","created":"Mar. 25, 2025, 10:28 AM","description":"Pseudomonas fluorescens was cultured in casamino acids media with either normal or depleted iron via Chelex-treatment and analyzed for metabolites with DDA.","fileCount":"35","fileSizeKB":"555867","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"casamino acids;Pseudomonas;fluorescens;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b500bb3237d64b60b0e98ba95ba15aac","id":"1077"}, {"dataset":"MSV000097443","datasetNum":"97443","title":"GNPS - GC-MS metabolomics of different wood fungi species","user":"LPN_IKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742920090000","created":"Mar. 25, 2025, 9:28 AM","description":"GC-MS metabolomics analysis of secondary metabolites present in the different fungi species.","fileCount":"109","fileSizeKB":"4060152","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ganoderma parvulum (NCBITaxon:1227451);Trametes menziesii (NCBITaxon:1140397);Trametes versicolor (NCBITaxon:5325);Trametes villosa (NCBITaxon:47662);Ganoderma stipitatum (NCBITaxon:1368614);Annulohypoxylon stygium (NCBITaxon:326628);Ascomycota sp. (NCBITaxon:1709939);Ganoderma ecuadoriense (NCBITaxon:1837094);Programme epimiltina;Bjerkandera sp. (NCBITaxon:1897508);Phlebiopsis sp. (NCBITaxon:1968779);Trametes meyenii (NCBITaxon:526243);Ganoderma resinaceum (NCBITaxon:34465)","instrument":"GCMS-QP2020NX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Gas Chromatography-Mass Spectrometry;Wood fungi;Untargeted Metabolite Profiling;DatasetType:Metabolomics","pi":[{"name":"CIPRIANI AVILA EVA ISABEL","email":"ECIPRIANI111@puce.edu.ec","institution":"Pontificia Universidad Catolica del Ecuador","country":"Ecuador"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"bab4a1efafc6406a9cb91c0b97058252","id":"1078"}, {"dataset":"MSV000097441","datasetNum":"97441","title":"Xiong_kinetochore_APMS_P124_6600","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742915347000","created":"Mar. 25, 2025, 8:09 AM","description":"This dataset consists of 8 raw MS files and associated peak lists and results files, acquired on AB Sciex TripleTOF 6600 mass spectrometer operated in Data Dependent Acquisition mode. \nSamples were generated by Emily Xiong. GFP-AP and Mass spectrometry acquisition was performed by Zhen-Yuan Lin. Analysis was performed by Cassandra Wong and Emily Xiong. \nThe files are associated with a manuscript submitted for publication by Emily Xiong et al. The main goal of this paper was to identify and characterize components of the Candida albicans kinetochore.\nLeah Cowen is the corresponding author of the manuscript (leah.cowen@utoronto.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 3 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence\nTable 3 lists the SAINTexpress interactions \n","fileCount":"55","fileSizeKB":"11937509","spectra":"0","psms":"100746","peptides":"13601","variants":"16184","proteins":"10935","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Candida albicans (NCBITaxon:5476)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"AP-MS;kinetochore;Candida albicans;DatasetType:Proteomics","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD062214","task":"d634234fa45c4d20822347fd6abda92b","id":"1079"}, {"dataset":"MSV000097439","datasetNum":"97439","title":"Bacteria induces the release of alkaloids in plankton","user":"MarineValletMPICE","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742902757000","created":"Mar. 25, 2025, 4:39 AM","description":"Marine bacteria modulate the plankton composition and induce the release of harmine alkaloids.","fileCount":"391","fileSizeKB":"22305696","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Kordia algicida (NCBITaxon:221066)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bacteria;Exometabolome;Alkaloids;Plankton;Kordia;LCMS;Zic-hilic Chromatography;DatasetType:Metabolomics","pi":[{"name":"Dr. Marine Vallet","email":"mvallet@ice.mpg.de","institution":"Friedrich Schiller University Jena, Max Planck Institute for Chemical Ecology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9b3bef799dc445b084f08bbda0c47e3a","id":"1080"}, {"dataset":"MSV000097436","datasetNum":"97436","title":"Cardiomyocyte-specific deletion of PTP1B protects against obesity-induced cardiomyopathy by regulating cardiac metabolic signaling","user":"mdoor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742856698000","created":"Mar. 24, 2025, 3:51 PM","description":"Cardiomyocyte-specific PTP1B KO mice are protected from high fat diet-induced cardiomyopathy. Whole tissue lysates from hearts of these mice were reduced, alkylated, trypsin digested, and phospho-enriched using Thermo Fisher's Fe NTA High Select columns. 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"13C-SIP, soil lipidomics, yearlong incubation;DatasetType:Other (Lipidomics)","pi":[{"name":"Kirsten Hofmockel","email":"kirsten.hofmockel@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c80af5590fdd4ebf9ad1a7f95337056d","id":"1082"}, {"dataset":"MSV000097432","datasetNum":"97432","title":"NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742847598000","created":"Mar. 24, 2025, 1:19 PM","description":"WT-Mock-1: WT cells treated with vehicle for 24 hours, replicate-1: 126\n\nWT-Mock-2: WT cells treated with vehicle for 24 hours, replicate-2: 127N\n\nWT-Mock-3: WT cells treated with vehicle for 24 hours, replicate-3: 127C\n\nWT-Mock-4: WT cells treated with vehicle for 24 hours, replicate-4: 128N\n\nWT-6-TG-1: WT cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-1: 128C\n\nWT-6-TG-2: WT cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-2: 129N\n\nWT-6-TG-3: WT cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-3: 129C\n\nWT-6-TG-4: WT cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-4: 130N\n\nNUDT5-Mock-1:\tNUDT5 KO cells treated with vehicle for 24 hours, replicate-1: 130C\n\nNUDT5-Mock-2:\tNUDT5 KO cells treated with vehicle for 24 hours, replicate-2: 131N\n\nNUDT5-Mock-3:\tNUDT5 KO cells treated with vehicle for 24 hours, replicate-3: 131C\n\nNUDT5-Mock-4:\tNUDT5 KO cells treated with vehicle for 24 hours, replicate-4: 132N\n\nNUDT5-6-TG-1: NUDT5 KO cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-1: 132C\n\nNUDT5-6-TG-2:\tNUDT5 KO cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-2: 133N\n\nNUDT5-6-TG-3:\tNUDT5 KO cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-3: 133C\n\nNUDT5-6-TG-4:\tNUDT5 KO cells treated with 0.5ug\/mL 6-TG for 24 hours , replicate-4: 134N","fileCount":"25","fileSizeKB":"31930424","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - 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Post-translational modifications (PTMs) and ligand binding significantly affect the activity and function of AMPK. However, the dynamic interplay of PTMs, non-covalent interactions, and higher-order structures of the kinase complex remain poorly understood. Herein, we report the structural heterogeneity of the AMPK complex arising from ligand binding and proteoforms, protein products derived from PTMs, alternative splicing, and genetic variants, using integrated native and denatured top-down mass spectrometry (TDMS). The fully intact AMPK heterotrimeric complex exhibits heterogeneity due to phosphorylation and multiple adenosine monophosphate (AMP) binding states. Native TDMS provides valuable insights into the higher-order structure of AMPK, subunit composition, and AMP binding stoichiometry, whilst denatured TDMS characterizes the proteoforms and localizes the phosphorylation site. This is the first study to structurally characterize AMPK proteoform-ligand complexes. Notably, using native TDMS and AlphaFold, we resolve a flexible regulatory region that has been difficult to visualize with traditional structural biology tools. These findings offer new perspectives on protein kinase regulation and establish a powerful framework for elucidating other kinase complexes.","fileCount":"947","fileSizeKB":"2668276","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"solariX;impact II","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"top-down mass spectrometry;native top-down mass spectrometry;AMP-activated protein kinase;post-translational modifications;protein-ligand binding;DatasetType:Proteomics","pi":[{"name":"Ying Ge","email":"ge2@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062177","task":"2b57c7dc913a4c40b3a497bc11b469f1","id":"1084"}, {"dataset":"MSV000097429","datasetNum":"97429","title":"GNPS_Metabolites from methylobacterium aquaticum","user":"alaronlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742841964000","created":"Mar. 24, 2025, 11:46 AM","description":"This dataset contains mass spectrometry data from a metabolomics experiment focused on metabolites from a lanthanide-utilizing bacteria known as methylobacterium aquaticum. Lanthanides are used in alcohol dehydrogenation for this species.","fileCount":"61","fileSizeKB":"1359385","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Methylobacterium aquaticum (NCBITaxon:270351)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"methylobacteria;lanthanide-binding;gram-negative;metallophores;lanthanophores;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f196719f0ccd41dc966672f2cb7c1244","id":"1085"}, {"dataset":"MSV000097423","datasetNum":"97423","title":"OL 16:0\/15:0 analysis by MS\/MS analysis. 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The fecal samples from these mice were collected and extracted with 50% methanol for LC-MS\/MS metabolomics. The sample extracts were chromatographed using a Phenomenex polar C18 column, and MS\/MS data was acquired on a Thermo Q Exactive in positive ionization mode.","fileCount":"299","fileSizeKB":"20440446","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile Salt Hydrolase;Engineered strains;Time restricted feeding (TRF);Fecal;DatasetType:Metabolomics","pi":[{"name":"Pieter C. 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ACQUITY BEH C8 column (100 mm×2.1 mm, 1.7 ?m, Waters, Milford, MA, USA) was used for the LC system in positive (ESI+) ionization modes, respectively. The temperature was set to 50°C, and the gradient elution flow rate was set at 0.35 mL\/min. The mobile phase consisted of water (A) and acetonitrile with 0.1% formic acid (B) in ESI+ ionization mode. The initial gradient started with 5% B for 1 min, followed by a linear increase to 100% B within 23 min, and then maintained for an additional 4 min. Finally, the gradient was reduced to 5% B for system equilibration.\r\nAstral MS analysis. Mass spectrometry was performed on Orbitrap Astral (Thermo Fisher Scientific, Rockford, IL, USA) in full scan MS\/ddMS2 mode. For the full scan properties of the Orbitrap detector, the MS1 scan range was 85-1250 m\/z. Orbitrap resolution was 120,000. RF lens was set as 50%. Full-scan orbitrap MS1 was performed in parallel with fast and sensitive DDA MS2 (top 30) on the Astral mass analyzer, with an MS\/MS acquisition rate of 150 Hz. The isolation window was 1 m\/z. Normalized collision energy type was used in our work, and the HCD collision energy was set as 15%, 30%, 45% and 80%, respectively. The MS2 scan range was 50-1250 m\/z. The normalized AGC target and injection time were 10% and 5 ms, respectively. The spray voltages were 3.5 kV and 3.0 kV in positive and negative ionization modes, respectively. The aux gas heater temperature and capillary temperature were 350°C and 320°C, respectively. The sheath gas and aux gas were 45 and 10 (in arbitrary units), respectively.","fileCount":"6","fileSizeKB":"2123494","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolite annotation;molecular networking;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Xinxin Wang","email":"xxwang96@dicp.ac.cn","institution":"DICP","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"396c1b478b7843459494b3757a07f47f","id":"1091"}, {"dataset":"MSV000097410","datasetNum":"97410","title":"GNPS - NOZ Coral Reef DOM 2018 collection 2019 analysis","user":"MilouArts","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742634310000","created":"Mar. 22, 2025, 2:05 AM","description":"Dataset containing multiple sample sets of coral reef associated dissolved organic matter","fileCount":"143","fileSizeKB":"3381622","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coral Reef;Dissolved organic matter;DOM;Marine metabolomics;Caribbean;DatasetType:Metabolomics","pi":[{"name":"Andreas Haas","email":"andi.haas@nioz.nl","institution":"NIOZ","country":"Netherlands"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"5b48f73c412944329db314099452423b","id":"1092"}, {"dataset":"MSV000097408","datasetNum":"97408","title":"Guard Cell Mitochondria Prefer Alternative Substrates and Energy-Conserving Electron Transfer","user":"NoahDitz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742592572000","created":"Mar. 21, 2025, 2:29 PM","description":"Proteomics of plant mitochondria usually is based on a bulk mixture of organelles originating from different leaf cell types. Here, a novel isolation technique was applied, fusing an affinity tag under control of cell type specific promotors to a mitochondrial outer envelope protein. The construct allowed isolation of mitochondria from the mesophyll, guard cells, and total leafs, serving as a control. Isolated organelles were subjected to a shotgun MS workflow employing single pot, solid phase enhanced sample preparation (SP3, Hughes et al. 2019) protocol. Tryptic peptides were separated using a 60 min gradient on a Aurora 25cm column, connected to a nanoElute2 LC that was coupled to a timsTOF Pro MS. Spectra were acquired in DDA-PASEF and used to compute intensity based abundance quantification (iBAQ, Schwanhausser et al. 2011) values to assess organelle purity. Total leaf protein extracts were analyzed to estimate enrichment factors for mitochondrial proteins. Label free quantification values were used to compare the mitochondrial proteomes originating from different leaf tissues. Additionally, differences of mitochondrial protein complexes were investigated by complexome profiling. For this, mitochondria from different tissues were fractionated by blue native polyacrylamide gel electrophoresis, resulting in 39 fractions for each tissue that were subjected to tryptiv in-gel digestion and nanoElute2-timsTOF-MS to generate abundance profiles from iBAQ values. Last, abundance of complex I was estimated to calculate its NADH oxidase activity between the different tissues. For this, an Evosep was operated using the Whisper Zoom 40 SPD, coupled to a timsTOF Pro operating in DDA-PASEF. Abundance was estimated using iBAQ values of identified complex I subunits and their contribution to the summed up iBAQ intensity within each sample. 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Mouse models have been developed to study PGRN functions. However, PGRN deficiency in the commonly used C56BL\/6 mouse strain background leads to very mild phenotypes, and pathways regulating PGRN deficiency phenotypes remain to be elucidated. We generated PGRN-deficient mice in the FVB\/N background and compared PGRN deficiency phenotypes between C56BL\/6 and FVB\/N background via immunostaining, western blot, RNA-seq, and proteomics approaches. We also identified sPLA2-IIA as a novel binding partner of PGRN and demonstrated the importance of sPLA2-IIA in modifying PGRN deficiency phenotypes using inhibitor treatment and AAV-mediated overexpression in mouse models. We report that PGRN loss in the FVB\/N mouse strain results in earlier onset and stronger FTLD-related and lysosome-related phenotypes. We found that PGRN interacts with sPLA2-IIA, a member of the secreted phospholipase A2 (sPLA2) family member and a key regulator of inflammation that is expressed in FVB\/N but not C56BL\/6 background. sPLA2-IIA inhibition rescues PGRN deficiency phenotypes and sPLA2-IIA overexpression drives enhanced gliosis and lipofuscin accumulation in PGRN-deficient mice. Additionally, RNA-seq and proteomics analysis revealed that mitochondrial pathways are upregulated in the PGRN-deficient C57BL\/6 mice but not in the FVB\/N mice. Our studies establish a better mouse model for FTLD-GRN and uncover novel pathways modifying PGRN deficiency phenotypes.","fileCount":"17","fileSizeKB":"25084797","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Proganulin;Inflammation;Lysosome;mouse strain background;sPLA2-IIA;Mitochondria;DatasetType:Proteomics","pi":[{"name":"Fenghua Hu","email":"fh87@cornell.edu","institution":"Cornell University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cee66c3bf9d74055807ed1aed8eeabac","id":"1100"}, {"dataset":"MSV000097390","datasetNum":"97390","title":"APOE-isogenic iPSC-derived astrocytes","user":"ctackenberg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742508807000","created":"Mar. 20, 2025, 3:13 PM","description":"APOE-isogenic iPS cells were differentiated into astrocytes and analyzed for APOE genotype-mediated metabolic differences.","fileCount":"45","fileSizeKB":"6878184","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"APOE, astrocytes;DatasetType:Metabolomics","pi":[{"name":"Christian Tackenberg","email":"christian.tackenberg@uzh.ch","institution":"University of Zurich","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b7a0aa0e11fb4ede95bb30b4f7ac895c","id":"1101"}, {"dataset":"MSV000097385","datasetNum":"97385","title":"GNPS U2OS HA-TIPIN HA-IP & MS under camptothecin DNA damage","user":"jhaley55","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742503466000","created":"Mar. 20, 2025, 1:44 PM","description":"This study analyzes the function of TIPIN and its PTMs in DNA repair in a U2OS model. Four sample conditions were used: Control untreated, TIPIN WT untreated, TIPIN WT CPT, TIPIN S222A CPT. Spectra were acquired using an orbital trap and LFQ analysis was performed using Proteome Discoverer 3.1.","fileCount":"10","fileSizeKB":"11215299","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"homo","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"TIPIN DNA repair;DatasetType:Proteomics","pi":[{"name":"Hyungjin Kim","email":"hyungjin.kim@stonybrook.edu","institution":"Stony Brook University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5909908c8a054378a7ef2d07457df2f4","id":"1102"}, {"dataset":"MSV000097382","datasetNum":"97382","title":"GNPS_P rubens P03MB2_Neo Oct 2024","user":"SizweM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742420248000","created":"Mar. 19, 2025, 2:37 PM","description":"Untargeted metabolomics of an endophtic fungus, Penicillium rubens exhibiting anti-HIV activity","fileCount":"36","fileSizeKB":"2311379","spectra":"205054","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Penicillium rubens (NCBITaxon:1108849)","instrument":"LCMS-9030","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Untargeted metabolomics, endophytic fungi, anti-HIV;DatasetType:Metabolomics","pi":[{"name":"Sizwe Ndlovu","email":"sizwe.ndlovu@nwu.ac.za","institution":"North-West University","country":"South Africa"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3f511f52fc494953ac9ddd3c902cb4c3","id":"1103"}, {"dataset":"MSV000097381","datasetNum":"97381","title":"Msc_Fractions_Lc_Ms Grape&Olive","user":"islammarey77","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742419792000","created":"Mar. 19, 2025, 2:29 PM","description":"Analysis of Food natural products of grape pomace and olive leaves","fileCount":"37","fileSizeKB":"7186923","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vitis vinifera (NCBITaxon:29760);Vitis sp. 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Plasma membrane subdomains known as MCC (Membrane Compartment of Can1) or eisosomes are important for these processes. MCC\/eisosome domains are furrow-shaped invaginations of the plasma membrane that are about 250 nm long and 50 nm deep. Two proteins that localize to these domains, Sur7 and Lsp1, are critical for virulence. Identifying additional proteins that localize to MCC\/eisosomes has been hindered by the technical challenges of working with membrane proteins. Therefore, the proximity labeling method TurboID was used to identify MCC\/eisosome proteins in C. albicans. Candidate proteins were identified by fusing a variant of BirA known as TurboID to either Sur7 or Lsp1, to promote biotinylation of nearby proteins. Analysis of 19 of these proteins by tagging with the Green Fluorescent Protein (GFP) identified 7 proteins that detectably overlapped with MCC\/eisosomes. Deletion mutant analysis showed that one of these, a poorly studied protein known as Ker1, was important for hyphal growth in liquid culture, invasive growth into agar medium, and resistance to stress caused by copper and cell wall perturbing agents. Altogether, these approaches identified novel MCC\/eisosome proteins and show that TurboID can be applied to better define the molecular mechanisms of C. albicans pathogenesis and aid in discovery of targets novel therapeutic strategies.","fileCount":"71","fileSizeKB":"44804928","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Candida albicans (NCBITaxon:5476)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Candida albicans TurboID;DatasetType:Proteomics","pi":[{"name":"James B. 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","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742383206000","created":"Mar. 19, 2025, 4:20 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Carbaryl using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Carbaryl (in Acetonitrile)(working concentration of 5 microMolar (Organocarbamate) for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Carbaryl is Human serum albumin treated with Carbaryl and HSA_Carbaryl_2NA is Human serum Albumin treated with Carbaryl and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"5179055","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Organocarbamate;Pseudoesterase;Albumin;Pesticide;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"PGIMER, Chandigarh","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"123029e10b2342fca1c8d2191328de04","id":"1108"}, {"dataset":"MSV000097371","datasetNum":"97371","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Aminocarb using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. ","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742382054000","created":"Mar. 19, 2025, 4:00 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Aminocarb using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Aminocarb (in Acetonitrile)(working concentration of 5 microMolar (Organocarbamate) for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Aminocarb is Human serum albumin treated with Aminocarb and HSA_Aminocarb_2NA is Human serum Albumin treated with Aminocarb and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"6749223","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Pesticide;Organocarbamate;Pseudoesterase;Albumin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"PGIMER, Chandigarh","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a7ca405124dc43e79e037579ba003064","id":"1109"}, {"dataset":"MSV000097370","datasetNum":"97370","title":"To study the acetylation of human serum albumin (HSA) in presence and absence of Aldicarb using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. ","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742381046000","created":"Mar. 19, 2025, 3:44 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- To study the acetylation of human serum albumin (HSA) in presence and absence of Aldicarb using 2-Naphthyl Acetate (2NA) as substrate and digestion with Pepsin. Project File No. 5\/4\/1-25\/2020-NCD-1. Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with Aldicarb (in Acetonitrile)(working concentration of 5 microMolar (Organocarbamate) for 1 hour at 37 degree Celsius. Further, acetylation was done using 2NA (prepared in Acetonitrile) for 45 minutes at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 minutes followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Next, samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. Pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. Description of the raw files is as follow. HSA_Aldicarb is Human serum albumin treated with Aldicarb and HSA_Aldicarb_2NA is Human serum Albumin treated with Aldicarb and then substrate (2NA) was added.","fileCount":"7","fileSizeKB":"5151453","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"pesticide;organocarbamate;Pseudoesterase;Albumin;Poisoning;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"PGIMER, Chandigarh","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aaf4403802cd4d80ae1dca04f1afad4a","id":"1110"}, {"dataset":"MSV000097369","datasetNum":"97369","title":"Epithelial-fibroblast crosstalk initiates protective mechanisms in epithelial cells upon acute injury","user":"alexcampos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742360880000","created":"Mar. 18, 2025, 10:08 PM","description":"Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal lung disease characterized by excessive fibrotic scar tissue accumulation, compromising lung function. While the precise etiology of IPF remains elusive, emerging evidence suggests that sustained lung epithelial injury is a key driver in the disease's development and progression. This persistent injury, unlike normal wound healing, maintains a pro-fibrotic niche that continually fuels the fibrotic process. Consequently, the question remains whether there is a way to alter this niche signaling, counteract the pro-fibrotic signals, and restore physiological wound healing. By approaching an epithelial-fibroblast coculture model, we investigated in the intercellular communication in chronic and acute injury situations. We identified that epithelial cells and fibroblasts together, create a protective niche signaling preventing further damage in acute injuries. Within epithelial cells, we observed that a switch of the metabolic state towards increased aerobic fatty acid metabolism initiates regenerative processes. While delineating secreted regulators responsible for inducing these positive responses, we identified pentraxin 3 (PTX3) as a top hit harboring antifibrotic characteristics. Modifying the niche by addition of PTX3 on chronically injured epithelial cells causes an amelioration of the pro-fibrotic phenotype and maintained the epithelial barrier integrity. These findings offer valuable insights in key differences of acute and chronic injuries and underscore the importance of understanding the complex interplay between epithelial cells and fibroblasts in lung injury and repair.","fileCount":"64","fileSizeKB":"79258871","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Pulmonary fibrosis;Epithelial-fibroblast crosstalk;Fatty acid metabolism;PTX3;DatasetType:Proteomics","pi":[{"name":"Matthew J. Thomas","email":"matthew_james.thomas@boehringer-ingelheim.com","institution":"Boehringer Ingelheim Pharma GmbH","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD062012","task":"0b2786c6d3064f4fa5485362f7936f0f","id":"1111"}, {"dataset":"MSV000097367","datasetNum":"97367","title":"Overexpression of ATase1 and ATase2 in the mouse disrupts the quality of the secretome and causes a progeria phenotype ","user":"Feixuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742351432000","created":"Mar. 18, 2025, 7:30 PM","description":"Acetylation in the lumen of the endoplasmic reticulum requires two acetyltransferases, ATase1\/NAT8B and ATase2\/NAT8. They are type II membrane proteins and belong to the larger GNAT superfamily of acetyltransferases. Their enzymatic activity is tightly coupled to the import of acetyl-CoA in the lumen of the endoplasmic reticulum by AT-1\/SLC33A1. Gene duplication events involving 3q25.31 (harboring AT-1\/SLC33A1) and 2p13.1 (harboring ATase1\/ NAT8B and ATase2\/NAT8) are associated with autism spectrum disorder with intellectual disability and progeria-like dysmorphism. Here, we report the generation and phenotypic characterization of mice with systemic overexpression of ATase1 (ATase1 sTg) and ATase2 (ATase2 sTg). Overexpression of either ATase at conception was found to be lethal while overexpression at birth was found to cause a progeria-like phenotype that included skin alterations, lordokyphosis, reduced bone density, sarcopenia, splenomegaly, adenomegaly, and systemic inflammation. The phenotype of ATase1 sTg mice displayed incomplete penetrance, while the phenotype of ATase2 sTg displayed full penetrance and was more severe. Mechanistically, the phenotype was linked to altered dynamics of the secretory pathway with defects affecting the quality of the secretome. ","fileCount":"53","fileSizeKB":"43707353","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos;Q Exactive HF","modification":"UNIMOD:1 - \\\"Acetylation.\\\";N-linked glycosylation","keywords":"ATase1, ATase2, AT-1, acetyl-CoA, acetylation;DatasetType:Proteomics;DatasetType:Other (Glycoproteomics)","pi":[{"name":"Luigi Puglielli","email":"lp1@medicine.wisc.edu","institution":"University of Wisconsin-Madison","country":"The United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD062005","task":"574c42c665f44ff9bf21fba4b9ef308c","id":"1112"}, {"dataset":"MSV000097363","datasetNum":"97363","title":"GNPS - Untargeted Metabolomic Analysis of Extracts of the Marine Dinoflagellate Amphidinium eilatiense","user":"Mayca90","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742331609000","created":"Mar. 18, 2025, 2:00 PM","description":"Untargeted metabolomics mapping of non-polar active fractions produced by the benthic dinoflagellate Amphidinium eilatiense (previously A. eilatiensis). The dataset includes peak absorption spectra of detected features using LC-HMRS. Active fractions were obtained by bioassay-guided fractionation tested against human breast and lung cancer cell lines and a normal human lung fibroblast cell line. Data-dependent Acquisition was employed under positive and negative ionization mode.","fileCount":"17","fileSizeKB":"1205326","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Amphidinium eilatiense ","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"anticancer;bioactive compounds;secondary metabolites;phycotoxins;DatasetType:Metabolomics","pi":[{"name":"Lorena M. Duran-Riveroll","email":"lduran@secihti.mx","institution":"Centro de Investigacion Cientifica y de Educacion Superior de Ensenada","country":"Mexico"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"841c8b5f4b0b4ef8a92923115b726c95","id":"1113"}, {"dataset":"MSV000097361","datasetNum":"97361","title":"GNPS - Bacterial fractions produced by Moon snail egg mass associated bacteria from Puerto Rico","user":"lkyei","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742329573000","created":"Mar. 18, 2025, 1:26 PM","description":"Bacterial fractions produced by Moon snail egg mass associated bacteria from Puerto Rico with S. aureus biofilm inhibition activity.","fileCount":"12","fileSizeKB":"7402589","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria","instrument":"Exactive","modification":"NA","keywords":"Moon snail egg mass;DatasetType:Metabolomics","pi":[{"name":"Emily Mevers","email":"emevers@vt.edu","institution":"Virginia Tech","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"73716ba28fae4c0989c935ed95a104cc","id":"1114"}, {"dataset":"MSV000097355","datasetNum":"97355","title":"Pilocarpine inhibits Candida albicans biofilm maturation by altering lipid, sphingolipid, and protein content","user":"micheledeicas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742307914000","created":"Mar. 18, 2025, 7:25 AM","description":"Candida albicans filamentation and biofilm formation are key virulence factors tied to tissue invasion and antifungal tolerance. Pilocarpine hydrochloride (PHCl), a muscarinic receptor agonist, inhibits biofilm maturation, though its mechanism remains unclear. We explored PHCl effects by analyzing sphingolipid and lipid composition and proteomics in treated biofilms. PHCl significantly decreased polar lipid and ergosterol levels in biofilms while inducing phytoceramide and glucosylceramide accumulation. PHCl also induced reactive oxygen species and early apoptosis. Proteomic analysis revealed that PHCl treatment downregulated proteins associated with metabolism, cell wall remodeling, and DNA repair in biofilms to levels comparable to those observed in planktonic cells. Consistently with ergosterol reduction, Erg2 was found reduced.\nOverall, PHCl disrupts key pathways essential for biofilm integrity, resulting in reduced stability and increased detachment, underscoring its potential as a versatile antifungal compound.","fileCount":"139","fileSizeKB":"5063301","spectra":"50342","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Candida albicans (NCBITaxon:5476)","instrument":"Triple TOF 6600 Sciex","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"untargeted lipidomics;DatasetType:Other (lipidomics)","pi":[{"name":"Elisa Borghi","email":"elisa.borghi@unimi.it","institution":"Department of Health Sciences, Universita degli Studi di Milano, 20142 Milan, Italy","country":"Italy"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD061975","task":"ff41568c4ea1401db92ba1832b0c034b","id":"1115"}, {"dataset":"MSV000097353","datasetNum":"97353","title":"Longitudinal Monkey Plasma Metabolomics and Lipidomics","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742289108000","created":"Mar. 18, 2025, 2:11 AM","description":"Caloric restriction (CR) without malnutrition delays aging in diverse species, including primates, with metabolic changes implicated in this process. To facilitate exploration of CR metabolism with aging, we developed a 15-minute LC-MS\/MS metabolomics and lipidomics method, leveraging monophasic extractions and wide elution-strength solvents. We analyzed 494 plasma samples collected over 25 years from male and female rhesus monkeys (Macaca mulatta) on a Control or CR (30% restricted) diet. Quantitation of 359 biomolecules revealed that aging, followed by sex and diet, had the largest impact on metabolite abundances. In both sexes, aging was associated with significantly lower plasma levels of sphingomyelins (SMs) and higher levels of diglycerides (DGs) and triglycerides (TGs), each of which was opposed by CR. Sex dimorphism was evident by increased abundance of phosphocholine (PC)-containing lipids in females. These results highlight the utility of a rapid metabolomics and lipidomics approach to elucidate complex biology in large-scale studies.","fileCount":"941","fileSizeKB":"136319617","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Macaca mulatta (NCBITaxon:9544)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"omics;mass spectrometry;metabolomics;lipidomics;rhesus macaque;aging;caloric restriction;lipid metabolism;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Josh J. Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin - Madison","country":"USA"},{"name":"Katherine A. Overmyer","email":"kovermyer@morgridge.org","institution":"University of Wisconsin - Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"240138b7b2a2488ab46b2b393d32f810","id":"1116"}, {"dataset":"MSV000097352","datasetNum":"97352","title":"Comprehensive Dynamic Interaction Landscape of the Mammalian Hh Signaling Pathway","user":"XIOLIU","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742275193000","created":"Mar. 17, 2025, 10:19 PM","description":"The Hedgehog (Hh) signaling pathway is essential for embryonic development and tissue homeostasis, and its dysregulation contributes to severe developmental disorders and various cancers. Despite its biological importance, a detailed understanding of the dynamic interactions and phosphorylation events that regulate this pathway remains incomplete. To address this gap, we employed a comprehensive systems-level approach combining proximity-dependent biotinylation (BioID), phosphoproteomics, and advanced computational analyses to generate an extensive and dynamic map of the mammalian Hh signaling pathway. Using stable NIH-3T3 and HEK293 cell lines expressing key Hh components, we systematically characterized protein-protein interactions (PPIs) and phosphorylation dynamics in response to pathway activation and during primary cilia progression. Our workflow identified numerous ciliary proteins, highlighting the essential role of primary cilia and phosphorylation in Hh signaling regulation. To further explore the contribution of primary cilia, we analyzed interaction networks during cilia absence, formation, and resorption. These analyses revealed that the mammalian Hh signaling network is modular, consisting of four distinct functional groups: core membrane\/ciliary regulators, intracellular signaling regulators, trafficking\/scaffolding regulators, and downstream transcriptional regulators. Each module displayed specialized roles within the signaling cascade, closely linked to cell cycle regulation.","fileCount":"3681","fileSizeKB":"560166243","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive;timsTOF Pro","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Hh signaling;interactome;DatasetType:Proteomics","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6deb28043c1c4437ada087e950cce1e0","id":"1117"}, {"dataset":"MSV000097351","datasetNum":"97351","title":"Growth-rate dependent regulation of anabolism and catabolism in the thermophilic acetogen T. kivui under glucose limitation and phosphate limitation","user":"fnia","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742273856000","created":"Mar. 17, 2025, 9:57 PM","description":"Allocation of resources in the costly and competitive cellular proteome reflects trade-offs in cellular functions. As in many fast-growing bacteria, proteome composition of Escherichia coli growing aerobically on glucose is strictly regulated by growth rate. An increasing anabolic, especially ribosomal, proteome fraction leads to a decreasing catabolic proteome fraction at faster growth, resulting in shifted metabolism. Our systems-level studies of the thermophilic anaerobic acetogen Thermoanaerobacter kivui revealed a substantially different strategy: Over a range of two orders of magnitude, proteome allocation is minimally controlled by growth rate and metabolic rates are primarily controlled posttranslationally. Composition of the catabolic proteome is uncoupled from catabolic rates as indicated by product formation and flux analysis. At slower growth, ribosome numbers are controlled by rRNA concentrations, leading to an excess of ribosomal proteins. This points at a complex landscape of ecophysiological strategies and advantages for a more lenient regulation of proteome allocation.","fileCount":"296","fileSizeKB":"42175238","spectra":"0","psms":"445006","peptides":"16698","variants":"20649","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Thermoanaerobacter kivui (NCBITaxon:2325)","instrument":"TripleTOF 5600","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"T. kivui;Bectaria;Acetogen;Clostridia;Thermophile;Proteome allocation;Growth rate;DatasetType:Proteomics","pi":[{"name":"Alfred M. Spormann","email":"spormann@stanford.edu","institution":"Stanford University","country":"United States"},{"name":"James R. Williamson","email":"jrwill@scripps.edu","institution":"The Scripps Research Institute","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"009af5f31ae848f6b7369a2c3ce5e259","id":"1118"}, {"dataset":"MSV000097347","datasetNum":"97347","title":"Exo-metabolome profiling of soybean endophytes","user":"Haleema","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742235116000","created":"Mar. 17, 2025, 11:11 AM","description":"The present study explored the antifungal metabolites produced by soybean endophytes","fileCount":"94","fileSizeKB":"9640368","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus velezensis (NCBITaxon:492670);Bacillus thuringiensis (NCBITaxon:1428)","instrument":"Q Exactive","modification":"no","keywords":"Untargeted metabolomics of bacteria;DatasetType:Metabolomics","pi":[{"name":"Haleema Tariq","email":"haleema.tariq@mail.mcgill.ca","institution":"McGill University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5a545b8bffdf43cea42ec51b8edcf9c7","id":"1119"}, {"dataset":"MSV000097346","datasetNum":"97346","title":"NBC_Collection_Pekiskomycin_Producers","user":"sam_will92","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1742233395000","created":"Mar. 17, 2025, 10:43 AM","description":"Metabolomics data from 3 strains in the NBC collection that carry a Pekiskomycin BGC.\n\nThe strains were grown in R5 media and represent a WT strain, strain with a StrR regulator or LmbU regulator heterologously expressed to activate the cluster.\n\nStreptomyces sp. 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Next to the well-studied and explored IgG1, several other classes (e.g. IgA, IgM) and sub-classes (e.g., IgG2, IgG3 and IgG4) exist in humans. In particular IgG4 is worth a closer examination as it has unique natural properties and is regularly used as a scaffold in biologicals. In contrast to IgG1, endogenous IgG4 comes in two co-existing structural isomers, owing to the distinct properties of the hinge disulfide-bond connecting the two heavy chains. In one isomer, this disulfide bridge is opened, allowing the release and exchange of one half of the IgG4 molecule, and consequently the formation of bispecific IgG4. Here, we present a LC-MS-based approach enabling the analysis of IgG4 repertoires with clonal resolution, which we used to monitor endogenous serum IgG4 repertoires from seven healthy donors. Most strikingly, our data reveal the combinatorial explosion in diversity of the serum IgG4 clonal repertoire. This phenomenon is explained by the stochastic behavior of Fab-arm exchange, making virtually each IgG4 molecule in serum bispecific. Although the endogenous IgG4 clonal repertoire is therefore extremely diverse, we demonstrate that this IgG4 repertoire persists over time within an individual healthy donor, at least for more than one year.","fileCount":"417","fileSizeKB":"41241498","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Antibody repertoire;Clonal profiling;IgG4;DatasetType:Other (Intact protein)","pi":[{"name":"Albert J.R. 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Data was acquired on Orbitrap Exploris 240 with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 100 x 2.1 mm). Reversed-phase, ESI positive.","fileCount":"158","fileSizeKB":"12163964","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Diet, untargeted metabolomics, LC\/MS-MS, mouse, feces;DatasetType:Metabolomics","pi":[{"name":"Monica Guma","email":"mguma@ucsd.edu","institution":"UCSD","country":"USA"},{"name":"Pieter C. 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Diabetes mellitus (DM) affects all structures of the eye including the cornea, which can result in delayed wound healing and potential vision loss. MicroRNAs (miRNAs) are short non-coding oligonucleotides that regulate various cellular functions, including oxidative stress response, by repressing protein translation. MiR-10b-5p was previously identified to be upregulated in diabetic vs. non-diabetic limbal cells, and our purpose was to understand the role of miR-10b-5p in human limbal epithelial cells in healthy and diabetic conditions. Through integrated transcriptomic and proteomic analyses, we identified GCLM and LANCL1 as key miR-10b-5p targets, revealing its profound impact on glutathione metabolism, sulfur compound biosynthesis processes, and antioxidant defenses. Our findings suggest that overexpression of miR-10b disrupts redox balance, which potentially leads to heightened oxidative stress and increased cellular vulnerability in diabetic corneas. Understanding miR-10b function in corneal epithelial cells may pave the way for novel therapeutic strategies to mitigate oxidative stress and normalize corneal health in diabetic patients.","fileCount":"14","fileSizeKB":"19247107","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"diabetic cornea;limbal stem cells;miR-10b;oxidative stress;DatasetType:Proteomics","pi":[{"name":"Mehrnoosh Saghizadeh Ghiam","email":"Mehrnoosh.ghiam@cshs.org","institution":"Cedars-Sinai Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061853","task":"a4ae4736efe04d81ab567a097fe06733","id":"1129"}, {"dataset":"MSV000097326","datasetNum":"97326","title":"Enterococcal gelatinase mediated cleaving of IL-1beta proform","user":"harisantypas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741958822000","created":"Mar. 14, 2025, 6:27 AM","description":"Human IL1beta proform was incubated with Enterococcus faecalis OG1RF for 0, 6 and 18h in brain heart infusion media. 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Using an experimental design involving gentamicin protection and liquid chromagraphy followed by mass-spectrometry, a multi-species proteomic dataset was analyzed at different time points of the infection assay. Several previously undescribed Corynebacterium proteins were differentially regulated, as well as key macrophage components of the phagolysosome. Overall, Bacteria responded to phagocytosis by changes in DNA repair, transcription and cell wall synthesis proteins, while macrophages showed changes in components of the innate immune system.\r\n\r\nThis dataset consists of:\r\n\r\n- ThermoFisher's .raw files of three biological replicates of the infection assays (total proteome mixture of bacteria and eukaryotic cells and tagged using TMT-10). They can be downloaded all at once via the .zip file. \r\n- Protein abundance data for Macrophage THP-1 cells (M0) obtained by LC-MS\/MS followed by peptide sequencing using Proteome Discoverer (ThermoFisher) -see .zip folder.\r\n- Protein abundance data for Macrophage C. diphtheriae ISS3319 (CD) obtained by LC-MS\/MS followed by peptide sequencing using Proteome Discoverer (ThermoFisher) - see .zip folder.\r\n- Differential protein abundance analysis for CD and M0 using LIMMA. \r\n- Data underlying the growth curves observed in CD in RPMI + 10% FBS conditions (infection assay conditions). \r\n- BLASTP searches, PFAM clans, and InterPro annotations for CD.\r\n- STRING-based PPI network (baseline) and APSPs between differentially abundant proteins in CD. \r\n- Related R scripts.","fileCount":"52","fileSizeKB":"56030566","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Corynebacterium diphtheriae NCTC 13129 (NCBITaxon:257309);Corynebacterium diphtheriae bv. mitis str. 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Triggers and pathogenic pathways leading to podocyte cytoskeleton rearrangements are however incompletely explained. Here, we aimed to contribute to the understanding of these pathways using tissue bottom-up proteomic profiling of laser capture micro dissected glomeruli from MCD and FSGS.","fileCount":"844","fileSizeKB":"238392438","spectra":"0","psms":"20037","peptides":"2763","variants":"3421","proteins":"482","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"focal segmental glomerulosclerosis;minimal change disease;glomerular disease;label-free proteomics;DatasetType:Proteomics","pi":[{"name":"Iuga Cristina-Adela","email":"iugac@umfluj.ro","institution":"MEDFUTURE Research Center for Advanced Medicine","country":"Romania"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD061755","task":"716dd46a93f84eddbc8900a26e8d96e1","id":"1142"}, {"dataset":"MSV000097296","datasetNum":"97296","title":"HUVEC cell extracts for the investigation of collagen-induced cell signalling","user":"HanneDevos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741776575000","created":"Mar. 12, 2025, 3:49 AM","description":"We demonstrated that an abundant Collagen type I alpha 1-derived peptide inhibited collagen type I-induced endothelial cell migration in Human Umbilical Vein Endothelial Cells. 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Intraductal calcium deposition is a hallmark of aggressive premalignant lesions. This study tested the hypothesis that microbiome-derived extracellular vesicles (EVs) influence calcium modulation within premalignant breast cancer lesions. Based on the analysis of plasma, serum, saliva, and tissue collected from breast cancer patients and controls (N=150), Lactobacillus rhamnosus (Lr) was chosen as the model microbiota. In a BT-474 human breast cancer cell line monolayer culture under acute calcium stress, Lr EVs enhanced intracellular calcium intake. In a BT474 3D spheroid model under chronic calcium stress, Lr EVs increased extracellular calcium deposition and the mRNA expression of calcium export channel calcium pump isoform 2 (PMCA2) and stromal interaction molecule 1 (STIM1) in a dose-dependent manner. We propose that Lr EVs influence calcium regulation and mineral deposition, thereby affecting premalignant breast cancer progression.","fileCount":"767","fileSizeKB":"355287130","spectra":"0","psms":"18544","peptides":"3528","variants":"4521","proteins":"2268","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Lactobacillus (NCBITaxon:1578)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Breast cancer, calcium handling, microbiome;DatasetType:Proteomics","pi":[{"name":"Alessandra Luchini","email":"aluchini@gmu.edu","institution":"George Mason University","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD061715","task":"3cd9957cf0a244eab83f912f547a4c67","id":"1147"}, {"dataset":"MSV000097289","datasetNum":"97289","title":"Glycosylation of serine\/threonine-rich intrinsically disordered regions of membrane-associated proteins in streptococci ","user":"mmra250","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741715085000","created":"Mar. 11, 2025, 10:44 AM","description":"Despite lacking a tertiary structure, intrinsically disordered regions (IDRs) of proteins play a range of functional roles including cell signaling and protein folding in eukaryotes. 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Despite significant advancements in sample preparation, instrumentation, and data analysis, single-cell proteomics is currently limited by proteomic depth and quantitative performance. We combine a zero dead-end volume chromatographic column running at high throughput with the Thermo Scientific? Orbitrap? Astral? mass spectrometer running in DIA mode. We yield unprecedented depth of proteome coverage as well as accuracy and precision for quantification of ultra-low input amounts. Using a tailored library, we identify up to 7400 protein groups from as little as 250 pg HeLa at a throughput of 50 samples per day (SPD). We benchmark multiple data analysis strategies, estimate their influence on FDR and show that FDR on protein level can easily be maintained at 1 %. Using a two-proteome mix, we check for optimal parameters of quantification and show that fold change differences of 2 can still be successfully determined at single-cell level inputs. Eventually, we apply our workflow to A549 cells yielding a proteome coverage of up to 5200 protein groups from a single cell, which allows the observation of heterogeneity in a cellular population and studying dependencies between cell size and cell-cycle phase. Additionally, our workflow enables us to distinguish between in vitro analogs of two human blastocyst lineages: naïve human pluripotent stem cells (epiblast) and trophectoderm (TE)-like cells. Gene Ontology analysis of enriched proteins in TE-like cells harmoniously aligns with transcriptomic data, indicating that single-cell proteomics possesses the capability to identify biologically relevant differences between these two lineages within the blastocyst.","fileCount":"989","fileSizeKB":"748243393","spectra":"8389378","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Astral;Orbitrap Exploris 480","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Liquid chromatography;Mass spectrometry;Astral;A549;Aurora column;Single-cell proteomics;Trophectoderm-like cells;Naïve human stem cells;DatasetType:Proteomics","pi":[{"name":"Karl Mechtler","email":"karl.mechtler@imp.ac.at","institution":"Research Institute of Molecular Pathology (IMP), Vienna-Bio-Center (VBC), Vienna, Austria","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049412","task":"0e4988293ea7450fbd9b5582e3aa71f8","id":"1151"}, {"dataset":"MSV000097279","datasetNum":"97279","title":"GC-MS Profile for Cultured Anaerobic Gut Fungi - Anaeromyces robustus and Caecomyces churrovis","user":"lbutkovich","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741636789000","created":"Mar. 10, 2025, 12:59 PM","description":"Untargeted metabolomic profiling with gas chromatography-mass spectrometry (GC-MS) was performed for two gut fungal strains, Anaeromyces robustus S4 and Caecomyces churrovis A, enabling putative identification of metabolites and providing insights into gut fungal metabolic capabilities. Metabolites were extracted using the Metabolite, Protein, and Lipid Extraction (MPLEx) method and derivatized using a modified version of the protocol used to create FiehnLib. Samples underwent methoximation to protect carbonyl groups and reduce tautomeric isomers, followed by silylation with N-methyl-N-trimethylsilyltrifluoroacetamide and 1% trimethylchlorosilane (MSTFA) to derivatize hydroxy and amine groups to trimethylsilated (TMS) forms.","fileCount":"50","fileSizeKB":"550190","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Anaeromyces robustus (NCBITaxon:1754192);Caecomyces churrovis (NCBITaxon:2019372)","instrument":"Agilent GC 7890A-MSD 5975C","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Anaerobic Gut Fungi;MPLEx;Neocallimastigomycota;DatasetType:Metabolomics","pi":[{"name":"Michelle O'Malley","email":"butkovichlaza@gmail.com","institution":"University of California Santa Barbara","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"","task":"b9df38b012dd47d08eb1f6315ea430e6","id":"1152"}, {"dataset":"MSV000097269","datasetNum":"97269","title":"GNPS - Bacterial cultures of new gut microbes syncom","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741456913000","created":"Mar. 8, 2025, 10:01 AM","description":"Gut microbes were cultured with bile acids and drugs. Data was acquired on Orbitrap Exploris 240 with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 100 x 2.1 mm). Reversed-phase, ESI positive.","fileCount":"385","fileSizeKB":"24635137","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bacterial, bile acids, drug, LC-MS\/MS, untargeted metabolomics;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a0669877adb44e2d8681d8e2cdfc5720","id":"1153"}, {"dataset":"MSV000097266","datasetNum":"97266","title":"Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets","user":"jkreuzer","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741355473000","created":"Mar. 7, 2025, 5:51 AM","description":"Biliary tract cancers (BTCs) are lethal malignancies, including intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Through multi-omics profiling and CRISPR screens of 63 BTC cell lines, we identify widespread EGFR dependency and subtype-specific vulnerabilities with predictive markers. Strategies to overcome targeted therapy resistance include EGFR inhibition potentiating mutant-KRAS and FGFR inhibition, while SHP2 inhibition counters FGFR inhibitor resistance. Clustering by gene\/protein expression and dependencies reveals functional subtypes ductal, squamous, and bi-lineage each with distinct survival dependencies. Transcriptional analysis of patient samples highlights the prognostic value of this classification. This BTC cell line atlas uncovers therapeutic targets, defines disease subtypes, and serves as a critical resource for BTC research. Multiplexed proteomics was performed using TMT tags (TMT1 to TMT12) and TMTpro tags (TMT13 to TMT17) and the SPS3 method on an Orbitrap Fusion Lumos instrument. The sample key is provided as an excel file as a metadata file.","fileCount":"478","fileSizeKB":"318409661","spectra":"41385569","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"229.162932 (TMT10\\\/11), lysine, N-terminus, static;15.9949146221 (oxidation), methionine, variable;57.02146374 (IAA), cysteine, static;304.207146 (TMTpro16\\\/18), lysine, N-terminus, static","keywords":"Biliary Tract Cancer, Cholangiocarcinoma, Gallbladder Carcinoma, Cell line atlas, CRISPR screens, Tumor classification, Multi-omics, Integrative analysis, Orbitrap Fusion Lumos, TMT, TMTpro, SPS MS3;DatasetType:Proteomics","pi":[{"name":"Nabeel Bardeesy","email":"bardeesy.nabeel@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School, Boston","country":"USA"},{"name":"Vindhya Vijay ","email":"vvijay1@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a01db7b6d59e4d3f915282e58122692a","id":"1154"}, {"dataset":"MSV000097265","datasetNum":"97265","title":"Oncogenic Proteome of Pancreatic Cancer Extracellular Vesicle SLC5A3","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741355355000","created":"Mar. 7, 2025, 5:49 AM","description":"We performed proteome analysis of plasma-derived sEVs (8 PDAC patients and 4 healthy controls (Figure 1b). We demonstrate that SLC5A3 expression is elevated in sEV-derived PDAC patients relative to non-disease (highly elevated for patients 2 and 4). ","fileCount":"72","fileSizeKB":"68780642","spectra":"1710507","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"biomarker;Pancreatic Cancer;Extracellular Vesicles;SLC5A3;DatasetType:Proteomics","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061577","task":"c293fa2c058748a7a42a647d840e2021","id":"1155"}, {"dataset":"MSV000097263","datasetNum":"97263","title":"GNPS - Dataset Creation from GNPS Molcular Networking - 514832a6bd36459a97669c26a2f28845","user":"MarineValletMPICE","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741352323000","created":"Mar. 7, 2025, 4:58 AM","description":"This is the molecular network done using ddMS files of QC pool sample analyzed with C18 (positive, negative polarities) and Zic-Hilic (Positive, negative polarities). DMSP was identified in cold-adapted Antarctic Ulva and its holobiont, and several other polar compounds were up-regulated during heat stress.\nThe full dataset can be found under the MassIVE Accession MSV000097253","fileCount":"13","fileSizeKB":"198631","spectra":"15448","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ulva (NCBITaxon:3118)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Seaweed;Holobiont;Ulva;Bacteria;Antarctic;Heat Stress;C18;Zic-Hilic;Cell extracts;DatasetType:Metabolomics","pi":[{"name":"Dr. Marine Vallet","email":"mvallet@ice.mpg.de","institution":"Friedrich Schiller University Jena, Max Planck Institute for Chemical Ecology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"68c1ce081a25468a93def0fef3047ef6","id":"1156"}, {"dataset":"MSV000097257","datasetNum":"97257","title":"Cell therapy mesenchymal stem cell secretome for cardioprotection ","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741311189000","created":"Mar. 6, 2025, 5:33 PM","description":"Mesenchymal stem cells (MSCs) offer promising therapeutic effects for cardiac repair, primarily through their secretome, a complex array of bioactive factors with broad, multi-target effects on various cell types and pathological processes. However, current delivery and retention methods lack the ability to provide sustained, stable therapeutic benefits in ischaemic heart disease. This study addresses this limitation by introducing an innovative approach for the prolonged and clinically feasible delivery of MSC-derived secretome for cardioprotection. To evaluate the cardioprotective effects of MSC secretome in a human context, a human-iPSC-derived cardiac organoid model of simulated ischaemia-reperfusion injury was employed. Proteomic analysis of the Cymerus secretome, collected at both pre- and post-implantation, was conducted to investigate the mechanisms underlying its cardiac benefits. Proteomic analysis revealed the secretome of Cymerus comprised 3,851 proteins, with functional enrichment in pathways related to tissue homeostasis, apoptosis regulation, wound healing, and antioxidant defence . Furthermore, the post-implantation MSC secretome demonstrated an upregulation of proteins related to extracellular matrix organization, immune modulation, and tissue remodelling, indicating a temporal and adaptive response of the MSCs to ischaemic conditions.","fileCount":"42","fileSizeKB":"28800067","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\"","keywords":"heart;secretome;therapeutic;stem cells;Ischaemia-reperfusion injury;DatasetType:Proteomics","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061555","task":"c699e535e82b4608aea2b9cb817f371e","id":"1157"}, {"dataset":"MSV000097253","datasetNum":"97253","title":"GNPS - 20250306_Antarctic_Ulva_Metabolomics","user":"MarineValletMPICE","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741304348000","created":"Mar. 6, 2025, 3:39 PM","description":"The algal holobiont, which consists of algae and the bacteria living on it, has developed strategies to handle environmental stresses, such as changes in temperature. The green alga Ulva (Chlorophyta) is home to bacteria that help the algae grow and develop, from germlings to mature plants. These bacteria release chemicals like thallusin, N-acyl homoserine lactone, and ectoine, which support the health and growth of the algae. However, there is limited research on the metabolome of cold-adapted Ulva holobionts, especially those from hard-to-reach regions like Antarctica, and how they respond to environmental changes. In this study, we examine the metabolites found in Ulva and its associated bacteria from Antarctica (Potter Cove) using high-resolution mass spectrometry. We identified small polar and zwitterionic metabolites, such as cysteinolic acid, ectoine, glutamine, glycerol, and proline, in the surface tissues of the algae with MALDI-MS. By profiling these metabolites using UHPLC-HRMS and ZIC-HILIC chromatography, we found that their levels change significantly in response to heat-stressed Antarctic Ulva holobionts. Our results suggest that environmental change can affect the interaction between seaweeds and their microbes by altering the metabolites involved in their chemical exchanges.\r\nThe Data contains the Ulva metabolome profiles (.mzXML) analyzed using ZIC-HILIC chromatography coupled with HRMS (QExactive). Acquisition was conducted with the polarity switch mode and ddMS acquisition was done on the QC pool samples. The Metadata, normalization factor and results files from CD 3.3 can be found in the supplementary files.","fileCount":"263","fileSizeKB":"6431258","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ulva (NCBITaxon:3118)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Seaweed;Holobiont;Ulva;Antarctic;MALDI-MS;LCMS;ZIC-HILIC chromatography;Bacteria;Ectoine;Glycerol;Heat Stress;DatasetType:Metabolomics","pi":[{"name":"Dr. Marine Vallet","email":"mvallet@ice.mpg.de","institution":"Friedrich Schiller University Jena, Max Planck Institute for Chemical Ecology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"005ce2afdb554e4a9396f74c161a6771","id":"1158"}, {"dataset":"MSV000097251","datasetNum":"97251","title":"Danshen mzmL MASSIVE submit test","user":"manzhuo81","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741304314000","created":"Mar. 6, 2025, 3:38 PM","description":"Salvia miltiorrhiza Bunge;TCM\nDanshen POS NEG IDA; SCIEX ZenoTOF7600; \nChina,Beijing\n","fileCount":"9","fileSizeKB":"1159367","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"danshen;TCM","instrument":"ZenoTOF 7600","modification":"no","keywords":"Danshen;TCM;DatasetType:Other (TCM)","pi":[{"name":"zhuo man","email":"zhuo.man@sciex.com","institution":"sciex","country":"china"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6af844d401b44390aba373a262e8b017","id":"1159"}, {"dataset":"MSV000097249","datasetNum":"97249","title":"Mechanistic insight into the regulation of virulence factors in pathogenic E. coli by rhomboid protease GlpG","user":"srphanse","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741304272000","created":"Mar. 6, 2025, 3:37 PM","description":"With the rise in antimicrobial resistance, understanding the virulence factors utilized by pathogenic E. coli is essential for the development of alternative therapeutics. While previous work has shown that disruption of the rhomboid protease gene glpG leads to defects in bacterial colonization, here we provide mechanistic insight into the loss of fitness. We show GlpG is essential for the formation of virulence factors, namely type 1 pili, required for the colonization of eukaryotic cells. As adhesion is critical for biofilm formation and bacterial persistence, the absence of GlpG proteolytic activity also reduces the production of biofilm. Working towards new potential antimicrobial targets for treating infections, we show that biofilm formation is hampered by GlpG inhibition. Our data demonstrates that GlpG plays a key role in protein quality control of virulence factors and alters the paradigm for GlpG proteolysis, previously implicated in the cleavage of only membrane embedded substrates.","fileCount":"10","fileSizeKB":"1720449","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli K-12 (NCBITaxon:83333)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"GlpG, Rhomboid protease, FimA, UPEC, UTI, proteostasis, protein quality control;DatasetType:Proteomics","pi":[{"name":"M. Joanne Lemieux","email":"mlemieux@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9eac13582094497498976b2b8f7d5438","id":"1160"}, {"dataset":"MSV000097248","datasetNum":"97248","title":"MS-based amyloidosis typing in FFPE tissue samples ","user":"eyyub_bag","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741304159000","created":"Mar. 6, 2025, 3:35 PM","description":"Amyloidoses are characterized by the pathological deposition of non-degradable misfolded protein fibrils. Precise identification of the fibril-forming protein is crucial for prognosis and correct therapeutic intervention. Here, we present a reproduceable method for amyloid typing using relative quantification to enhance the accuracy and reliability of proteomic amyloid typing. In this study, we analyzed 62 FFPE tissue samples (+4 replicates of one tissue sample using different set-ups), using liquid chromatography-tandem mass spectrometry and employed internal normalization of iBAQ values of amyloid-related proteins relative to serum amyloid-P component (APCS) for amyloidosis typing. This method demonstrated robust performance across multiple LC-MS\/MS platforms, as well as for samples with low amounts of amyloid, and achieved complete concordance with IHC typed amyloidosis cases. More importantly, it resolved several unclear amyloid cases with inconclusive staining results. Finally, we established machine learning approach (XGBoost) achieving 94% accuracy by using ~160 amyloid-related proteins as input variables.","fileCount":"163","fileSizeKB":"51838386","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus;Q Exactive HF;LTQ Velos;timsTOF;Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\"","keywords":"Amyloidosis;Mass Spectrometry;FFPE-proteomics;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Stephan Singer","email":"stephan.singer@med.uni-tuebingen.de","institution":"Department of Pathology and Neuropathology, University Hospital Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061551","task":"2341dc2feb6c46509b56d7ec24066e30","id":"1161"}, {"dataset":"MSV000097245","datasetNum":"97245","title":"GNPS - retention time matching bile acid Molecular networking community structure","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741214241000","created":"Mar. 5, 2025, 2:37 PM","description":"Retention time matching of new bile acid found in human datasets ","fileCount":"10","fileSizeKB":"508064","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bile acid, 6-mix, retention time matching;DatasetType:Metabolomics","pi":[{"name":"Alexander Aksenov","email":"aaaksenov@health.ucsd.edu","institution":"University of California San Diego","country":"USA"},{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aa228860ad8c4dbaa31ac73cb0aae25b","id":"1162"}, {"dataset":"MSV000097244","datasetNum":"97244","title":"fdsafsdafcasdgvfagvdsf sadcfdsafdasfcdsafda","user":"KecskemetiGabor2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741205254000","created":"Mar. 5, 2025, 12:07 PM","description":"dsfadfvcacdsadcasfewqfwqsacdsafgrgsrgsergesgresgsegewa","fileCount":"8","fileSizeKB":"1611481","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sdffafvqeveavdadcas;DatasetType:Proteomics","pi":[{"name":"Kecskemeti Gabor","email":"kecskemeti.gabor8907@gmail.com","institution":"University of Szeged","country":"Magyarorszag"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"388a2332a2a846ec9fa56b9de7cd920f","id":"1163"}, {"dataset":"MSV000097243","datasetNum":"97243","title":"GNPS - Botswana Metsi Chabo Babayani 2025","user":"KenosiK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741204625000","created":"Mar. 5, 2025, 11:57 AM","description":"Non-targeted LC-MS\/MS analysis of organic matter obtained from PPL, HLB and MCX SPE extracts from water pans and flood plain pools in the Okavango Region. Babayani collected in 2020, Chabo in 2022 and Metsi in 2024. Positive and Negative mode. ","fileCount":"884","fileSizeKB":"83068045","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;Organic Matter;Botswana;Water pans;Solid Phase Extraction;DatasetType:Metabolomics","pi":[{"name":"Lihini Aluwihare","email":"laluwihare@ucsd.edu","institution":"UCSD SIO","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6bab22beba974fc7a44c6c3b90c8b099","id":"1164"}, {"dataset":"MSV000097236","datasetNum":"97236","title":"Mechanistic insight into the regulation of virulence factors in pathogenic E. coli by rhomboid protease GlpG","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741106910000","created":"Mar. 4, 2025, 8:48 AM","description":"Characterization of E. coli periplasmic proteins associated with bacterial virulence. In-gel digestion for proteomic changes in extracts (increased\/decreased abundance) after incubation with active or inactive GlpG (n=4 each) using Orbitrap Fusion Lumos. In-gel digestion of substrates for MG1655 GlpG-KO separated by SDS-PAGE incubated with inactive or active GlpG (n=6; by molecular weight) using Q Exactive.","fileCount":"21","fileSizeKB":"18217320","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Fusion Lumos;Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"GlpG;Rhomboid protease;FimA;UPEC;UTI;proteostasis;protein quality control;DatasetType:Proteomics","pi":[{"name":"M. Joanne Lemieux","email":"mlemieux@ualberta.ca","institution":"University of Alberta","country":"Canada"},{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"80ea0ea7a5ea42cab5b6fc2f3387520f","id":"1165"}, {"dataset":"MSV000097234","datasetNum":"97234","title":"Wavelength Dependence of Intact Protein Extraction Using Femtosecond Laser Ablation","user":"AAC_Wainwright","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741100707000","created":"Mar. 4, 2025, 7:05 AM","description":"Raw files for the paper named: Wavelength Dependence of Intact Protein Extraction Using Femtosecond Laser Ablation","fileCount":"19","fileSizeKB":"2327766","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Equine Myoglobin ;Lysozyme from chicken egg white;Mastigocladopsis repens rhodopsin\\t","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Myoglobin;Lysozyme;Mastigocladopsis repens rhodopsin;Top-down proteomics;Lasers;Ultrafast Lasers;DatasetType:Proteomics","pi":[{"name":"R.J. Dwayne Miller","email":"dmiller@lphys.chem.utoronto.ca","institution":"University of Toronto","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aa8b7645a7ae43e282c43a765ab7b0e5","id":"1166"}, {"dataset":"MSV000097233","datasetNum":"97233","title":"The Association of Biomolecular Resource Facilities Proteomics Standards Research Group (sPRG) 2022 Multi-Species Standard to Assist Quantitative Proteomics","user":"sprg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741100673000","created":"Mar. 4, 2025, 7:04 AM","description":"Authors:\nBenjamin A. Neely\nJosue Baeza\nMagnus Palmblad\nLindsay K. Pino\nBrian C. Searle\nSusan T. Weintraub\nStudy Participants\n\nThe Proteomics Standards Research Group (sPRG) has record of creating successful materials and standards for the proteomics community. With the increased capacity and diversity of platforms, these materials have increased in complexity from the two synthetic peptides in the 2003 standard to the 147 synthetic phosphopeptides in the 2018 standard. The new standard builds on the rationale of a multi-species mixture for benchmarking label-free quantification and is composed of three proteome digests (over 10 000 proteins per species) in different ratios, where a complete detection by current techniques is unlikely. The materials were freeze-dried human, cow, and fish standards from NIST that are available for purchase. This new sPRG material may be used for evaluating systems and quantification workflows. Human liver, cow liver, and lake trout filet were purchased from NIST (RM 8461, SRM 1577c, and SRM 1947, respectively), and 8 to 12 mg of each was digested with TPCK-treated Worthington trypsin using S-Trap midi columns (ProtiFi). Resulting peptides were mixed at different levels across three aliquots, dried down, and distributed to participants for testing. Homogeneity and stability were evaluated within the sPRG; testing of data of sPRG members demonstrated the utility of the material when employing different label-free quantification methods. Sample sets were then disseminated to interested researchers across the globe to run in their own labs, with the goal of comparing the performance of the standard across different instrumentation, quantitative acquisition approaches and data processing workflows and software. The raw data from 13 participating labs are included here where the filename pattern is \"ID_instrument_data type_sample_modifier\", where sample is A, B or C premixed samples, and the modifier can be things like short_gradient or other user given information. Suggested fasta as well as verbose directions to participants is also given (please consult this). The participant data acquisition methods, reported ratios and additional analysis will be presented in a paper currently in preparation. Preliminary results from participant-submitted data showed two general observations. The reported species ratios were generally within the expected species ratios. Additionally, post data analysis showed that some peptides used to determine species ratios were shared between species. After filtering out the shared species peptides, the new species ratios showed greater accuracy and precision. The preliminary results suggest this multi-species mixture, and the data generated from it, are suitable for comparing analysis workflows with respect to protein inference and quantitative accuracy. This sPRG standard is the first step to a commercially available standard for benchmarking label-free proteomics platforms and workflows.","fileCount":"953","fileSizeKB":"231011727","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Bos taurus (NCBITaxon:9913);Salvelinus namaycush (NCBITaxon:8040)","instrument":"timsTOF HT;Orbitrap Fusion Lumos;Orbitrap Fusion;timsTOF Pro;Q Exactive;Orbitrap Exploris 480;Q Exactive HF;Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"standards;DDA;DIA;multi-species;label-free quantification;DatasetType:Proteomics","pi":[{"name":"Benjamin Neely","email":"benjamin.neely@nist.gov","institution":"NIST","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061455","task":"b0fd815f0798467d83c37dd5ef89c7d2","id":"1167"}, {"dataset":"MSV000097232","datasetNum":"97232","title":"NEDD4L BioID - Hyperosmosis_Rotin-Raught","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741095242000","created":"Mar. 4, 2025, 5:34 AM","description":"Dataset contains LC-MS results from BioID of NEDD4L fused with miniTurbo and expressed in T-REx Flp-In HEK293 cells. Following Tet-dependent induction and addition of biotin, cells were collected, lysed in RIPA, cleared and incubated with streptavidin sepharose. Captured proteins were digested with trypsin and analyzed on an Easy nLC 1200 pump in-line with a Q Exactive HF instrument operated in ESI positive mode. Spectral count results were analyzed with SAINT by comparison with miniTurbo-only BioID samples to generate a list of proximity interactors.","fileCount":"83","fileSizeKB":"19437097","spectra":"0","psms":"775489","peptides":"59245","variants":"95814","proteins":"25647","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"NEDD4L, T-REx Flp-In HEK293, miniTurbo, BioID, LC-MS, biotin, streptavidin;DatasetType:Proteomics","pi":[{"name":"Brian Raught","email":"brian.raught@uhn.ca","institution":"Princess Margaret Cancer Centre, University Health Network","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD061451","task":"dfce8337d055496884c03d6321533039","id":"1168"}, {"dataset":"MSV000097229","datasetNum":"97229","title":"Uridine Phosphorylase-1 supports metastasis by altering immune and extracellular matrix landscapes ","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741091408000","created":"Mar. 4, 2025, 4:30 AM","description":"Understanding mechanisms that facilitate early events in metastatic seeding is key to developing therapeutic approaches to reduce metastasis. We have identified uracil as a prominent metastasis-associated metabolite in genetically engineered mouse models of cancer and in patients with metastatic breast cancer. Uracil is generated by the enzyme uridine phosphorylase-1 (UPP1), and we find that neutrophils are a significant source of UPP1 in metastatic cancer. UPP1 increases expression of adhesion molecules on the neutrophil surface, leading to decreased neutrophil motility in the pre-metastatic lung. UPP1-expressing neutrophils suppress T cell proliferation, and the UPP1 product uracil increases fibronectin deposition in the extracellular microenvironment. Consistently, knockout or inhibition of UPP1 in mice with mammary tumours increases T cell numbers and reduces fibronectin content in the lung and decreases the proportion of mice that develop lung metastasis. These data indicate that UPP1 influences neutrophil behaviour and extracellular matrix deposition in the lung and suggest that circulating uracil could be a marker of metastatic disease, and that pharmacological inhibition of UPP1 could be a strategy to reduce metastasis. ","fileCount":"848","fileSizeKB":"109194571","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fibronectin;Metastasis;Neutrophils;T cells;Uridine Phosphorylase;DatasetType:Metabolomics","pi":[{"name":"Cassie Clarke","email":"c.clarke@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Institute","country":"United Kingdom"},{"name":"David Sumpton","email":"d.sumpton@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Jim Norman","email":"j.norman@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Institute","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4e350a90e51d494399860358dc4a2453","id":"1169"}, {"dataset":"MSV000097228","datasetNum":"97228","title":"GNPS - Metabolic profile of human bone marrow hematopoietic stem and progenitor cells upon differentiation, aging and leukemia","user":"joergbuescher","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741083393000","created":"Mar. 4, 2025, 2:16 AM","description":"Metabolic cues are crucial for regulating hematopoietic stem and progenitor cells (HSPCs). However, the metabolic profile of human HSPCs remains poorly understood due to the limited number of cells and the scarcity of bone marrow samples. Here, we present the integrated metabolome, lipidome and transcriptome of human adult HSPCs (lineage-, CD34+, CD38-) upon differentiation, aging and acute myeloid leukemia (AML). The combination of low-input targeted metabolomics with our newly optimized low-input untargeted lipidomics workflow allows us to detect up to 219 metabolites and lipids from a starting material of 3,000 and 5,000 HSPCs, respectively. Among other findings, we observe elevated levels of the essential nutrient choline in HSPCs compared to downstream progenitors, which decline upon aging and further decrease in AML. Functionally, we show that choline supplementation fuels lipid production in HSPCs and enhances stemness. Overall, our study provides a comprehensive resource identifying metabolic changes that can be utilized to promote and enhance human stem cell function.","fileCount":"328","fileSizeKB":"460873059","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hematopoiesis;stem cell;leukemia;aging;DatasetType:Metabolomics;DatasetType:Other (Lipidomics, 13C label tracing)","pi":[{"name":"Joerg Buescher","email":"buescher@ie-freiburg.mpg.de","institution":"MPI Immunbiology and Epigenetics","country":"Germany"},{"name":"Nina Cabezas-Wallscheid","email":"cabezas@ie-freiburg.mpg.de","institution":"MPI Immunbiology and Epigenetics","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b989df95d313469498f50d74d35250e6","id":"1170"}, {"dataset":"MSV000097227","datasetNum":"97227","title":"GNPS - The purpose of this experiment is to investigate the chemical composition of the plant, with the plant samples collected in Hainan, China.","user":"92649264","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741080681000","created":"Mar. 4, 2025, 1:31 AM","description":"The purpose of this experiment is to investigate the chemical composition of the plant, with the plant samples collected in Hainan, China.","fileCount":"4","fileSizeKB":"23726","spectra":"997","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Piper nigrum L.","instrument":"angilent","modification":"0000398","keywords":"Alkaloid;DatasetType:Metabolomics","pi":[{"name":"shixiong wang","email":"hnwangshixiong@163.com","institution":"Guangdong Pharmaceutical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"40f9e667e47949dc904c96bba8eadea0","id":"1171"}, {"dataset":"MSV000097225","datasetNum":"97225","title":"Proteome of human glioblastoma and meningioma tissue small extracellular vesicles","user":"huaqisu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741072995000","created":"Mar. 3, 2025, 11:23 PM","description":"Small extracellular vesicles (EVs) have gained attention in the neurology field due to their role in cell-to-cell communication and their potential diagnostic and therapeutic applications. Despite progress in the field, there remains a gap in our understanding of the composition and function of EVs in brain tumours. Previous studies have primarily evaluated EVs obtained from patient fluids or cell cultures, rather than directly from the tumour tissue. \n\nHere we successfully isolated EVs from biopsies of glioblastoma (GBM) or meningioma (MNG) tumors obtained during surgery, marking the first report of in situ EV isolation from brain tumors. The protein content of the tumors and their EVs was characterized using tandem mass spectrometric proteomics, revealing proteins exclusively detected or enriched in EVs relative to tumor. While our study confirmed the presence of proteins previously identified in GBM and MNG EVs from various sources, it also identified novel proteins and pathways associated with EVs from these tumour types. This study underscores the benefit of analyzing in situ EVs direct from brain tissue for insights into tumor biology and highlights the need for further research comparing various types and grades of brain tumors. ","fileCount":"35","fileSizeKB":"29906222","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"extracellular vesicles;glioblastoma;meningioma;proteomics;exosomes;DatasetType:Proteomics","pi":[{"name":"Dr. Laura Vella","email":"laura.vella@unimelb.edu.au","institution":"The Florey Institute of Neuroscience and Mental Health","country":"Australia"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD061430","task":"2dabee7c5e0c43f5895429122b65fc4a","id":"1172"}, {"dataset":"MSV000097222","datasetNum":"97222","title":"Chemically-induced degradation of the endoplasmic-reticulum 1 stress sensor IRE1 2 by a VHL-recruiting chimera","user":"tcheung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1741051004000","created":"Mar. 3, 2025, 5:16 PM","description":"The endoplasmic-reticulum (ER) transmembrane protein IRE1 mitigates ER stress through kinase-ribonuclease (KR) and scaffolding activities. Cancer cells often co-opt IRE1 to facilitate growth. An IRE1-RNase inhibitor has entered clinical trials; however, recent work uncovered a significant nonenzymatic IRE1 dependency in cancer. To fully disrupt IRE1, we designed a proteolysis-targeting chimera (G6374) that couples an IRE1-kinase ligand to a compound that binds the ubiquitin Cullin RING Ligase (CRL) adapter VHL. G6374 induced stable interaction between IRE1 and VHL, driving VHL-dependent IRE1 K48-linked ubiquitination on two principal kinase sites and inducing proteasomal IRE1 degradation. Cryogenic electron microscopy and mutational studies revealed a 2:2 IRE1:VHL ternary-complex topology and critical interactional features, informing future designs. G6374 blocked growth of IRE1-dependent cancer cells irrespective of their dependency mode, while sparing IRE1-independent cells. We provide the first proof-of-concept for VHL-based degradation of an ER-transmembrane protein, advancing strategies to fully disrupt IRE1. ","fileCount":"45","fileSizeKB":"9571604","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\"","keywords":"IRE1;DatasetType:Proteomics","pi":[{"name":"Christopher M. Rose","email":"rose.christopher@gene.com","institution":"Genentech","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1aa403d6dc3647fb9157d230f9d7d2f6","id":"1173"}, {"dataset":"MSV000097220","datasetNum":"97220","title":"Pseudomonas fluorescens - metabolism of and response to serotonin","user":"thomenu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740566519000","created":"Feb. 26, 2025, 2:41 AM","description":"Pseudomonas fluorescens MFY63 (isolated from human) was incubated with 10 or 100 micromolar serotonin. The culture supernatants were collected after 12 or 24 hours of incubation and extracted using ethyl acetate. Negative (NEG) and positive (POS) polarity data were obtained on a HR-LC-MS\/MS setup.","fileCount":"58","fileSizeKB":"2483648","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"LCMS-9030;Shimadzu Nexera X2 UHPLC system, with attached PDA, coupled to Shimadzu 9030 QTOF mass spectrometer, standard ESI source","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"untargeted metabolomics;Serotonin;5-HT;Pseudomonas fluorescens;5-HIAA;Indole metabolite;amino acids catabolism;DatasetType:Metabolomics","pi":[{"name":"Gilles van Wezel","email":"g.wezel@biology.leidenuniv.nl","institution":"Institute of Biology, Leiden University","country":"The Netherlands"},{"name":"Sahar El Aidy","email":"s.elaidy@uva.nl","institution":"Swammerdam Institute for Life Sciences (SILS), University of Amsterdam","country":"The Netherlands"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"bf8c503b054e4714b5da88695816559b","id":"1174"}, {"dataset":"MSV000097219","datasetNum":"97219","title":"GNPS - StM16 standards mixture spiked into Pseudomonas aeruginosa extract","user":"raimofranke","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740565586000","created":"Feb. 26, 2025, 2:26 AM","description":"Preparation of PA14 extract spiked with StM16-Mix at different concentrations.\r\nA mixture of 16 compounds - 2-methoxybenzoic acid, biochanin A, trans-ferulic acid, 3-indoleacetonitrile, indole-3-carboxaldehyde, kinetin, p-coumaric acid, L-(+)-alpha-phenylglycine, phloridzin dihydrate, rutin trihydrate, indole-3-acetyl-L-valine, quercetin, naproxen, nortriptyline, trimethoprim, and novobiocin - was prepared at a concentration of 120 uM per compound in a 1:1 mixture of acetonitrile and water.\r\nThe StM16-Mix was then spiked into a Pseudomonas aeruginosa PA14 extract, prepared according to Franke et al. (mSystems, 2021), to achieve final concentrations of 10, 8, and 4 uM.\r\n\r\nLC-MS analysis. For each concentration, 1 uL of the StM16-spiked PA14 extract was analyzed by reversed phase ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry with n= 3 technical replicates. The samples were analyzed by positive mode electrospray ionization quadrupole time-of-flight mass spectrometry on a maXis HD QTOF (Bruker, Bremen, Germany) in full scan mode (50 to 1500 Da). Accurate masses were obtained by internal calibration using an ion cluster of sodium formate and lock mass calibration. The StM16-Mix was also analyzed using data-dependent MS\/MS by collision-induced dissociation of the five most abundant ions in each scan, making use of the Bruker smart exclusion algorithm.","fileCount":"22","fileSizeKB":"764997","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa UCBPP-PA14 (NCBITaxon:208963)","instrument":"maXis","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"spiked standards, Pseudomonas aeruginosa, PA14;DatasetType:Metabolomics","pi":[{"name":"Raimo Franke","email":"raimo.franke@helmholtz-hzi.de","institution":"Helmholtz Centre for Infection Research","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4205c28a3e2e483b8d9004bfc3e03232","id":"1175"}, {"dataset":"MSV000097218","datasetNum":"97218","title":"Exploration of the visual streak of the Mongolian gerbil as a model for the human central retina","user":"Dali77","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740563995000","created":"Feb. 26, 2025, 1:59 AM","description":"The Mongolian gerbil (MG), a day-active rodent, features a particular retinal region of high visual acuity, the visual streak (VS). Optimized for vision in desert-like environments, the VS allows for a particularly good view of the horizon between the projection areas of the sky and the ground. Here, we assess the structural basis of this specialized region and compare the findings to the conditions at the human retinal center. The VSs of MG retinas (n=5) were evaluated morphologically with immunohistochemistry for cone, rod, and RPE cell-specific markers in dorsoventral cross-sections, and the results were compared to data from the near (adjacent) and far periphery. Mass spectrometry of the VS and peripheral retina\/RPE was used for analysis of the proteomic differential expression between these regions. In the VS of the MG, we found an increased density of cones, elongated photoreceptor outer segments (OSs), and a rod-to-cone ratio lying within the zone of descent between the border of the macula and the fovea (macular shoulder). Likewise, the base area of retinal pigment epithelium (RPE) cells in the VS was significantly reduced, while cells were taller than those in the periphery. Accordingly, proteomic data provided evidence for an enhanced abundance of key proteins relevant for photoreceptor and RPE function and pathophysiology of macular diseases in the VS. The high degree of conformance between the VS data of the MG and the human central retina renders the MG a promising rodent, non-primate model of the central human retina","fileCount":"66","fileSizeKB":"50286448","spectra":"2363350","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Meriones unguiculatus (NCBITaxon:10047)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"DIA, LFQ, GErbil, Eye, Retina;DatasetType:Proteomics","pi":[{"name":"Mohamed Ali Jarboui","email":"mohamed-ali.jarboui@uni-tuebingen.de","institution":"core facility medical proteomics, University klinikum Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD061216","task":"053a3f845bba4e4fb903f1b069a898d6","id":"1176"}, {"dataset":"MSV000097216","datasetNum":"97216","title":"GNPS-fenziwangluo-GQD-danzhisuan-NEG","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740537143000","created":"Feb. 25, 2025, 6:32 PM","description":"rat \tUHPLC-Q-Exactive Orbitrap\/MS colon metabolism","fileCount":"4","fileSizeKB":"109696","spectra":"7467","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"rat","instrument":"UHPLC-Q-Exactive Orbitrap\\\/MS","modification":"No PTMs included in the dataset","keywords":"rat colon;DatasetType:Metabolomics","pi":[{"name":"Li Yu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1f2151ec905d4ad8a960093394a83df0","id":"1177"}, {"dataset":"MSV000097215","datasetNum":"97215","title":"coffea_arabica_analisecromatograficaoleo5","user":"jayneferreira12","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740521237000","created":"Feb. 25, 2025, 2:07 PM","description":"Chromatographic analysis of oil samples from green coffea arabica seeds.","fileCount":"12","fileSizeKB":"341063","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Coffea arabica (NCBITaxon:13443)","instrument":"GCMS-QP2010SE","modification":"no","keywords":"coffea;oil;DatasetType:Metabolomics","pi":[{"name":"Jayne Ferreira da Silva Oliveira","email":"jaynefsoliveira@gmail.com","institution":"Universidade Federal da Bahia","country":"Brasil"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6b823edd8f0d434f8243fa5eb88de687","id":"1178"}, {"dataset":"MSV000097213","datasetNum":"97213","title":"Survey of megadalton protein assemblies from Dictyostelium discoideum","user":"ghooger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740512586000","created":"Feb. 25, 2025, 11:43 AM","description":"The analysis of high-abundance megadalton protein complexes in Dictyostelium discoideum cell lysates was conducted as follows: the solubilized protein fraction was subjected to size-exclusion chromatography isolating fractions corresponding to the megadalton region, followed by ion-exchange chromatography to further resolve the protein complexes. The fractions obtained after both chromatographic steps were then analyzed using mass spectrometry to identify the constituent protein complexes, which provided the necessary data for cryo-EM.","fileCount":"25","fileSizeKB":"9396034","spectra":"0","psms":"9944","peptides":"1293","variants":"1510","proteins":"284","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Dictyostelium discoideum AX2 (NCBITaxon:366501)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\"","keywords":"mass spectrometry;Dictyostelium discoideum;cryo-EM;DatasetType:Proteomics","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD061189","task":"6d7ceb8b993c4d6181bb312bb6350cbd","id":"1179"}, {"dataset":"MSV000097212","datasetNum":"97212","title":"Wu Selective Inhibition of Matrix Mechanosensing AP-MS","user":"acaudal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740511731000","created":"Feb. 25, 2025, 11:28 AM","description":"AP-MS of primary cardiac fibroblasts (Lonza, #CC-2904), 8 samples (n = 3 replicates per group): Undiff CF, MyoFb, TGFbi, Soft, Soft+TGFbi, SAR, SAR+TGFbi, IgG. 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The detected peptide data were annotated to both human and bacterial references, and the human data showed that the profiles of cancer EVs were distinct from those of patients with benign tumors.","fileCount":"356","fileSizeKB":"221250495","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lactobacillus gasseri (NCBITaxon:1596)","instrument":"LC-MS\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bacteria, ovarian cancer, ascites, extracellular vesicles;DatasetType:Proteomics","pi":[{"name":"Akira Yokoi","email":"ayokoi@med.nagoya-u.ac.jp","institution":"Nagoya University","country":"Japan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061094","task":"7e92709349c44b5182b7b0f26673d9b3","id":"1184"}, {"dataset":"MSV000097197","datasetNum":"97197","title":"An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling-Sciex7600","user":"TomLin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740284722000","created":"Feb. 22, 2025, 8:25 PM","description":"Protein arginylation is an essential posttranslational modification (PTM) catalyzed by arginyl-tRNA-protein transferase 1 (ATE1) in mammalian systems. 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Covalent inhibitor-modified oncoproteins are presented as MHC-restricted hapten-peptides (p*MHC) on the cancer cell surface, creating an opportunity to combine targeted therapy with immunotherapy to overcome drug resistance. Building on previous indirect evidence of KRASG12C-derived p*MHCs, we used immunopeptidomics to identify and directly quantify these synthetic neoantigens. Prompted by their low copy number, we developed AETX-R114, a T cell engaging bispecific antibody with picomolar affinity for MHC-restricted sotorasib-modified KRASG12C peptides presented by three alleles belonging to the HLA-A3 supertype. AETX-R114 dramatically increases the half-life and thereby the number of presented p*MHCs, enabling selective and potent killing of resistant cancer cells in vitro and in vivo. To broaden the therapeutic potential of creating and targeting synthetic neoantigens we developed AETX-R302, which recognizes divarasib-modified KRASG12C peptides presented on alleles from the HLA-A2 and HLA-A3 supertypes. Cryo-EM structure determination revealed the molecular basis for breaking HLA supertype restriction. 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The most common form of kidney cancer, clear cell renal cell carcinoma, is frequently caused by loss of the pVHL tumor suppressor protein and the resulting upregulation of the HIF2 transcription factor. We show that PTHLH, which resides on a ccRCC amplicon on chromosome 12p, is a direct HIF2 transcriptional target in ccRCC. Further, we show that the increased PTHLH expression is both necessary and sufficient for the induction of hypercalcemia and cachexia in preclinical orthotopic cell line tumor models. Consistent with these observations, two different allosteric HIF2 inhibitors, belzutifan and NK-2152, rapidly ameliorated hypercalcemia and cachexia in ccRCC patients, including in patients who did not exhibit objective tumor shrinkage. 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Each BN-gel lane was cut into 43 fraction, proteins of each fraction digested with trypsin and peptides of each fraction each fraction was analyzed on an Q Exactive mass spectrometer. 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Proteins were extracted and digested via the SP3 protocol. Peptides were cleaned up via solid-phase extraction. All samples were measured with three different ion mobility ranges (TIMS fractionation). 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Each BN-gel lane was cut into 43 fraction, proteins of each fraction digested with trypsin and peptides of each fraction each fraction was analyzed on an Q Exactive mass spectrometer. ","fileCount":"90","fileSizeKB":"81698352","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Plant;Arabidopsis thaliana;RNA Editing;Complex I;Q Exactive;DDA;MaxQuant;DatasetType:Proteomics;Mitochondria;Multiple Organellar RNA Editing Factor 3 (MORF3);Liquid Cell Culture;Complexome Profiling","pi":[{"name":"Nils Rugen","email":"rugen@genetik.uni-hannover.de","institution":"Leibniz University Hannover","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD061041","task":"372b442b4b7042b4b58e8aeb5a39db63","id":"1195"}, {"dataset":"MSV000097173","datasetNum":"97173","title":"Hard Tissue paleometabolomics of early human sites yield metabolic and ecologic profiles - B: Proteomics Data Set","user":"hbromage","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740083656000","created":"Feb. 20, 2025, 12:34 PM","description":"The science of metabolic profiling exploits the chemical compound byproducts of biological functions called metabolites that, when analysed, not only explain internal biological functions and physiological well-being, but also provide evidence of external influences specific to the habitat in which an organism lives. \nHere, we advance a new ultra fine-scale bio molecular approach to understand the paleo environment of early human localities in eastern, central, and southern Africa using six fossil bones derived from 1.7-1.8 myr Bed I and 1.3 myr Bed II sites at Olduvai Gorge, Tanzania, one 2.4 myr sample from the Chiwondo Beds, Malawi, and one sample from the 3 myr site at Makapansgat, South Africa.","fileCount":"26","fileSizeKB":"14533289","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Dendromus (NCBITaxon:106344);Saccostomus mearnsi (NCBITaxon:1582484);Gerbilliscus gentryi;Gerbilliscus (NCBITaxon:410297);Xerus inauris (NCBITaxon:234690);Kolpochoerus majus;Elephas recki;Loxondonta africana;Bovidae (NCBITaxon:9895);Kobus ellipsiprymnus (NCBITaxon:9962)","instrument":"Q Exactive HF","modification":"Hydroxyproline;Pyroglutamine;pyroxyglutamate;MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\"","keywords":"Paleometabolome, metabolomics and ecologic profiling, fossil bone proteomics, polarized light microscope;DatasetType:Proteomics","pi":[{"name":"Dr. Thomas A. Neubert","email":"Thomas.Neubert@med.nyu.edu","institution":"New York University School of Medicine","country":"USA"},{"name":"Dr.Timothy G. Bromage","email":"tim.bromage@nyu.edu","institution":"New York University Department of Anthropology","country":"U.S.A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD061016","task":"f3c174cd9fe24d5dadc76c2868054f1d","id":"1196"}, {"dataset":"MSV000097171","datasetNum":"97171","title":"GNPS ColemanETAL2025 Data and Result Files for Silverstoneia flotator and taxonomically diverse Panamanian invertebrates","user":"jcole844","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740077915000","created":"Feb. 20, 2025, 10:58 AM","description":"mzXML files generated from metabolomic extracts of frog (Silverstoneia flotators) skins as well as taxonomically mixed samples of their dietary and leaf litter invertebrates, supplementary files from these raw files (generated using SIRIUS v5.8.6, MZmine v.3.9.0, GNPS), and feature tables with curated data from all these softwares (generated on R4.2.2) are included","fileCount":"290","fileSizeKB":"11353617","spectra":"357219","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Silverstoneia flotator (NCBITaxon:384859);Formicidae (NCBITaxon:36668);Acari (NCBITaxon:6933);Gastropoda (NCBITaxon:6448);Blattodea (NCBITaxon:85823);Isoptera (NCBITaxon:7499);Araneae (NCBITaxon:6893);Coleoptera (NCBITaxon:7041);Collembola (NCBITaxon:30001);Diptera (NCBITaxon:7147);Hemiptera (NCBITaxon:7524);Hymenoptera (NCBITaxon:7399);Lepidoptera (NCBITaxon:7088);Isopoda (NCBITaxon:29979);Diplura (NCBITaxon:29997);Myriapoda (NCBITaxon:61985);Orthoptera;Archaeognatha (NCBITaxon:29994);Opiliones (NCBITaxon:43271);Thysanoptera (NCBITaxon:30262);Schizomida (NCBITaxon:43267)","instrument":"Thermo Fisher Scientific (MA, USA) Q Exactive hybrid quadrupole-orbitrap mass spectrometer;Thermo Fisher Scientific Vanquish Horizon Duo ultra-high performance liquid chromatography (UHPLC) system with an Accucore C18 column with 150 mm length, 2.1 mm internal diameter, and 2.6 micron particle size","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dendrobatidae;Silverstoneia flotator;invertebrates from Panama;inconspicuous;frog;skin;invertebrate tissues;alkaloids;metabolomics;UHPLC-HESI-MSMS;DatasetType:Metabolomics","pi":[{"name":"Brian Sedio","email":"sediob@utexas.edu","institution":"University of Texas at Austin","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"99f20cb30d05402eb38a7c25ed20d6b5","id":"1197"}, {"dataset":"MSV000097169","datasetNum":"97169","title":"Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold","user":"Rolandoo1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740075721000","created":"Feb. 20, 2025, 10:22 AM","description":"For core peptide analysis, enzyme assays were performed using 50 uL volumes containing either copper(II) chloride (CuCl2) from JT Baker Chemical Co. or water. Assays for BURP-domain proteins comprised 300 uM GheBURP-1xQLFVWGW\/100 uM ManBURP-1xQLFFWRY, 1 mM CuCl2, and a citrate:phosphate buffer (pH 7) with final concentrations of 18 mM citrate and 165 mM Na2HPO4. The enzyme reactions were incubated for 24 h at 20 C. Subsequently, 1 ug of trypsin (Sigma-Aldrich, T7575-1KT) in 20 uL of 1 M Tris-HCl (pH 8)\/1 ug of LysC (NEB, P8109S) in 10 uL of 10 mM Tris-HCl (pH 8) buffer was added to GheBURP\/ManBURP assay, respectively, and further incubated at 37 C for 24 h. Each digest was centrifuged, added to ChromacolTM LC-MS vial, and subjected to LC-MS\/MS analysis. LC-MS\/MS settings: Injection volume 15 uL, LC - Higgins Analytical PROTO300 C4 5 um 250 x 4.6 mm, solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0.7 mL\/min, LC gradient: 0 min: 10% B, 10 min: 50% B, 11 min: 95% B, 13 min: 95% B, 13.1 min: 10% B, 20min: 10% B, MS - Positive ion mode, Full MS: Resolution 35000, mass range: 700-1250 m\/z for GheBURP digest and 700-1450 m\/z for ManBURP digest, dd-MS2: resolution 17500, AGC target 1e5, loop count 5, isolation window 0.4 m\/z, collision energy 25 eV, dynamic exclusion 2 s. Scaled enzyme assays for exoproteolytic cyclic peptide formation were conducted on a 2 mL scale using purified GheBURP-1xQLFVWGW\/ManBURP-1xQLFFWRY obtained from a 4 L\/2 L expression and purification process. These assays included 130-350 uM of the BURP domain cyclase and 1 mM CuCl2 in a citrate:phosphate buffer at pH 7. The assays were incubated for 24 h at 20 C. Following incubation, trypsin\/LysC was introduced into the GheBURP\/ManBURP reaction mixtures at a protease-substrate molar ratio of 1:250\/1:100, with the pH adjusted to 8 using a 1 M Tris-HCl (pH 8) buffer and incubated at 37 C for 24 h. Two digests were subjected to preparative HPLC, respectively (LC settings, Phenomenex Kinetex 5 um C18 100 A LC Column 150 x 21.2 mm, 7.5 mL\/min; solvent A, 0.1% TFA; solvent B, acetonitrile (0.1% TFA); LC gradient, 0 min, 10% B; 1 min, 10% B; 36 min, 50% B; 39 min, 95% B; 42 min, 95% B; 42.5 min, 10% B; 60.1 min, 10% B). HPLC fractions were analyzed by LC-MS analysis for target masses of modified core peptides with the following LC-MS parameters: injection volume 2 uL; LC, Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 50 x 3 mm LC column; LC gradient. solvent A, 0.1% formic acid; solvent B, acetonitrile (0.1% formic acid); 0 min, 5% B; 2.5 min, 95% B; 3.0 min, 95% B; 3.1 min, 5% B; 5.0 min, 5% B, 0.5 mL\/min; MS, positive ion mode; full MS, resolution 35000, mass range 400-1200 m\/z; dd-MS2, resolution 17500; loop count 5, collision energy 25 eV and dynamic exclusion 0.5 s. LC fractions containing target peptides were dried and resuspended in 30 uL DMSO for further analysis. Exopeptidase assays were conducted with approximately 25-50 ug of peptides (with 4% DMSO), carboxypeptidase Y (from S. cerevisiae, Sigma-Aldrich), and aminopeptidase N (from Rat, Sigma Aldrich) at a peptidase:peptides ratio of 1:10 (w\/w). These assays were performed in 100 mM Tris-HCl buffer at pH 7 and 37 C for 24 h. Following incubation, the assays were centrifuged and analyzed by LC-MS\/MS as follows: Injection volume 15 uL, LC - Higgins Analytical PROTO300 C4 5 um 250 x 4.6 mm, all gradients: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0.7 mL\/min, LC gradient: 0 min: 15% B, 60 min: 40% B, 61 min: 95% B, 63 min: 95% B, 63.1 min: 15% B, 80 min: 15% B, MS - Positive ion mode, Full MS: Resolution 35000, mass range: 800-1300 m\/z for GheBURP and 700-1450 m\/z for ManBURP, dd-MS2: resolution 17500, AGC target 1e5, loop count 5, isolation width 0.4 m\/z, collision energy 25 eV, dynamic exclusion 0.6 s. The analysis was compared to purified glechomanin\/mercurialin standards.","fileCount":"19","fileSizeKB":"1983718","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Glechoma hederacea (NCBITaxon:28509);Mercurialis annua (NCBITaxon:3986)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset;UNIMOD:1222 - \\\"Val->Trp substitution.\\\";UNIMOD:1102 - \\\"Phe->Trp substitution.\\\"","keywords":"Burpitide;Burpitide cyclase;BURP domain protein;Plant RiPP biosynthesis;DatasetType:Proteomics","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan, Ann Arbor","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"811455e7894e47659396e322f5a0e5f4","id":"1198"}, {"dataset":"MSV000097168","datasetNum":"97168","title":"BioPlex Human AP-MS Dataset: U2OS Cells","user":"EdHuttlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1740068292000","created":"Feb. 20, 2025, 8:18 AM","description":"RAW Files from the BioPlex project profiling protein-protein interactions for specific human bait proteins in U2OS cells. 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The abstract is as follows: The advent of large molecule therapeutics has revolutionized treatment options for previously unmet medical needs. This advent has also led to an increased impact of immunogenicity on drug efficacy and safety. In order to maximize the potential of large molecule therapeutics, immunogenicity-related liabilities must be identified as early in development as possible, using an integrated risk assessment that takes into account the various cell types and processes involved. Here, we describe the development of an ex vivo B-cell immunogenicity assay, to capture a key component of the immune response that has been missing from previously published ex vivo immunogenicity assays. Plasmablasts\/plasma cells were preferentially expanded in this assay, a subset of which were drug-specific and presented drug-specific peptides on MHC Class II. 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Polar C18 column attached to Qexactive.","fileCount":"545","fileSizeKB":"11962902","spectra":"448543","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mouse;fecal;infant;mother;DatasetType:Metabolomics","pi":[{"name":"Shirley M. Tsunoda","email":"smtsunoda@ucsd.edu","institution":"University of California San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"82947523d63e4ceebb6cbd622cb5651f","id":"1216"}, {"dataset":"MSV000097136","datasetNum":"97136","title":"GNPS - Automated mass spectrometry-based profiling of multi-glycosylated glycosyl inositol phospho ceramides (GIPC) in barley","user":"marlene_5454","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739798655000","created":"Feb. 17, 2025, 5:24 AM","description":"LC-HRMS based profiling of glycosyl inositol phospho ceramides (GIPC) in barley at different development stages and after heat-stress application.","fileCount":"32","fileSizeKB":"6341730","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hordeum vulgare (NCBITaxon:4513)","instrument":"Orbitrap IQ-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-HRMS;barley;Hordeum vulgare;GIPC;glycosphingolipids;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Marlene Puehringer","email":"marlene.puehringer@univie.ac.at","institution":"University of Vienna","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d06c86fe4d094890a41bcf8423d752b9","id":"1217"}, {"dataset":"MSV000097135","datasetNum":"97135","title":"Coupled transcriptome and proteome analysis of the L3 and L4 developmental stages of Anisakis simplex s.s.: Insights into target genes under glucose influence","user":"robertstr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739782505000","created":"Feb. 17, 2025, 12:55 AM","description":"According to the European Food Safety Authority (EFSA), A. simplex has been classified as a biohazardous organism. Most developmental stages of parasitic nematodes occur under anaerobic conditions, and larvae obtain most of their energy from saccharides. The effect of glucose from the external environment has not been described in L3 and L4 larvae of A. simplex. Another advantage is that only these stages have been identified as pathogenic in humans. In this study, we aimed to uncover genes and pathways controlling glucose (10 mg\/mL) action by an integrated analysis of the transcriptome and proteome of L3 and L4 larval stages of A. simplex. The proteome results yielded a total of 6,441 proteins that were filtered for further analysis. The final repository consists of 464 proteins, which were identified in a group as up-regulated DEPs, e.g., malate dehydrogenase, and down-regulated DEPs, e.g., methylmalonyl-CoA epimerase. The results obtained should lead to a better understanding of the molecular processes underlying the development of A. simplex infection in humans and will add to the existing knowledge on the role of nutrients of this parasite.","fileCount":"17","fileSizeKB":"7213233","spectra":"285672","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Anisakis simplex (NCBITaxon:6269)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Anisakis simplex;glucose uptake;proteomics;DatasetType:Proteomics","pi":[{"name":"Robert Stryinski ","email":"robert.stryinski@uwm.edu.pl","institution":"University of Warmia and Mazury in Olsztyn","country":"Poland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b7898dfe12654683a45b4bceb029dfbd","id":"1218"}, {"dataset":"MSV000097132","datasetNum":"97132","title":"GNPS_mapp_project_00007_mapp_batch_00020_and_00059","user":"pmallard","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739724100000","created":"Feb. 16, 2025, 8:41 AM","description":"An untargeted metabolomics dataset of nodules of Sinorhizobium meliloti in Medicago truncatula. For the publiction \"Medicago truncatula inhibits cheating rhizobial endosymbionts with a multilayered sanctioning syndrome involving induction of defense and repression of symbiotic services.\" (Chen et al. 2025) Positive and negative ionisation mode.","fileCount":"215","fileSizeKB":"8056552","spectra":"231299","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Medicago truncatula (NCBITaxon:3880);Sinorhizobium meliloti (NCBITaxon:382)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Medicago truncatula;Sinorhizobium meliloti;nodules;DatasetType:Metabolomics","pi":[{"name":"Didier Reinhardt","email":"didier.reinhardt@unifr.ch","institution":"University of Fribourg","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aeeb0476e79c4f218698b57bcf4b79cd","id":"1219"}, {"dataset":"MSV000097131","datasetNum":"97131","title":"GNPS - Bile extracts from 75 animals","user":"ipmohanty","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739723037000","created":"Feb. 16, 2025, 8:23 AM","description":"This dataset consists of data collected in positive ionization mode profiling bile extracts from 75 different animal species. MS\/MS data acquisition was carried out on a Thermo Q Exactive mass spectrometer in positive ionization mode, with chromatographic separation achieved using a Phenomenex Polar C18 column.","fileCount":"448","fileSizeKB":"44701363","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"animalia","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acids;Bile extract;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"fe43c1fdb0c0416382bfb6929774d2d7","id":"1220"}, {"dataset":"MSV000097130","datasetNum":"97130","title":"1. Mitochondrial Protein Identification; 2. Redox Proteomics Identification; 3. Quantitative Cellular Proteomics","user":"luxin722","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739722045000","created":"Feb. 16, 2025, 8:07 AM","description":"1. Quantitative Proteomic Analysis of Isolated Mitochondria. Each group has three replicates: Glc group: Glucose starvation group.\nGlcFH group: FH activity inhibition combined with glucose starvation group.\n2. Quantitative proteomics analysis was performed to assess intracellular protein disulfide bond levels. The experiment included the following groups, each with three replicates:UOK group: UOK262 cells under glucose starvation; UOKFH group: UOK262 cells overexpressing FH under glucose starvation. V786O group: 786-O cells under glucose starvation; XCT786O group: 786-O cells overexpressing XCT under glucose starvation.\n3. Quantitative Proteomics Analysis of Cellular Protein Expression Differences, Each group has three replicates: Glcn group: glucose starvation group. Glcp group: glucose sufficiency group\n","fileCount":"5","fileSizeKB":"5893734","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human;1. Human; 2. Human; 3. Human","instrument":"1. Orbitrap melting fluorescence coupled to an EASY nanoLC 1200 system (Thermo Fisher Scientific, MA, USA); 2.Orbitrap Astral mass spectrometer coupled with a Vanquish Neo UHPLC system (Thermo Fisher Scientific); 3. Tandem EASY-nanoLC1200 with Orbitrap Fusion Lumos (Thermo Fisher Scientific, MA, USA)","modification":"NO","keywords":"Mitochondrial, Redox, Quantitative, Cellular, Proteomics, Disulfide Stress;DatasetType:Proteomics","pi":[{"name":"Guowang Xu","email":"xugw@dicp.ac.cn","institution":"DICP","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc159f9b2ea34b15bbbdaeac2aa7c756","id":"1221"}, {"dataset":"MSV000097127","datasetNum":"97127","title":"GNPS-A series of eremophilane sesquiterpenoids were isolated from the marine-derived fungus Phoma sp. DXH009.","user":"Vivi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739611366000","created":"Feb. 15, 2025, 1:22 AM","description":"Four new eremophilane sesquiterpenoids, together with five known analogues, were isolated from the marine-derived fungus Phoma sp. DXH009.","fileCount":"19","fileSizeKB":"81341","spectra":"10519","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phoma sp. ","instrument":"HPLC HRESIMS","modification":"NO","keywords":"DXH009;eremophilane;DatasetType:Other (natural compounds)","pi":[{"name":"mengweinQin","email":"1014296214@qq.com","institution":"Hainan university","country":"CHINA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f55bf235fb8a43cd929a51082ce19e53","id":"1222"}, {"dataset":"MSV000097126","datasetNum":"97126","title":"Lipidome data of environmental samples","user":"zff9900","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739599042000","created":"Feb. 14, 2025, 9:57 PM","description":"This study examined archaeal lipidome of a total of 52 sediment and soil samples across a wide range of environmental gradients, including sediment from hot springs in Tengchong, Yunan Province, sediment from acid mine drainages in Anhui and Guangdong provinces, permafrost soil from Tibet Plateau, soil from Western Sichuan Plateau, surface sediment of cold seeps and sediment core material from the South China Sea, and sediment from the East China Sea.","fileCount":"115","fileSizeKB":"24250460","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Waters SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"environmental samples;lipidome;archaea;hotspring;soils;marine sediment;DatasetType:Other (Lipidomics)","pi":[{"name":"Chuanlun Zhang","email":"zhangcl@sustech.edu.cn","institution":"Southern University of Science and Technology","country":"China"},{"name":"Fengfeng Zheng","email":"zff9900@163.com","institution":"Southern University of Science and Technology","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1b533b61395542c88bc7a2f24c44d677","id":"1223"}, {"dataset":"MSV000097125","datasetNum":"97125","title":"Lipidome data of two wildtype pure cultures and two mutant strains of archaea","user":"zff9900","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739589520000","created":"Feb. 14, 2025, 7:18 PM","description":"The lipidome of two wildtype pure cultures and two mutant strains of archaea were examined in this study, which included Nitrosopumilus maritimus strain SCM1, a Haloferax larsenii (JCM 13917), a Methanococcus maripaludis mutant strain (pMEV4-ma_1486) and a mutant strain of Sulfolobus acidocaldarius (p1561-grsB-grsA). The lipids were analyzed using a Waters SYNAPT G2-Si quadrupole time-of-flight mass spectrometer (qTOF) coupled to an electrospray ionization (ESI) source operated at positive ion mode.","fileCount":"31","fileSizeKB":"4527398","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Archaea (NCBITaxon:2157)","instrument":"Waters SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"archaeal lipidome;GDGTs;spectral library;ArchLipid;pure cultures;DatasetType:Other (Lipidomics)","pi":[{"name":"Chuanlun Zhang","email":"zhangcl@sustech.edu.cn","institution":"Southern University of Science and Technology","country":"China"},{"name":"Fengfeng Zheng","email":"zff9900@163.com","institution":"Southern University of Science and Technology","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e1b7c2716cd441dca03c0945e2b97415","id":"1224"}, {"dataset":"MSV000097124","datasetNum":"97124","title":"Discovery of mammalian collagens I and III within ancient poriferan biopolymer 2 spongin","user":"miksik","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739572811000","created":"Feb. 14, 2025, 2:40 PM","description":"Discovery of mammalian collagens I and III 1 within ancient poriferan biopolymer 2 spongin","fileCount":"14","fileSizeKB":"1738174","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sponges (Porifera)","instrument":"maXis","modification":"proline hydroxylation;lysine hydroxylation;UNIMOD:7 - \\\"Deamidation.\\\";methionine oxidation","keywords":"spongin;collagen;DatasetType:Proteomics","pi":[{"name":"Ivan Miksik","email":"imiksik@seznam.cz","institution":"University of Pardubice","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060839","task":"6846e72ccca54a79bd78f8db1a971bfc","id":"1225"}, {"dataset":"MSV000097121","datasetNum":"97121","title":"Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein","user":"FHproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739560826000","created":"Feb. 14, 2025, 11:20 AM","description":"Saccharomyces cerevisiae kinetochores were isolated from a NUF2-3V5 background via Dsn1-His-Flag purifications. (AAL020924_02154_SBY23028) and (AAL020924_021524_SBY23066) were grown at 30 C and harvested once cell cultures reached OD600nm = ~3. Cells were resuspended in Buffer H (25mM HEPES pH8.0, 2mM MgCl2 , 0.1 mM EDTA pH 8.0, 0.5 mM EGTA-KOH pH8.0, 15% Glycerol, 0.1% NP-40, and 150 mM KCl) containing phosphatase inhibitors (1 mM sodium-pyrophosphate, 2 mM sodium-beta-glycerophosphate, 0.1 mM sodium orthovanadate, and 5 mM NaF), 0.1 mM microcystin-LR, 0.2 mM PMSF, and protease inhibitors (10 mg\/mL for each of the following leupeptin, pepstatin A, and chymostatin). In which cells were spun down and flash frozen in liquid nitrogen. Pellets were lysed via Freezer Mill (SPEX SamplePrep) and treated with 50 units\/ml of benzonase (EMD Milipore Corp) for 30 minutes on ice. Lysate proteins were extracted after undergoing ultracentrifugation at 24,000 RPM for 90 minutes at 4 °C. The Pierce BCA Protein Assay Kit (Thermo Scientific) was used to measure the protein concentration within each extract which were subsequently normalized. Extracts were incubated with a-M3DK (GenScript) magnetic Protein G Dynabeads (Invitrogen) for 3 hours at 4 °C with rotation. Beads were washed three times with BH0.15 containing phosphatase inhibitors, protease inhibitors, 0.1 mM microcystin-LR, and 2 mM DTT. Then two times with BH0.15 containing protease inhibitors and LPC. Then rinsed two times with pre-elution rinse buffer (50 mM Tris pH 8.3, 75 mM KCl, and 1 mM EGTA). Purified kinetochores were eluted from beads into 70 ml of 0.2% RapiGest (Waters Corporation) in 50 mM ammonium bicarbonate. This was achieved via gentle agitation on a Vortex-Genie 2 (Scientific Industries) set to the lowest setting for 30 minutes at room temperature. 60 ml of each elution sample was sent for mass spectrometry processing.","fileCount":"14","fileSizeKB":"10739131","spectra":"298686","psms":"17038","peptides":"6421","variants":"9380","proteins":"1417","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae W303 (NCBITaxon:580240)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Saccharomyces cerevisiae;kinetochores;phosphorylation;DatasetType:Proteomics","pi":[{"name":"Susan Biggins","email":"sbiggins@fredhutch.org","institution":"Fred Hutchinson Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060835","task":"7682b7fab7164fa1b70d2682f1c596e4","id":"1226"}, {"dataset":"MSV000097120","datasetNum":"97120","title":"The immune NIK1 RPL10 LIMYB signaling module regulates photosynthesis and translation under biotic and abiotic stresses","user":"patricksn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739557663000","created":"Feb. 14, 2025, 10:27 AM","description":"Photosynthesis and translation are targets of metabolic control and development in plants, yet how stress signals coordinately regulate these opposing energy-producing and consuming processes remains enigmatic. Here, we described a growth control circuit that ties the photosynthetic function to translational control in response to biotic and abiotic signals. We showed first that the downstream component of the NIK1\/RPL10 antiviral signaling module, LIMYB, which represses translation-related genes and translation, also suppresses photosynthesis-related genes and photosynthesis. LIMYB repressing activity was the primary determinant for the decrease in the photosynthetic function in the LIMYB-overexpressing lines, which was linked to the NIK1 antiviral signaling and stunted growth. NIK1 activation by viral or bacterial PAMPs, or expressing a constitutively activated NIK1 mutant, T474D, repressed the photosynthesis-related genes and photosynthesis in control lines but not in lymyb.\n","fileCount":"17789","fileSizeKB":"266694338","spectra":"396647","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"nanoACQUITY UPLC","modification":"UNIMOD:903 - \\\"Lys->Cys substitution and carbamidomethylation.\\\"","keywords":"Photosynthesis, biotic and abiotic stress, translational control, Arabidopsis, LIMYB, NIK1;DatasetType:Proteomics","pi":[{"name":"Elizabeth Pacheco Batista Fontes ","email":"bbfontes@ufv.br","institution":"University Federal of Vicosa - UFV","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060833","task":"1720848d46cf4cf0aba6fac809df5daa","id":"1227"}, {"dataset":"MSV000097115","datasetNum":"97115","title":"Hypertrophic Cardiomyopathy-Associated CRYABR123W Activates Calcineurin, Reduces Calcium Sequestration, Alters the CRYAB Interactome and the Proteomic Response to Pathological Hypertrophy","user":"athorkelsson","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739544578000","created":"Feb. 14, 2025, 6:49 AM","description":"Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular condition in the world affecting around 1:500 people. HCM is characterized by ventricular wall thickening, decreased ventricular chamber volume and diastolic dysfunction. Inherited HCM is most commonly caused by sarcomere gene mutations, however approximately 50% of patients do not present with a known mutation highlighting the need for further research into additional pathologic mutations. CRYABR123W was previously identified as a novel sarcomere-independent mutation causing HCM associated with pathologic NFAT signaling in the setting of pressure overload. We generated stable H9C2 cell lines expressing FLAG tagged wild type and mutant CRYAB, which demonstrated that CRYABR123W has increased calcineurin activity. Using Alphafold to predict structural and interaction changes we generated a model where CRYABR123W uniquely binds to the autoinhibitory domain of calcineurin. Co-immunoprecipitation using the CRYAB FLAG tag fol-lowed by mass spectrometry showed novel and distinct changes in the protein interaction patterns of CRYABR123W. Finally, mouse hearts extracted from our wild type and CRYABR123W model with and without pressure overload caused by transverse aortic constriction (TAC) were used in global proteomic and phosphoproteomic mass spectrometry analysis which showed dysregulation in cytoskeletal, metabolomic, cardiac and immune function. 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The molecular mechanism underlying Dnajb11-related kidney disease involves an impairment in the processing of Polycystin-1, which is the protein most often mutated in Autosomal Dominant Polycystic Kidney Disease (ADPKD). Whether additional co-factors are necessary for DNAJB11-dependent PC-1 processing has so far remained unclear.\nIn this study, we perform an unbiased interaction proteomics screen for DNAJB11 interacting proteins. We identify two highly homologous proteins, SDF2 and SDF2L1, as strong interaction partners of DNAJB11. Using newly established knockout cell lines we demonstrate a profound interdependence of DNAJB11 and SDF2\/SDF2L1. Furthermore, we show that concomitant loss of SDF2 and SDF2L1 impairs PC-1 processing and that SDF2 or SDF2L1 are elementary subunits of the DNAJB11 complex required for normal PC-1 processing.\n","fileCount":"22","fileSizeKB":"6448290","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DNAJB11;DatasetType:Proteomics","pi":[{"name":"Prof. Dr. Michael Koettgen","email":"michael.koettgen@uniklinik-freiburg.de","institution":"University Medical Center Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060623","task":"b6addb729f344721861a4c98e9953e62","id":"1244"}, {"dataset":"MSV000097085","datasetNum":"97085","title":"Nunziata Maio_Tracey Rouault_8LFQ_nsp14","user":"psfuserdata","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739133890000","created":"Feb. 9, 2025, 12:44 PM","description":"Mass spectrometry-based label-free quantitation analysis to identify interacting partners of the SARS-CoV-2 helicase, nsp14.","fileCount":"28","fileSizeKB":"26194784","spectra":"0","psms":"27344","peptides":"4955","variants":"5604","proteins":"952","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00483 - \\\"A protein modification that is produced by reaction with N-ethylmaleimide.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Label free quantitation;Mass Spectrometry;DatasetType:Proteomics","pi":[{"name":"Tracey Rouault","email":"rouault@mail.nih.gov","institution":"Institute: National Institute of Child Health and Human Development, National Institutes of Health","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060605","task":"d845210ce8184b1a80699e4b1421763a","id":"1245"}, {"dataset":"MSV000097081","datasetNum":"97081","title":"Integrative analysis of proteome and O glycoproteome mediated by OGT in high glucose induced podocyte","user":"songwenze","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739029016000","created":"Feb. 8, 2025, 7:36 AM","description":"Diabetic kidney disease, a major microvascular complication of diabetes, is the primary cause of end-stage renal disease globally 1. Current treatments mainly target glycemic, blood pressure, and lipid control but often fail to prevent renal impairment. Early DKD is characterized by tubular damage, glomerular hypertrophy, thickening of the glomerular basement membrane, and loss of podocytes. Podocyte damage and loss are potentially significant in the pathogenesis of DKD. Hyperglycemia, a critical factor in podocyte injury, can contribute to the progression of DKD. Therefore, mitigating podocyte injury may be a crucial factor in the future management and alleviation of DKD. Chronic hyperglycemia leads to podocyte dysfunction through inflammation, oxidative stress, autophagy, and apoptosis. As is well known, the non-enzymatic glycation of proteins, leading to the formation of advanced glycation end-products (AGEs), constitutes a significant contributing factor to DKD. Notably, recent studies underscore the crucial role of O-linked-N-acetylglucosamine (O-GlcNAc) modification (also known as O-GlcNAcylation) in DKD progression. The hexosamine biosynthesis pathway (HBP) converts glucose to UDP-N -acetylglucosamine (UDP-GlcNAc), a substrate for O-GlcNAcylation, which is catalyzed by O-GlcNAc transferase (OGT) and removed by O-GlcNAcase (OGA). Aberrant O-GlcNAcylation is linked to renal fibrosis, inflammation, and apoptosis, which worsen diabetic kidney function. Elevated levels of O-GlcNAcylation have been observed in renal tissues of diabetic patients, indicating a potential link between hyperglycemia and dysregulated O-GlcNAc signaling. However, the exact molecular mechanisms of O-GlcNAcylation in DKD are not well understood. This study explores the changes in protein and glycosylated protein in podocytes after OGT knockdown to learn the molecular mechanisms of podocyte injury induced by high glucose (HG). A total of 128 up-regulated proteins and 45 down-regulated proteins in OGT knockdown group than in the control group were identified. Furthermore, 55 significantly changed glycosylation modification sites on 43 proteins were identified. To the best of our knowledge, this is the first study to conduct a global analysis of O-GlcNAcylation in podocytes.","fileCount":"15","fileSizeKB":"105850950","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"UNIMOD:934 - \\\"Photocleavable Biotin + GalNAz on O-GlcNAc.\\\"","keywords":"O-glycoproteome;OGT;proteome;podocytes;diabetic kidney disease;DatasetType:Proteomics","pi":[{"name":"Jiao Wang","email":"wangjiao@ncu.edu.cn","institution":"The First Affiliated Hospital of Nanchang University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060596","task":"7312c2e171aa48bb865b65888936e3ce","id":"1246"}, {"dataset":"MSV000097080","datasetNum":"97080","title":"Proteogenomic and expression profiling of virulent and attenuated Gallid alphaherpesvirus 1 ","user":"jvolkening","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1739014745000","created":"Feb. 8, 2025, 3:39 AM","description":"Virulent (1874C5) and attenuated (vaccine strain LaryngoVac) strains of infectious laryngotracheitis virus (ILTV) were characterized in vivo for transcript expression via short-read mRNA-Seq and in vitro for transcript and protein expression using full-length cDNA sequencing and high-resolution LC-MS\/MS.","fileCount":"48","fileSizeKB":"31639061","spectra":"0","psms":"722790","peptides":"175983","variants":"232392","proteins":"28827","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gallus gallus (NCBITaxon:9031)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"ILTV;GaHV-1;infectious laryngotracheitis virus;Gallid alphaherpesvirus 1;proteogenomics;DatasetType:Proteomics","pi":[{"name":"Stephen J. Spatz","email":"stephen.spatz@usda.gov","institution":"US National Poultry Research Center, USDA-ARS","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060595","task":"0cb45b9bb8ba419c9f551b176f125d57","id":"1247"}, {"dataset":"MSV000097079","datasetNum":"97079","title":"Ryanodine receptor 1 protein complex from WT, Ryr1Y524S\/+, and Ryr1 S2902D mice","user":"syjung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738963560000","created":"Feb. 7, 2025, 1:26 PM","description":"RYR1 was immunoprecipitated (IP) from the gastrocnemius muscles of WT S2902D HET, S2902D HOM, YS, and YS\/S2902D mice.","fileCount":"266","fileSizeKB":"157189001","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Ryanodine receptor 1;DatasetType:Proteomics","pi":[{"name":"Sung Jung","email":"syjung@bcm.edu","institution":"Baylor College of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060589","task":"8aff256bffa34d188e9e67a2382b26a6","id":"1248"}, {"dataset":"MSV000097078","datasetNum":"97078","title":"GNPS Maculalactone BGC transformed in Ecoli","user":"vuka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738958443000","created":"Feb. 7, 2025, 12:00 PM","description":"This dataset includes samples of the Maculalctone biosynthetic gene cluster (mac BGC) captured in Nodularia sp. NIES-3585 and heterologously expressed in E. coli.\nTotal = complete BGC\nCDEF = minimal BGC\nEmpty vector = control","fileCount":"7","fileSizeKB":"4274144","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nodularia sp. NIES-3585 (NCBITaxon:1973477)","instrument":"impact II","modification":"NA","keywords":"cyanobacteria, furanolides, heterologous expression, E.coli;DatasetType:Metabolomics","pi":[{"name":"Tobias A.M. Gulder","email":"tobias.gulder@tu-dresden.de","institution":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Natural Product Biotechnology, Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University, 66123, Saarbrucken, Germany","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f05c9193276344ada459c2c2e4ab26a0","id":"1249"}, {"dataset":"MSV000097077","datasetNum":"97077","title":"EGFR inhibitor-resistant lung cancers exhibit collateral sensitivity to a covalent, cysteine-independentKEAP1 oligomerizing molecular bridge","user":"hbc8","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738950967000","created":"Feb. 7, 2025, 9:56 AM","description":"Targeted therapies have revolutionized cancer care. Unfortunately, most patients develop refractory, multifocal resistance to these therapies within a matter of months. Here, we demonstrate that the evolution of resistance to EGFR inhibitors in EGFR-mutant non-small cell lung cancer endows cells with hypersensitivity to a small molecule compound, MCB-613. Systematic proteomic, functional genomic, and biochemical studies revealed that MCB-613 binds KEAP1 in a covalent, cysteine-independent fashion, acting as a divalent molecular bridge that relies upon lysine residues in the KEAP1 dimerization domain to join monomers of KEAP1 together. Oligomerization of KEAP1 by MCB-613 sets into motion a fatal cascade of KEAP1 dysfunction, ROS accumulation, and ATF4\/CHOP-dependent cell death. Together, these findings demonstrate that diverse models of EGFR inhibitor-resistant NSCLC share the common feature of elevated integrated stress response activity, and that a covalent molecular bridge which activates non-canonical KEAP1-ATF4 signaling can exploit this feature to select against resistance evolution.","fileCount":"7","fileSizeKB":"2190163","spectra":"0","psms":"18549","peptides":"8826","variants":"13020","proteins":"3913","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"DBIA;DatasetType:Proteomics","pi":[{"name":"Kris Wood","email":"kris.wood@duke.edu","institution":"Duke University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060588","task":"175ddadd3cdf45799fd6e210fc3b27bc","id":"1250"}, {"dataset":"MSV000097075","datasetNum":"97075","title":"A conserved germline-specific Dsn1 alternative splice isoform supports oocyte and embryo development","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738950031000","created":"Feb. 7, 2025, 9:40 AM","description":"Alternative RNA splicing can generate distinct protein isoforms to allow for the differential control of cell processes across cell types. The chromosome segregation and cell division programs associated with somatic mitosis and germline meiosis display dramatic differences such as kinetochore orientation, cohesin removal, or the presence of a gap phase. These changes in chromosome segregation require alterations to the established cell division machinery. However, it remains unclear what aspects of kinetochore function and its regulatory control differ between the mitotic and meiotic cell divisions to rewire these core processes. Additionally, the alternative splice isoforms that differentially modulate distinct cell division programs have remained elusive. Here, we demonstrate that mammalian germ cells express an alternative mRNA splice isoform for the kinetochore component, DSN1, a subunit of the MIS12 complex that links the centromeres to spindle microtubules during chromosome segregation. This germline DSN1 isoform bypasses the requirement for Aurora kinase phosphorylation for its centromere localization due to the absence of a key regulatory region allowing DSN1 to display persistent centromere localization. Expression of the germline DSN1 isoform in somatic cells results in constitutive kinetochore localization, chromosome segregation errors, and growth defects, providing an explanation for its tight cell type-specific expression. Reciprocally, precisely eliminating expression of the germline-specific DSN1 splice isoform in mouse models disrupts oocyte maturation and early embryonic divisions coupled with a reduction in fertility. Together, this work identifies a germline-specific splice isoform for a chromosome segregation component and implicates its role in mammalian fertility.","fileCount":"45","fileSizeKB":"31613154","spectra":"452158","psms":"60850","peptides":"19386","variants":"22252","proteins":"3237","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MOD:01720 - \\\"A protein modification that effectively replaces a hydrogen atom of a residue with the Proteome Sciences TMT6plex-126 reporter+balance group.\\\"","keywords":"Kinetochore;Splicing;Meiosis;Mitosis;DatasetType:Proteomics","pi":[{"name":"Iain Cheeseman","email":"icheese@wi.mit.edu","institution":"Whitehead Institute and MIT","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054119","task":"b9a8165b69f64e4788781b90627d536a","id":"1251"}, {"dataset":"MSV000097074","datasetNum":"97074","title":"GNPS - LC-HRESI-MS\/MS data of lusichelins A-E","user":"mariana","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738930760000","created":"Feb. 7, 2025, 4:19 AM","description":"LC-HRESI-MS\/MS data of lusichelins A-E isolated from the cyanobacterium Lusitaniella coriacea LEGE 07167","fileCount":"16","fileSizeKB":"1456412","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lusitaniella coriacea LEGE 07167 ","instrument":"Q Exactive Focus Hybrid Quadrupole-Orbitrap","modification":"none","keywords":"cyanobacteria;DatasetType:Metabolomics","pi":[{"name":"Mariana Alves Reis","email":"mreis@ciimar.up.pt","institution":"CIIMAR","country":"Portugal"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0c6a6bb7e6c04b778a581c926e5a47ba","id":"1252"}, {"dataset":"MSV000097068","datasetNum":"97068","title":"GNPS - Raw MassSpec Data for TopDown Analysis of CALR Arginylation (SI)","user":"rsearfoss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738903389000","created":"Feb. 6, 2025, 8:43 PM","description":"Raw files of data used for Supplemental figures and tables in manuscript \"Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation\".","fileCount":"48","fileSizeKB":"8395500","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"Arginylation","keywords":"TopDown;CALR;Arginylation;UVPD;ETD;DatasetType:Proteomics","pi":[{"name":"Benjamin A. Garcia","email":"bagarcia@wustl.edu","institution":"Washington University School of Medicine in Saint Louis","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"51155ef25c074bcdbc383db7af4470b3","id":"1253"}, {"dataset":"MSV000097067","datasetNum":"97067","title":"Raw MassSpec Data for TopDown Analysis of CALR Arginylation (Main)","user":"rsearfoss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738902360000","created":"Feb. 6, 2025, 8:26 PM","description":"Raw files of data used for main figures in manuscript \"Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation\".","fileCount":"69","fileSizeKB":"2080926","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ZenoTOF 7600","modification":"Arginylation","keywords":"TopDown;CALR;EAD;Arginylation;DatasetType:Proteomics","pi":[{"name":"Benjamin A. Garcia","email":"bagarcia@wustl.edu","institution":"Washington University School of Medicine in Saint Louis","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a1c5e3fc3eb2447d9519436791794a1d","id":"1254"}, {"dataset":"MSV000097065","datasetNum":"97065","title":"Progressive Changes in Human Follicular Fluid Composition over the Course of Ovulation: Quantitative Proteomic Analyses.","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738886984000","created":"Feb. 6, 2025, 4:09 PM","description":"The composition of follicular fluid reflects crucial paracrine signalling between granulosa- and theca cells and the oocyte. Dynamic changes in the protein composition of human follicular fluid across multiple time points in the period where final meiotic maturation and release of the oocyte take place are previously undescribed. Twenty-five women undergoing IVF- or ICSI treatment in a standard antagonist protocol with agonist ovulation trigger were included in this prospective cohort study. From each patient one follicle was aspirated by transvaginal ultrasound guided puncture at one of five specific time points either before ovulation induction (T=0) or 12-, 17-, 32- or 36 hours after ovulation induction (five patients\/time point). Proteomics was carried out by liquid chromatography-mass spectrometry. In total, 400 proteins were identified (FDR<0.05) and 30 were significantly regulated across time points (one-way ANOVA, adjusted p<0.05). Compared to compiled human plasma proteome sets, 47 proteins were unique to follicular fluid. Enriched biological functions among differentially expressed proteins included immune functions, wound healing and functions related to blood coagulation (FDR<0.02). The most profound changes occurred shortly after ovulation induction. We confirmed parallel protein expression to known granulosa cell mRNA changes and described many hitherto unknown protein expression profiles during ovulation. Thus, the study endorsed important biological functions of some proteins and suggested additional proteins, which may be crucial to intrafollicular signalling and oocyte competence that should be further investigated.","fileCount":"53","fileSizeKB":"97024846","spectra":"1868504","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Ovulation;Human;Oocyte maturation;Follicular fluid;Proteome;DatasetType:Proteomics","pi":[{"name":"Johan Malm","email":"johan.malm@med.lu.se","institution":"Deputy head of department at Department of Translational Medicine. Lund University. Principal investigator at CEBMMS PI. Professor at Clinical Chemistry, Malm\uFFFD Professor at Clinical Protein Science and Imaging Professor at Department of Clinical Sciences, Lund","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD012561","task":"675b43eb8b0541eea6c9163cb8b4cb70","id":"1255"}, {"dataset":"MSV000097063","datasetNum":"97063","title":"Proteomic profile of endothelial cells exposed to plasma from preeclamptic pregnant women","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738870541000","created":"Feb. 6, 2025, 11:35 AM","description":"Preeclampsia (PE) is a multifactorial disease with a complex pathophysiology and no specific treatment currently available. The release of harmful factors into maternal circulation and endothelial dysfunction play a key role in the development of preeclampsia. This study aims to identify altered proteins in endothelial cells exposed to the plasma of pregnant women with early and late onset PE comparing them with cells exposed to plasma from healthy pregnant women.","fileCount":"19","fileSizeKB":"11446299","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Preeclampsia;endothelial cells;pregnant women plasma;DatasetType:Proteomics","pi":[{"name":"Bruno Cesar Rossini","email":"bruno.rossini@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Mariana Bertozzi Matheus","email":"mariana.bertozzi@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Valeria Cristina Sandrim","email":"valeria.sandrim@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7faf19568e0045be9b5b0885728c0df7","id":"1256"}, {"dataset":"MSV000097062","datasetNum":"97062","title":"O-GlcNAc transferase senses influenza viral RNA and restricts viral infection by integrating innate immunity and lipid metabolism","user":"yayu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738869166000","created":"Feb. 6, 2025, 11:12 AM","description":"Viral infection induces robust reprogramming of metabolic pathways in host cells. However, whether host metabolic enzymes detect viral components remains unknown. Our group and others previously identified O-GlcNAc transferase (OGT), an important glucose metabolic enzyme, as a crucial mediator of the antiviral immune responses. Here, by studying a mouse model with a catalytically impaired OGT, we discover a catalytic activity-independent function of OGT in restraining influenza A virus (IAV) infection in addition to its catalytic activity-dependent effect on MAVS-mediated antiviral immunity. Biochemical studies reveal a critical antiviral effect based on OGT interacting with IAV genomic RNA that requires its N-terminal tetracopeptide repeat-4 motif. This interaction causes the translocation of nuclear OGT to cytosolic lipid droplets (LDs) to destabilize LDs-coating perilipin 2, thereby limiting LDs accumulation and in turn virus replication. In sum, our findings reveal OGT as a multifaceted metabolic sensor that integrates MAVS signaling and lipid metabolism to combat viral infection.","fileCount":"37","fileSizeKB":"2904439","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Quantitative proteomics;E3technology;Viral infection;Innate immunity;DatasetType:Proteomics","pi":[{"name":"Haitao Wen","email":"Haitao.Wen@osumc.edu","institution":"Ohio State University College of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dffa2d6a49a04a69a79cf1df8218c2c4","id":"1257"}, {"dataset":"MSV000097061","datasetNum":"97061","title":"Circulating proteins in the plasma of pregnant women with early and late onset preeclampsia versus healthy pregnant women","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738866750000","created":"Feb. 6, 2025, 10:32 AM","description":"Preeclampsia (PE) is a multifactorial disease with a complex pathophysiology and no specific treatment currently available. Therefore, investigating altered pathways, proteins, and metabolites, as well as identifying potential biomarkers and therapeutic targets, becomes essential. Thus, the objective of this work is to identify the proteins altered or involved in the pathophysiology of PE.","fileCount":"41","fileSizeKB":"92005885","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive (Thermo Fisher)","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Preeclampsia;biomarkers;blood human;DatasetType:Proteomics","pi":[{"name":"Bruno Cesar Rossini","email":"bruno.rossini@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brazil"},{"name":"Joao Leandro Chaguri","email":"joao.leandro@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Mariana Bertozzi Matheus","email":"mariana.bertozzi@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"},{"name":"Valeria Cristina Sandrim","email":"valeria.sandrim@unesp.br","institution":"Sao Paulo State University (UNESP)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e4e9503ffbff43c4bfd2748414c3a4f1","id":"1258"}, {"dataset":"MSV000097055","datasetNum":"97055","title":"Evaluating Drug Therapeutic Effects and Molecular Mechanisms via Human LC-MS Analysis","user":"NDMCKuoTungTai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738821222000","created":"Feb. 5, 2025, 9:53 PM","description":"The experiment aims to evaluate the therapeutic effects of the drug and to investigate its underlying molecular mechanisms. This involves analyzing the drug's impact on specific biological pathways, cellular responses, and molecular interactions to better understand its mode of action. By correlating observed therapeutic outcomes with detailed molecular changes, the study provides critical insights into both the efficacy and mechanistic basis of the treatment.","fileCount":"15","fileSizeKB":"7781290","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap XL","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"human;DatasetType:Proteomics","pi":[{"name":"Kuan-Yin Tseng","email":"neuronsurgery@gmail.com","institution":"Department of Neurological Surgery, Tri-Service General Hospital Taipei, Taiwan (R.O.C.)","country":"Taipei, Taiwan (R.O.C.)"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"63f58bb25afe46eda0847156f01e7877","id":"1259"}, {"dataset":"MSV000097053","datasetNum":"97053","title":"Activity-based protein profiling of beta-lactam targets in Mycobacterium tuberculosis","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738810767000","created":"Feb. 5, 2025, 6:59 PM","description":"Activity-based protein profiling data from Mycobacterium tuberculosis (Mtb) H37Rv grown under replicating and carbon-starvation conditions with beta lactam (meropenem) probe labeling or no probe control (npc). Proteins were obtained from Mtb cultures lysed by bead beating, digested with trypsin, and then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"227","fileSizeKB":"23454791","spectra":"0","psms":"442461","peptides":"152261","variants":"173933","proteins":"7830","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium tuberculosis (NCBITaxon:1773)","instrument":"Q Exactive Plus;SYNAPT G2-Si","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"proteomics;H37Rv;activity-based protein profiling;ABPP;DatasetType:Proteomics","pi":[{"name":"Kimberly Beatty","email":"beattyk@ohsu.edu","institution":"Oregon Health and Science University (OHSU)","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD060534","task":"e3d482a75ad143eeb8586d1d6f0f0766","id":"1260"}, {"dataset":"MSV000097050","datasetNum":"97050","title":"Protein degradation and growth dependent dilution substantially shape mammalian proteomes","user":"andrewleduc95","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738798323000","created":"Feb. 5, 2025, 3:32 PM","description":"In vivo metabolic pulse labeling data from mouse brain, lung, pancreas and bone marrow","fileCount":"67","fileSizeKB":"108278625","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MOD:01316 - \\\"A protein modification that effectively converts an L-lysine residue to 4x(13)C labeled N6-succinyl-L-lysine.\\\"","keywords":"SILAC;SILAM;Tissue;DatasetType:Proteomics","pi":[{"name":"Nikolai Slavov","email":"n.slavov@northeastern.edu","institution":"Northeastern University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD060531","task":"732135590e454112b315f6e610891080","id":"1261"}, {"dataset":"MSV000097049","datasetNum":"97049","title":"Podoplanin Positive Cell-derived Small Extracellular Vesicles Contribute to Cardiac Amyloidosis After Myocardial Infarction","user":"darukeshwara","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738798289000","created":"Feb. 5, 2025, 3:31 PM","description":"Cardiac amyloidosis is a secondary phenomenon of an already pre-existing chronic condition. Whether cardiac amyloidosis represents one of the complications of post-myocardial infarction (MI) is yet to be fully understood. Here, we show that amyloidosis occurs after MI and that amyloid fibers are composed of macrophage-derived Serum Amyloid A 3 (SAA3) monomers. SAA3 overproduction in macrophages is triggered by exosomal communication from cardiac stromal cells (CSC), which, in response to MI, activate the expression of a platelet aggregation-inducing type I transmembrane glycoprotein Podoplanin (PDPN). CSCPDPN+ derived small extracellular vesicles (sEVs) are enriched in SAA3, and exosomal SAA3 engages with macrophage by Toll-like receptor 2, triggering an overproduction, with consequent impaired clearance and aggregation of SAA3 monomers into rigid fibers. SAA3 amyloid deposits reduce cardiac contractility and increase scar stiffness. Inhibition of SAA3 aggregation by retro-inverso D-peptide, specifically designed to bind SAA3 monomers, prevents the deposition of SAA3 amyloid fibrils and improves heart function post-MI.","fileCount":"13","fileSizeKB":"60588891","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"QE-HF in DIA mode in the LC-MS\\\/MS ","modification":"no","keywords":"Exosomes;DatasetType:Proteomics","pi":[{"name":"Raj Kishore","email":"raj.kishore@temple.edu","institution":"Temple University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"35438bd629d74e03bba4940f95c52b51","id":"1262"}, {"dataset":"MSV000097047","datasetNum":"97047","title":"Novel antimicrobial peptides and peptide-microbiome crosstalk in Appalachian salamander skin","user":"tpcleland","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738759885000","created":"Feb. 5, 2025, 4:51 AM","description":"Host antimicrobial peptides (AMPs) are an ancient defense system found in all multicellular organisms that interact with host microbiomes. We used multi-omics and mathematical tools to discover new AMPs and examine AMP-microbial interactions in three Appalachian salamander species (Plethodon cinereus, Eurycea bislineata and Notophthalmus viridescens). We conducted skin transcriptomics (n = 13), proteomics (n = 91) and AMP database querying to identify candidate AMPs. With candidate AMPs, we identified correlations with the skin microbiome (16S rRNA amplicon) and synthesized 20 peptides to use in challenge assays with pathogens of amphibians (Batrachochytrium dendrobatidis: Bd) and humans (ESKAPEE pathogen panel). Using transcriptomics, candidate AMP genes (30-67 genes) were detected in all individuals with Cathelidicin-like peptides being most common. Using proteomics, detectable AMPs were only found in a subset of salamanders (31\/91) - predominately E. bislineata - with Kinin-like peptides being most common. Candidate AMP composition generally predicted skin bacterial composition. Crude and synthesized peptides showed limited activity against Bd. Two synthesized Cathelicidin-like peptides (from P. cinereus) showed moderate to strong killing activity against human pathogens, Acinetobacter baumannii and Escherichia coli. We show that mining under-studied taxa and using multi-omics fuels AMPs discovery, reveals dynamic AMPs-microbial relationships, and informs the therapeutic potential of AMPs usage in conservation and translational applications.","fileCount":"7424","fileSizeKB":"46369156","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Plethodon cinereus (NCBITaxon:141976);Eurycea bislineata (NCBITaxon:134758);Notophthalmus viridescens (NCBITaxon:8316)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Salamander;Antimicrobial peptides;DatasetType:Proteomics","pi":[{"name":"Carly Muletz-Wolz","email":"MuletzC@si.edu","institution":"Smithsonian Institution","country":"USA"},{"name":"Timothy Cleland","email":"clelandtp@si.edu","institution":"Smithsonian Institution","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060511","task":"9c5c4d64d69e4b1a93c4554462df74d3","id":"1263"}, {"dataset":"MSV000097043","datasetNum":"97043","title":"GNPS - Mass Spectral Data of Primary and Secondary Metabolites Changes in Medicinal Plants by Solvent Polarity","user":"cho_chae_yeon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738745095000","created":"Feb. 5, 2025, 12:44 AM","description":"MS raw file and mzML file of plant metabolite data from 83 family","fileCount":"5530","fileSizeKB":"331983188","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alismataceae (NCBITaxon:4449);Amaranthaceae (NCBITaxon:3563);Amaryllidaceae (NCBITaxon:4668);Anacardiaceae (NCBITaxon:4011);Araliaceae (NCBITaxon:4050);Araceae (NCBITaxon:4454);Aristolochiaceae (NCBITaxon:16727);Asclepiadoideae (NCBITaxon:167484);Berberidaceae (NCBITaxon:41773);Bignoniaceae (NCBITaxon:24079);Campanulaceae (NCBITaxon:4381);Caprifoliaceae (NCBITaxon:4200);Caryophyllaceae (NCBITaxon:3568);Bassia (NCBITaxon:83153);Asteraceae (NCBITaxon:4210);Convolvulaceae (NCBITaxon:4118);Cornaceae (NCBITaxon:42219);Cucurbitaceae (NCBITaxon:3650);Cupressaceae (NCBITaxon:3367);Cyperaceae (NCBITaxon:4609);Dioscoreaceae (NCBITaxon:4671);Dipsacaceae (NCBITaxon:40572);Dipterocarpaceae (NCBITaxon:40588);Ephedraceae (NCBITaxon:3386);Eriocaulaceae (NCBITaxon:26019);Eucommiaceae (NCBITaxon:4390);Gentianaceae (NCBITaxon:21472);Geraniaceae (NCBITaxon:4027);Ginkgoaceae (NCBITaxon:3309);Poaceae (NCBITaxon:4479);Illicium (NCBITaxon:13097);Iridaceae (NCBITaxon:26339);Lamiaceae (NCBITaxon:4136);Lardizabalaceae (NCBITaxon:22788);Lauraceae (NCBITaxon:3433);Fabaceae (NCBITaxon:3803);Lemnoideae (NCBITaxon:284551);Liliaceae (NCBITaxon:4677);Linaceae (NCBITaxon:4004);Loganiaceae (NCBITaxon:26468);Loranthaceae (NCBITaxon:3963);Magnoliaceae (NCBITaxon:3401);Meliaceae (NCBITaxon:43707);Menispermaceae (NCBITaxon:3455);Moraceae (NCBITaxon:3487);Myristicaceae (NCBITaxon:22274);Myrtaceae (NCBITaxon:3931);Nymphaeaceae (NCBITaxon:4410);Oleaceae (NCBITaxon:4144);Orchidaceae (NCBITaxon:4747);Orobanchaceae (NCBITaxon:91896);Paeoniaceae (NCBITaxon:24943);Arecaceae (NCBITaxon:4710);Papaveraceae (NCBITaxon:3465);Piperaceae (NCBITaxon:16739);Plantaginaceae (NCBITaxon:156152);Polygalaceae (NCBITaxon:4274);Polypodiaceae (NCBITaxon:3275);Polygonaceae (NCBITaxon:3615);Polyporaceae (NCBITaxon:5317);Portulacaceae (NCBITaxon:3581);Pyroloideae (NCBITaxon:217032);Ranunculaceae (NCBITaxon:3440);Rhamnaceae (NCBITaxon:3608);Rosaceae (NCBITaxon:3745);Rubiaceae (NCBITaxon:24966);Rutaceae (NCBITaxon:23513);Saururaceae (NCBITaxon:16748);Schisandraceae (NCBITaxon:16733);Scrophulariaceae (NCBITaxon:4149);Selaginellaceae (NCBITaxon:3245);Simaroubaceae (NCBITaxon:23808);Solanaceae (NCBITaxon:4070);Sparganium (NCBITaxon:4729);Stemonaceae (NCBITaxon:49662);Sterculioideae (NCBITaxon:214912);Styracaceae (NCBITaxon:20008);Thymelaeaceae (NCBITaxon:39987);Typhaceae (NCBITaxon:4731);Apiaceae (NCBITaxon:4037);Valerianaceae (NCBITaxon:19944);Violaceae (NCBITaxon:24921);Zingiberaceae (NCBITaxon:4642);Zygophyllaceae (NCBITaxon:43873)","instrument":"Orbitrap Exploris 120","modification":"No","keywords":"plant_metabolite, positive, negative;DatasetType:Metabolomics","pi":[{"name":"Heejung Yang","email":"heejyang@kangwon.ac.kr","institution":"Kangwon National University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6157c45a8a7a4013ba51e0fdf4684e17","id":"1264"}, {"dataset":"MSV000097038","datasetNum":"97038","title":"GNPS - 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Data were acquired following gradient LC separation and then a 65% water 35% ACN isocratic run (files designated with iso) to identify specific sesquiterpene lactones. Files designated Tulip correspond to L tulipifera samples (3 and B) and Chin correspond to L chinense samples (A and D).","fileCount":"15","fileSizeKB":"1946632","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Liriodendron tulipifera (NCBITaxon:3415);Liriodendron chinense (NCBITaxon:3414)","instrument":"LTQ XL","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Liriodendron, tulip free, sesquiterpene lactones;DatasetType:Metabolomics","pi":[{"name":"Matt Bertin","email":"mxb1224@case.edu","institution":"Case Western Reserve University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4a2ca69aaf314b7784c6d77156da9cab","id":"1266"}, {"dataset":"MSV000097036","datasetNum":"97036","title":"TEMI: Tissue Expansion Mass Spectrometry Imaging ","user":"LangDing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738681012000","created":"Feb. 4, 2025, 6:56 AM","description":"MALDI-MSI raw files for Main Figure 1, 2, 3, 4, 5, 6, and Extended Data Figure 3.","fileCount":"41","fileSizeKB":"42761172","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX MALDI-2","modification":"N-glycans","keywords":"lipids;peptides;PC-MT-IHC-MALDI-MSI;N-glycans;mouse cerebellum;mouse kidney;mouse pancreas;mouse melanoma tumor;DatasetType:Other (MALDI-MSI)","pi":[{"name":"Meng Wang","email":"wmeng@bcm.edu","institution":"Baylor College of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c484fdce3ef4056b84943be21bbb4b1","id":"1267"}, {"dataset":"MSV000097035","datasetNum":"97035","title":"Mitochondrial damage drives T-cell immunometabolic paralysis after major surgery","user":"kkleigrewe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738677165000","created":"Feb. 4, 2025, 5:52 AM","description":"Cytotoxic T cell (CTL) dysfunction is a key feature of immune paralysis following major surgery, significantly increasing the risk of severe nosocomial infections and contributing to elevated mortality in critically ill patients. The pathomechanisms of CTL dysfunction remain unclear. We report that reactive oxygen species (ROS) release by Myeloid-Derived Suppressor Cells, which transiently and unexpectedly emerge after major surgery, drives perioperative CTL immunoparalysis. This ROS release causes a critical accumulation of ROS within CTL, overwhelming their antioxidative defenses and severely compromising mitochondrial membrane potential. Consequently, oxidative phosphorylation is impaired, and CTL effector functions are inhibited. Additionally, stress-induced mitochondrial hyperfusion occurs, which disrupts fission-dependent mitochondrial translocation to the immunological synapse, exacerbating the bioenergetic failure. These processes result in substantial mitochondrial dysfunction, which could be partially reversed by treatment with the mitochondria-targeting antioxidant MitoTempo. Stabilizing mitochondrial function could serve as a promising clinical strategy for preventing and treating perioperative immune dysfunction.","fileCount":"275","fileSizeKB":"14816348","spectra":"356711","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"Metabolomics","keywords":"Mitochondrial damage;cytotoxic T cell dysfunction;DatasetType:Metabolomics","pi":[{"name":"Simone Kreth","email":"simone.kreth@med.uni-muenchen.de","institution":"Ludwig-Maximilian-University (LMU) Munich","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b04359ba2b2c4278a344d855d5d1a85b","id":"1268"}, {"dataset":"MSV000097033","datasetNum":"97033","title":"GNPS_WelO16_purified_HW_lysate_attempt_3","user":"AKania","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738672956000","created":"Feb. 4, 2025, 4:42 AM","description":"3rd attempt \nin vitro assay of WelO16 with h. welwtischii lysate\nlyophilized assay sample and solved in MeOH","fileCount":"13","fileSizeKB":"1501682","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hapalosiphon welwitschii (NCBITaxon:162986)","instrument":"6510 Quadrupole Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"WelO16;DatasetType:Metabolomics","pi":[{"name":"Alexander Kania","email":"akania@uni-bonn.de","institution":"University of Bonn","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5739784ffe8a4947b94a8caa62e19f8c","id":"1269"}, {"dataset":"MSV000097031","datasetNum":"97031","title":"GNPS - Green synthesis of silver nanoparticles using padina tetrastromatica against malaria and deciphering the mechanism through machine learning driven metabolomics and network pharmacology.","user":"msrinivas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738653735000","created":"Feb. 3, 2025, 11:22 PM","description":"Metabolomics was carried out to identify metabolic alterations using machine-learning models in both the infected and Ag-PT-treated mice models. ","fileCount":"91","fileSizeKB":"18719150","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 120","modification":"None","keywords":"Padina tetrastromatica, green synthesised silver nanoparticles, malaria, metabolomics, machine learning, network pharmacology;DatasetType:Metabolomics","pi":[{"name":"Dr. M. Srinivasa Rao","email":"msrinivas@iict.res.in","institution":"CSIR - Indian Institute of Chemical Technology","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b9a65f5022a546f09ce6783d85e3b70b","id":"1270"}, {"dataset":"MSV000097029","datasetNum":"97029","title":"GNPS - Caffeic acids utilization in the Phyllosphere ","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738607038000","created":"Feb. 3, 2025, 10:23 AM","description":"Non-target metabolomics analysis to track compounds utilization by plant`s bacteria isolated ","fileCount":"235","fileSizeKB":"10260697","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bacteria;natural products;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ae110f54282840a1a5cfb55445ba8586","id":"1271"}, {"dataset":"MSV000097027","datasetNum":"97027","title":"Sus scrofa WT and DMD cardiac decellularized ECM ","user":"Dds100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738592822000","created":"Feb. 3, 2025, 6:27 AM","description":"\nCardiac tissue decellularization was conducted on wild-type (WT) and dystrophic (DMD) pig heart tissues, derived from 1-day (1D) and 4-month-old (4M) animals. Briefly, the tissues were cut into pieces approximately 1 mm thick. The minced heart tissue was stirred in 0.3% SDS in a Milli-Q water for 48 h followed by treatment with a 3% Triton X-100 (Sigma-Aldrich, St. Louis, MO, USA; X100-500ML) solution for a further 48 h. The decellularized extracellular matrices were washed using Milli-Q water for at least 3 days, lyophilized, and stored at -80C.\n\nSamples have been prepared to nanoscale liquid chromatography coupled to tandem mass spectrometry (nLC-MS\/MS) analysis with the MS compatible detergent RapiGest SF Surfactant (Waters Corporation, Milford, MA, USA; 186001861). Briefly, after recovering samples from -80C freezer, they were centrifuged at 13.000 rpm, for 10 min and the supernatant was discarded. Pellets were resuspended in 0.1 M Ammonium bicarbonate (NH4HCO3), pH=7.9 and mechanically homogenized. RapiGest SF was added to each sample to reach a final concentration of 0.2% v\/v and samples were heated at 95C for 20 min. After centrifugation at 13.000 rpm for 10 min, samples were quantified using Qubit Protein Assay Kit on a QubitTM4 Fluorometer (Invitrogen, ThermoFisher Scientific, Waltham, MA, USA); 50 microg of proteins were recovered from each sample and digested overnight with trypsin (Trypsin Gold, Promega, Madison, WI, USA; V5280) 1:50 enzyme\/substrate ratio. Tryptic digestion was stopped with trifluoroacetic acid (TFA) to reach a final concentration of 0.5% v\/v and samples were centrifuged (13.000 rpm for 10 min) to remove any matrix debris. Eventually, resulting peptides have been desalted and enriched with PepClean C18 Spin Columns (ThermoFisher Scientific, Waltham, MA, USA), according to the manufacturer s instructions.\n\nEach sample was analysed in two technical replicates on LC-MS\/MS platform: Eksigent nanoLC-Ultra 2D System (Eksigent, Dublin, CA, USA) for nano liquid chromatography coupled with LTQ Orbitrap XLTM (Thermo Fisher Scientific, San Jose, CA, USA) for MS\/MS analyses. In particular, peptides were separated with the following eluent gradient: (A) 0.1% formic acid in water; (B) 0.1% formic acid in acetonitrile; the gradient profile was 10-50% B in 104 min, 50-95% B in 17 min; 95% B for 9 min.\n\n","fileCount":"17","fileSizeKB":"1709890","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sus scrofa (NCBITaxon:9823)","instrument":"LTQ Orbitrap XL ETD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Biomaterials;Extracellular matrix;Duchenne Muscular Dystrophy;Hydrogel;DatasetType:Proteomics","pi":[{"name":"Dario Di Silvestre","email":"dario.disilvestre@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Francesca Brambilla","email":"francesca.brambilla@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Pierluigi Mauri","email":"pierluigi.mauri@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Raffaello Vigano","email":"raffaello.vigano@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"931e235271d4413aabbd69a207167b2d","id":"1272"}, {"dataset":"MSV000097018","datasetNum":"97018","title":"Sacubitril treated mouse heart proteomics","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738365366000","created":"Jan. 31, 2025, 3:16 PM","description":"Mouse heart samples processed by S-trap. S: sacubitril (n=6), V: vehicle (n=5)","fileCount":"12","fileSizeKB":"43287687","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"sacubitril;chronic heart allograft vasculopathy;DatasetType:Proteomics","pi":[{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aaea6796575447ff81de26d102009616","id":"1273"}, {"dataset":"MSV000097016","datasetNum":"97016","title":"Plasma Extracellular Vesicle-Associated enolase 1 as a Diagnostic Biomarker for Early-Stage 1 Breast Cancer","user":"moravcor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738345202000","created":"Jan. 31, 2025, 9:40 AM","description":"For successful treatment of breast cancer, early and efficient diagnosis is paramount. However, the diagnosis of breast cancer in the earliest stage, stage 1, is challenging as small tumors are often left undetected by conventional imaging techniques. Additionally, 8 out of 10 breast masses are classified as benign which causes unnecessary psychological stress and increased costs to the medical system. To improve the detection of early-stage breast cancer, development of non-invasive approaches should be explored. Here, we investigated the potential of extracellular vesicles (EVs) to report on a breast cancer diagnosis. EVs contain unique cancer-associated proteins from the parental cell and have the potential to be used for early detection of tumor growth. We isolated EVs from healthy (19), benign (19), and early-stage breast cancer (86) patient plasma samples using size exclusion chromatography. Mass spectrometry analysis identified 94 significantly changed proteins in the plasma EVs from breast cancer patients . Using a cohort of pre- and post-surgery breast cancer patients, we identified enolase 1 as a promising biomarker for breast cancer detection. Enolase 1 was further validated using a larger cohort of healthy and breast cancer patients, by high-throughput ELISA of plasma, and was found to be elevated in breast cancer patient plasma at all stages, including Stage 1. Furthermore, enolase-1 plasma levels decreased post-operatively upon tumor removal. An enolase 1 liquid blood biopsy could be used to support breast cancer screening for the identification of high-risk individuals promoting the diagnosis of breast cancer at the very earliest and treatable stage. Furthermore, plasma-enolase 1 can decipher between individuals with a benign or cancerous mass, it could therefore be used alongside current imaging practices to direct physician decisions to carry out only necessary needle biopsy procedures.","fileCount":"2321","fileSizeKB":"592521107","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Enolase;Breast Cancer;Biomarker;Extracellular Vesicle;DatasetType:Proteomics","pi":[{"name":"Karla C. Williams","email":"karla.williams@ubc.ca","institution":"The University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060401","task":"5a68986cbba543db83666899dceb9717","id":"1274"}, {"dataset":"MSV000097015","datasetNum":"97015","title":"GNPS - Extended coverage of human serum glycosphingolipidome by 4D-RP-LC TIMS-PASEF unravels association with Parkinson's disease","user":"huovo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738342579000","created":"Jan. 31, 2025, 8:56 AM","description":"Glycosphingolipids (GSLs) are important targets in immune, infectious, lysosomal storage diseases, cancer, and neurodegenerative diseases. Circulatory GSL profiling in clinical samples is restricted by the lack of mid- and high-throughput analytical methods and deep coverage of long-chain sialylated glycosphingolipidome. \r\nWe present a 4-dimensional (4D)-glycosphingolipidomics platform for routine glycosphingolipidome profiling encompassing: extraction and fractionation of sialylated GSLs with 3 to 15 monosaccharides, neutral GSLs and sulfatides; µL-flow reversed-phase LC-TIMS-PASEF MS analysis; semi-quantification strategy adapted for fractionated glycosphingolipidome, and referential CCS, RT, and m\/z values for GSL annotation. 4D-glycosphingolipidomics of human serum reveals a high structural heterogeneity, amounting to 376 GSLs: 159 GSLs of ganglio- and neolacto-series, 145 neutral GSLs and 72 sulfatides. \r\nHere we demonstrate the platform\u2019s utility for clinical profiling of Parkinson\u2019s disease (PD) sera. 41 neolacto- and ganglio-species discriminate PD patients from controls and 14 GSLs differentiate sex subgroups, laying the foundation for further functional GSL studies with PD.","fileCount":"619","fileSizeKB":"9112933","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX;timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipidomics;glycosphingolipids;TIMS PASEF;ion mobility mass spectrometry;DatasetType:Other (Lipidomics)","pi":[{"name":"Laura Bindila","email":"bindila@uni-mainz.de","institution":"Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center Mainz","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7ea04cbbd9b04840a3d3dcb9c5c1b846","id":"1275"}, {"dataset":"MSV000097014","datasetNum":"97014","title":"Pseudomonas putida membrane vesicles","user":"jwal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738340919000","created":"Jan. 31, 2025, 8:28 AM","description":"Cellular and membrane vesicle proteomes from Pseudomonas putida KT2440 and engineered derivative strains. Proteomic quantification by diDO-IPTL (Waldbauer et al. 2017 Analytical Chemistry).","fileCount":"116","fileSizeKB":"125531967","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas putida KT2440 (NCBITaxon:160488)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:199 - \\\"DiMethyl-CHD2.\\\";UNIMOD:193 - \\\"O18 label at both C-terminal oxygens.\\\"","keywords":"vesicle;omv;pseudomonas;diDO-IPTL;IPTL;DatasetType:Proteomics","pi":[{"name":"Jacob Waldbauer","email":"jwal@uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060399","task":"0fdf97819b31421892e1ebd688349507","id":"1276"}, {"dataset":"MSV000097010","datasetNum":"97010","title":"TBRC13601_positive_diffmedia_GNPS_SCBmedium","user":"Natthaphongsombut","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738292866000","created":"Jan. 30, 2025, 7:07 PM","description":"Global Natural Products Social Molecular Networking (GNPS) platform with SIRIUS and Feature-Based Molecular Networking (FBMN) to analyze metabolites associated with the bacterial genus Yinghuangia under positive ionization mode with SCB medium( mzXML file 41-45 blank and 46-50 cultured).","fileCount":"21","fileSizeKB":"1329413","spectra":"34686","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Yinghuangia sp. TBRC 13601","instrument":"UPLC-ESI\\\/MS","modification":"Metabolomics","keywords":"Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Natthaphong Sombuttra","email":"Natthaphong.sombut@kmutt.ac.th","institution":"King Mongkut's University of Technology Thonburi","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"04aab05458ba4277bcfa8b3780f4eff5","id":"1277"}, {"dataset":"MSV000097009","datasetNum":"97009","title":"TBRC13601_positive_diffmedia_GNPS_ISP4medium","user":"Natthaphongsombut","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738292685000","created":"Jan. 30, 2025, 7:04 PM","description":"Global Natural Products Social Molecular Networking (GNPS) platform with SIRIUS and Feature-Based Molecular Networking (FBMN) to analyze metabolites associated with the bacterial genus Yinghuangia under positive ionization mode with ISP4 medium( mzXML file 31-35 blank and 36-40 cultured).","fileCount":"11","fileSizeKB":"572817","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Yinghuangia sp. TBRC 13601","instrument":"UPLC-ESI\\\/MS","modification":"Metabolomics","keywords":"Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Natthaphong Sombuttra","email":"Natthaphong.sombut@kmutt.ac.th","institution":"King Mongkut's University of Technology Thonburi","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d247aa97def5491e8eb09798e0c6b4a7","id":"1278"}, {"dataset":"MSV000097008","datasetNum":"97008","title":"TBRC13601_positive_diffmedia_GNPS_ISP2medium","user":"Natthaphongsombut","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738292437000","created":"Jan. 30, 2025, 7:00 PM","description":"Global Natural Products Social Molecular Networking (GNPS) platform with SIRIUS and Feature-Based Molecular Networking (FBMN) to analyze metabolites associated with the bacterial genus Yinghuangia under positive ionization mode with ISP2 medium( mzXML file 21-25 blank and 26-30 cultured).","fileCount":"11","fileSizeKB":"620681","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":" Species Yinghuangia sp. TBRC 13601","instrument":"UPLC-ESI\\\/MS","modification":"Metabolomics","keywords":"Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Natthaphong Sombuttra","email":"Natthaphong.sombut@kmutt.ac.th","institution":"King Mongkut's University of Technology Thonburi","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"688055554910482bb25d4936ec93e368","id":"1279"}, {"dataset":"MSV000097007","datasetNum":"97007","title":"TBRC13601_positive_diffmedia_GNPS_A1medium","user":"Natthaphongsombut","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738292048000","created":"Jan. 30, 2025, 6:54 PM","description":"Global Natural Products Social Molecular Networking (GNPS) platform with SIRIUS and Feature-Based Molecular Networking (FBMN) to analyze metabolites associated with the bacterial genus Yinghuangia under positive ionization mode with A1 medium( mzXML file 11-15 blank and 16-20 cultured).","fileCount":"11","fileSizeKB":"608335","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":" Species Yinghuangia sp. TBRC 13601","instrument":"UPLC-ESI\\\/MS","modification":"Metabolomics","keywords":"Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Natthaphong Sombuttra","email":"Natthaphong.sombut@kmutt.ac.th","institution":"King Mongkut's University of Technology Thonburi","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6c0db88ac7f44a5bafbd5b3db984c864","id":"1280"}, {"dataset":"MSV000097006","datasetNum":"97006","title":"TBRC13601_positive_diffmedia_GNPS_301medium","user":"Natthaphongsombut","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738291659000","created":"Jan. 30, 2025, 6:47 PM","description":"Global Natural Products Social Molecular Networking (GNPS) platform with SIRIUS and Feature-Based Molecular Networking (FBMN) to analyze metabolites associated with the bacterial genus Yinghuangia under positive ionization mode with 301 medium( mzXML file 1-5 blank and 6-10 cultured).","fileCount":"11","fileSizeKB":"620938","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Yinghuangia sp. TBRC 13601","instrument":"UPLC-ESI\\\/MS","modification":"Metabolomics","keywords":"Metabolomics;DatasetType:Metabolomics","pi":[{"name":"Natthaphong Sombuttra","email":"Natthaphong.sombut@kmutt.ac.th","institution":"King Mongkut's University of Technology Thonburi","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b808f959aee6484293ec4e44b77be79d","id":"1281"}, {"dataset":"MSV000097003","datasetNum":"97003","title":"VIPER-TACs leverage viral E3 ligases for disease-specific targeted protein degradation","user":"jliu19","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738272465000","created":"Jan. 30, 2025, 1:27 PM","description":"In targeted protein degradation (TPD) a protein of interest is degraded by chemically induced proximity to an E3 ubiquitin ligase. One limitation of using TPD therapeutically is that most E3 ligases have broad tissue expression, which can contribute to toxicity via target degradation in healthy cells. Many pathogenic and oncogenic viruses encode E3 ligases (vE3s), which de facto have strictly limited expression to diseased cells. Here, we provide proof-of-concept for Viral E3 Pan-Essential Removing Targeting Chimeras (VIPER-TACs) that are bi-functional molecules that utilize viral E3 ubiquitin ligases to selectively degrade pan-essential proteins and eliminate diseased cells. We find that the human papillomavirus (HPV) ligase E6 can degrade the SARS1 pan-essential target protein in a model of HPV-positive cervical cancer to selectively kill E6 expressing cancer cells. Thus, VIPER-TACs have the capacity to dramatically increase the therapeutic window, alleviate toxicity concerns, and ultimately expand the potential target space for TPD.","fileCount":"10","fileSizeKB":"21113235","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"targeted protein degradation, viral E3 ligase;DatasetType:Proteomics","pi":[{"name":"Patrick Ryan Potts","email":"ryan.potts@amgen.com","institution":"Amgen Research","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060380","task":"c5eb7485ef0443df88949868fb22a004","id":"1282"}, {"dataset":"MSV000097002","datasetNum":"97002","title":"GNPS - Metabolomics_Annotation_Collaboration_WS_Standards_Dataset","user":"pmanwill","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738271508000","created":"Jan. 30, 2025, 1:11 PM","description":"This MassIVE dataset contains the standard compounds used to verify Level 1 annotations for the Metabolomics Annotation Collaboration. It contains two folders, which are labeled with the instrument (Orbi), the polarity [Positive (POS)], and the file type (Raw or mzML). Each folder contains 42 files: the extraction blanks (EXBLANK), Methanol\/waste blanks (Wasteblank), the botanical of interest, Withania somnifera (WS03), a 10 uM mixture of 10 standards (WSSTDMix_10uM), and 10 individual standards (STD01-STD10), each in triplicate (ABC or 123).","fileCount":"128","fileSizeKB":"10144177","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Withania somnifera (NCBITaxon:126910)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Withania somnifera;Ashwagandha;AHP BRM WS Root;Pure standards;DatasetType:Metabolomics","pi":[{"name":"Nadja B. 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Despite its functional significance, the spatial organization of cell surface proteins remains poorly understood. High-resolution fluorescence microscopy and proximity labeling have advanced studies of surface protein arrangement, but a systematic analysis of the spatial organization of the complete surface proteome remains unexplored. In this study, we systematically mapped the surface proteome of human T-lymphocytes and B-lymphoblasts using proximity labeling of 85 antigens, identified from over 100 antibodies tested for binding to surface-exposed proteins. These experiments were coupled with an optimized data-independent acquisition (DIA) mass spectrometry workflow to generate a robust dataset. Unsupervised clustering of the resulting interactome revealed functional modules, including well-characterized complexes such as the T-cell receptor and HLA class I\/II, alongside novel clusters. Notably, we identified mitochondrial proteins localized to the surface, including the transcription factor TFAM, suggesting previously unappreciated roles for mitochondrial proteins at the plasma membrane. A high-accuracy machine learning classifier predicted over 6,000 surface protein associations, highlighting functional associations such as IL10RBs role as a negative regulator of type I interferon signaling. Spatial modeling of the surface proteome provided insights into protein dispersion patterns, distinguishing widely distributed proteins, such as CD45, from localized antigens, such as CD226. Interestingly, protein distribution appeared independent of abundance, pointing to active mechanisms regulating surface organization. This work provides a comprehensive map of the human surfaceome, offering a resource for exploring the spatial and functional dynamics of the cell membrane proteome.","fileCount":"1601","fileSizeKB":"735103988","spectra":"20388323","psms":"19902280","peptides":"107659","variants":"107659","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Surfaceomics;Membrane;Proximity labeling;DatasetType:Proteomics","pi":[{"name":"Brendan Floyd","email":"bmfloyd@stanford.edu","institution":"Stanford University","country":"United States"},{"name":"Carolyn Bertozzi","email":"bertozzi@stanford.edu","institution":"Stanford University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060303","task":"929ef0d728dd4594a5206c1f706927ea","id":"1288"}, {"dataset":"MSV000096981","datasetNum":"96981","title":"Retrobiosynthesis of unnatural lactams via reprogrammed polyketide synthase","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1738104459000","created":"Jan. 28, 2025, 2:47 PM","description":"Using discovery global proteomics to study the retrobiosynthesis of unnatural lactams via reprogrammed polyketide synthase.","fileCount":"76","fileSizeKB":"44249111","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas putida KT2440 (NCBITaxon:160488)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"proteomics;P. putida;polyketide synthase;DatasetType:Proteomics","pi":[{"name":"Kristin E. 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This in-depth N-glycoproteomic analysis, developed by us, integrates a new strategy for identifying sulfated and other rare N-glycans in IgA. In our study, we implemented two strategies for identifying the new N-glycan compositions: screening for rare glycopeptides using oxonium marker ions and wildcard search to identify glycans holding a rare modification attached to peptides. The dataset provided here contains primarily IgA N-glycopeptides identified from technical quadruplicates of two commercial human serum IgA samples. A comparison of the N-glycosylation profiles of two commercial human serum IgA samples demonstrated that sulfated N-glycans are mainly present in the tailpiece site. Also, complex-type N-glycan compositions with O-acetylated sialic acid were identified in the tailpiece. Surprisingly, N-glycans bearing glucuronic acid were identified in the commercial IgA samples, but from peptides of contaminant glycoproteins.These N-glycans have not been included in previously published IgA micro-heterogeneity analyses. 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Additionally, we find that NBR1 specifically interacts with phospho-Tau in human AD brain, underscoring the relevance of our findings to the human disease. 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This study utilized a multi-omics approach, integrating microbiome and metabolome analyses, to investigate adaptive strategies in sponges inhabiting the mesophotic (80-125 m), upper-rariphotic (125-200 m), and lower-rariphotic (200-305 m) zones of Curacao. 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Gates Foundation Sepsis Project. Untargeted LC-MS\/MS acquisition was performed on a UltiMate 3000 liquid chromatography system (Thermo Scientific) coupled to a QExactive Orbitrap (Thermo Scientific) mass spectrometer.","fileCount":"1723","fileSizeKB":"34146589","spectra":"1482205","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"feces;serum;milk;infant;microbiome;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b5b8f8469ac74836a59fcc460b2ebed8","id":"1301"}, {"dataset":"MSV000096941","datasetNum":"96941","title":"MB135 iDUX4ca EU labeled RICK Mass Spec","user":"srbennet","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737764270000","created":"Jan. 24, 2025, 4:17 PM","description":"RICK was performed as previously described (Bao et al., 2018). Briefly, cells were cultured in 15cm plates and 0.1mM 5-ethynyl uridine (ThermoFisher Scientific) was incubated with cells after dox-induction for 16-hrs followed by a washout and then fixed at 48-hrs. After washing 3x with 1X PBS, the plates were placed on ice and irradiated with 0.15 J\/cm2 UV light at 254 nm (Stratalinker). Cells were then fixed with 90% ethanol for 30 min, washed 3x with 1X PBS, and permeabilized with 0.5% Triton X-100 in 1X PBS for 15 min. Permeabilized cells were incubated with 15 mL of click reaction buffer (0.25M biotin-azide (Click Chemistry Tools, cat# 1265-25), 0.5M CuSO4, 0.25M THPTA, 0.1M sodium L-ascorbate in 1X PBS) for 30 minutes at RT. Reaction was quenched 3x in 0.5% Triton X-100 in 1X PBS with 2mM EDTA for 3 minutes at RT. Cells were then lysed in lysis buffer (20 mM Tris-HCl, pH 7.5, 500 mM LiCl, 1 mM EDTA pH 8.0, 0.5% lithium-dodecylsulfate (LiDS), and 5 mM DTT) supplemented with Pierce Protease Inhibitors EDTA-free (PIA32955) and Pierce Phosphatase Inhibitors (PIA32957) and RNase inhibitor (TaKaRa, cat# 2313A), and harvested by scraping. Samples were sonicated in a Biorupter (Diagenode) for 15 min on low, 30 sec on\/ 30 sec off to aid in lysis. Samples were centrifuged at 12,000 rcf for 10 min at 4C and 5% of the lysate was taken out as an input control. Complexes containing different RNA species, and their associated proteins, were isolated with streptavidin-conjugated magnetic beads (100 ul beads for each plate; Dynabeads MyOne Streptavidin C1, Thermo Fisher Scientific, cat# 65602). After incubation with the lysates overnight under continuous rotation at 4C, the beads were isolated on a magnetic stand and washed using lysis buffer, buffer 1 (20 mM Tris-HCl, pH 7.5, 500 mM LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, and 5 mM DTT), buffer 2 (20 mM Tris-HCl pH 7.5, 500 mM LiCl, 1 mM EDTA pH 8.0, and 5 mM DTT), and buffer 3 (20 mM Tris-HCl pH 7.5, 200 mM LiCl, 1 mM EDTA pH 8.0, and 5 mM DTT) for two times each under rotation (for 10 minutes at 4C). At last wash step beads were split to isolate RNA or proteins. Proteins were extracted from the captured complexes using RNase A\/T1 mix (ThermoFisher Scientific, cat# EN0551) and Ambion RNase III (ThermoFisher Scientific, cat# AM2290) at 37C for 1 hour at 1,000xg, then boiled for 10 minutes 95C. RNA was isolated in RNA elution buffer (10 mM EDTA, pH 8.0, 95% formamide (ThermoFisher Scientific)) and incubated at 95C for 5 minutes at 1,000xg. Proteinase K was added (20mg\/mL, ThermoFisher Scientific, cat# AM2546) and incubated at 55C for 1 hour. RNA was extracted using TRIzol. For LC-MS, eluted protein samples were electrophoresed into a NuPage 4-12% Bis-Tris gel, excised, and processed by the Fred Hutchinson Cancer Research Center Proteomics Core. Samples were reduced, alkylated, digested with trypsin, desalted, and run on the Orbitrap Eclipse Tribid Mass Spectrometer (ThermoFisher Scientific). Proteomics data were analyzed using Proteome Discoverer 2.4 against a UniProt human database that included common contaminants using Sequest HT and Percolator for scoring. Results were filtered to only include protein identifications from high-confidence peptides with a 1% false discovery rate. Proteins that were identified in all replicates from both independent experiments with at least two unique peptide matches and greater than 1.5 difference between sample and control were analyzed further.","fileCount":"34","fileSizeKB":"10045132","spectra":"0","psms":"16693","peptides":"6045","variants":"6656","proteins":"1539","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DUX4, HSATII RNA, RNP Complex, Splicing, RNA Processing;DatasetType:Proteomics","pi":[{"name":"Stephen J. Tapscott","email":"stapscot@fredhutch.org","institution":"Fred Hutchinson Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"Differential Abundance Results","status":"Complete","private":"false","hash":"","px":"PXD060176","task":"3acb2b0a68124293a163c5b6046a78d6","id":"1302"}, {"dataset":"MSV000096940","datasetNum":"96940","title":"GNPS - Metabolic cross-feeding of a dietary antioxidant enhances anaerobic energy metabolism by human gut bacteria","user":"zhezhou","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737762637000","created":"Jan. 24, 2025, 3:50 PM","description":"Untargeted and targeted LC\/MS analyses of ergothioneine metabolites produced by gut bacteria","fileCount":"855","fileSizeKB":"18209335","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Clostridium symbiosum ATCC 14940 (NCBITaxon:411472);Escherichia coli BL21(DE3) (NCBITaxon:469008);Mouse fecal samples;Bacteroides ovatus ATCC 8483 (NCBITaxon:411476);Bacteroides xylanisolvens XB1A (NCBITaxon:657309);Human fecal samples","instrument":"6490 Triple Quadrupole LC\\\/MS;6546 Q-TOF LC\\\/MS (Agilent instrument model)","modification":"No","keywords":"Untargeted and targeted metabolomics;DatasetType:Metabolomics","pi":[{"name":"Stavroula K. Hatzios","email":"stavroula.hatzios@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0831116465584d22a2ef7a37838bf954","id":"1303"}, {"dataset":"MSV000096938","datasetNum":"96938","title":"MB135-iDUX4ca HSATII RNP ChIRP LC\/MS","user":"srbennet","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737760547000","created":"Jan. 24, 2025, 3:15 PM","description":"ChIRP was performed as previously described (Chu et al., 2012) with modifications. 6-10 15 cm plates of cells were used per ChIRP-MS experiment. Cells are cross-linked in 2% paraformaldehyde for 15 minutes at RT, followed by 0.125 M glycine quenching for 5 minutes, scraped and pellet at 650xg for 5 minutes at 4C. Cells were then lysed in lysis buffer (50 mM Tris-HCl, pH 7.0, 10 mM EDTA, pH 8.0, 1% SDS supplemented with fresh 0.5 mM AEBSF (ThermoFisher Scientific, cat# BP635-500), Pierce Protease Inhibitors EDTA-free (PIA32955) and Pierce Phosphatase Inhibitors (PIA32957) and RNase inhibitor (TaKaRa, cat# 2313A)) for 10 minutes on ice. Samples were sonicated in a Biorupter (Diagenode) for 15 minutes on high, 30 sec on\/ 30 sec off pulse intervals for 4-cycles. Samples were centrifuged at 16,000xg for 10 minutes at 4C and 5% of the lysate was taken out as an input control. Lysates were pre-cleared with beads (Invitrogen Dynabeads M-280 Streptavidin, cat# 11205D) at 37C for 30 minutes at 800rpm. Hybridization was performed at 37C for 4 hours shaking at 800rpm using biotin-conjugated probes (HSATII probe: 5`-ATTCCATTCAGATTCCATTCGATC-3BioTEG-3`, Control probe: 5`-GTCCCGTTAGCTCAGGTGGTAGAGCAC-3BioTEG-3` or 5`-TGCTGATGAAGCAGAACAAC-3BioTEG-3`) in hybridization buffer (750 mM NaCl, 1% SDS, 50 mM Tris-HCl, pH 7.0, 1 mM EDTA, 15% formamide (Sigma-Aldrich) and supplemented with fresh 0.5 mM AEBSF (ThermoFisher Scientific, cat# BP635-500), Pierce Protease Inhibitors EDTA-free (PIA32955) and Pierce Phosphatase Inhibitors (PIA32957) and RNase inhibitor (TaKaRa, cat# 2313A)). Streptavidin magnetic beads (Invitrogen Dynabeads M-280 Streptavidin, cat# 11205D) were added (100 uL per 100 pmole of probes used) and incubated at 37C for 30 minutes at 800rpm. Beads were washed 3x in pre-warmed (37C) wash buffer (2X SSC (Invitrogen), 0.5% SDS and supplemented with Pierce Protease Inhibitors EDTA-free (PIA32955) and Pierce Phosphatase Inhibitors (PIA32957) and RNase inhibitor (TaKaRa, cat# 2313A) and 1 mM DTT) for 5 minutes at 37C at 800rpm. 10% of beads were removed for RNA isolation and 90% of remaining beads were used for protein isolation. RNA was isolated in RNA elution buffer (10 mM EDTA, pH 8.0, 95% formamide (ThermoFisher Scientific)) and incubated at 95C for 5 minutes at 1,000xg. Proteinase K was added (20mg\/mL, ThermoFisher Scientific, cat# AM2546) and incubated at 55C for 1 hour. RNA was extracted using TRIzol and validation of HSATII enrichment was performed using RT-qPCR. Protein was isolated by boiling beads for 30 minutes at 95C in 2X NuPage LDS sample buffer (ThermoFisher Scientific, cat#NP0007). Protein samples were using in immunoblotting or for LC-MS. For LC-MS, eluted protein samples were electrophoresed into a NuPage 4-12% Bis-Tris gel, excised, and processed by the Fred Hutchinson Cancer Research Center Proteomics Core. Samples were reduced, alkylated, digested with trypsin, desalted, and run on the Orbitrap Eclipse Tribid Mass Spectrometer (ThermoFisher Scientific). Proteomics data were analyzed using Proteome Discoverer 2.4 against a UniProt human database that included common contaminants using Sequest HT and Percolator for scoring. Results were filtered to only include protein identifications from high-confidence peptides with a 1% false discovery rate. Proteins that were identified in all replicates from both independent experiments with at greater than ten unique peptide matches and greater than 1.5 difference between sample and control were analyzed further.","fileCount":"82","fileSizeKB":"29292215","spectra":"0","psms":"205755","peptides":"50469","variants":"61005","proteins":"8655","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RICK, DUX4, HSATII RNA, RNP Complex, Splicing, RNA Processing;DatasetType:Proteomics","pi":[{"name":"Stephen J. Tapscott","email":"stapscot@fredhutch.org","institution":"Fred Hutchinson Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"Differential Abundance Results","status":"Complete","private":"false","hash":"","px":"PXD060172","task":"546c0ec23c2941a0882b8d3d907ae60d","id":"1304"}, {"dataset":"MSV000096931","datasetNum":"96931","title":"Shigella phage Sf14 structural proteins via shotgun proteomics","user":"sdoore","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737739027000","created":"Jan. 24, 2025, 9:17 AM","description":"This entry is for a shotgun proteomic analysis of Sf14 lysate to determine which proteins are present in virions. Peptides were compared to the proteome of Sf14 and 2457T, which is a close relative of CFS100 that was used to propagate the phage.","fileCount":"17","fileSizeKB":"678415","spectra":"0","psms":"8239","peptides":"1348","variants":"2202","proteins":"169","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Shigella phage Sf14","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bacteriophage;Shigella phage;Mooglevirus;Ounavirus;bacteriophage Sf14;DatasetType:Proteomics","pi":[{"name":"Sarah M Doore","email":"sdoore@ufl.edu","institution":"University of Florida","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060165","task":"d7348ebfd6414efeb599863669fe5b01","id":"1305"}, {"dataset":"MSV000096930","datasetNum":"96930","title":"GRHL2 methylation links KDM4C activity to cathepsin L-mediated histone H3 cleavage","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737736751000","created":"Jan. 24, 2025, 8:39 AM","description":"Basal breast cancer is a subtype with inferior prognosis necessitating novel therapeutic targets. Here, we describe a unique role for the KDM4C histone lysine demethylase in KDM4C-amplified basal breast cancers, where KDM4C inhibition triggers chromatin and transcriptomic remodeling without substantial changes of its canonical substrates H3K9me3 and H3K36me3. Rather KDM4C loss causes proteolytic cleavage of histone H3 mediated by cathepsin L (CTSL) resulting in decreased glutamate-cysteine ligase expression and increased reactive oxygen species (ROS). CTSL is recruited to the chromatin by the GRHL2 transcription factor that is methylated at lysine 453 following KDM4C inhibition triggering CTSL histone clipping activity. Deletion of CTSL or inhibition of ROS rescued KDM4-loss-mediated tumor suppression. Our study reveals a novel function for KDM4C that links cellular redox regulation to chromatin remodeling.","fileCount":"143","fileSizeKB":"50432925","spectra":"2037159","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus;Orbitrap Exploris 480","modification":"K-Acetylation, K-Methylation, K-Dimethylation, K-Trimethylation, STY-Phosphorylation, K-Ubiquitination, K,nterm-Propionylation","keywords":"global chromatin profiling, histone clipping, cathepsin L;DatasetType:Proteomics","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8d03d4ee66794a42a4970dda6ee7897a","id":"1306"}, {"dataset":"MSV000096928","datasetNum":"96928","title":"Proteomic characterization of checkpoint inhibitor-induced liver injury","user":"jfederspiel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737730864000","created":"Jan. 24, 2025, 7:01 AM","description":"Discovery proteomics of plasma samples from ChILI patients. EV enrichment was performed using Mag-Net protocol and samples were labelled with TMTpro.","fileCount":"94","fileSizeKB":"185977014","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"checkpoint inhibitor;ChILI;liver injury;biomarker;DatasetType:Proteomics","pi":[{"name":"Mireia Fernandez Ocana","email":"mireia.fernandezocana@pfizer.com","institution":"Pfizer, Inc","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060159","task":"aaf3c824cbae41cbb0b6d0e7c002e2c3","id":"1307"}, {"dataset":"MSV000096927","datasetNum":"96927","title":"Sucrose utilisation strategies in phototrophic purple bacteria: paving the way to sugar-rich by-product valorisation","user":"Manon_Gilson","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737723447000","created":"Jan. 24, 2025, 4:57 AM","description":"The circular bioeconomy has become a crucial strategy for sustainable development, especially by upcycling organic-rich by-products from various industrial processes. Purple non-sulphur bacteria (PNSB) have emerged as excellent candidates in this field, demonstrating exceptional metabolic versatility. While the growth of PNSB on sugar-rich streams has been extensively explored, the sugar assimilation metabolism remains poorly understood. Here, we explore the metabolic mechanisms of sucrose utilisation in two phototrophic purple non-sulphur bacteria (PNSB), Rhodospirillum rubrum and Rhodobacter capsulatus. Our findings demonstrate distinct carbohydrate hydrolysis and assimilation capacities, as well as the use of different redox strategies for each species. Moreover, Rhodospirillum rubrum could only grow on sucrose when co-cultivated with Rhodobacter capsulatus. This trophic link between Rhodospirillum rubrum and Rhodobacter capsulatus in sucrose containing co-culture was characterised and resulted in significantly enhanced productivity compared to pure cultures. Finally, we demonstrate that the synergy observed between Rhodospirillum rubrum and Rhodobacter capsulatus can be successfully scaled up in a photobioreactor system. Our study highlights how fundamental knowledge of the metabolism, trophic link and general microbial ecology concept might be useful for the development of biobased resource recovery strategies.","fileCount":"89","fileSizeKB":"43966482","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rhodospirillum rubrum ATCC 11170 (NCBITaxon:269796)","instrument":"TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Rhodospirillum rubrum;sugar;Proteomics;by-product valorisation;DatasetType:Other (Proteomics)","pi":[{"name":"Manon Gilson","email":"manon.gilson@umons.ac.be","institution":"University of Mons","country":"Belgique"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"7b3b5688ec954bb3850c158506d60c4d","id":"1308"}, {"dataset":"MSV000096926","datasetNum":"96926","title":"SWAPS: a modular deep-learning empowered peptide identity propagation framework beyond match-between-run","user":"KusterLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737711663000","created":"Jan. 24, 2025, 1:41 AM","description":"Mass spectrometry (MS)-based proteomics relies heavily on MS\/MS (MS2) data, which does not fully exploit the available MS1 information. Traditional peptide identification propagation (PIP) methods, such as Match-Between-Runs (MBR), are limited to similar runs, particularly with the same liquid chromatography (LC) gradients, thus potentially underutilizing available proteomics libraries. We introduce SWAPS, a novel and modular MS1-centric framework incorporating advances in peptide property prediction, extensive proteomics libraries, and deep learning-based post-processing to enable and explore PIP across more diverse experimental conditions and LC gradients. SWAPS substantially enhances precursor identifications, especially in shorter gradients. On the example of 30-, 15-, and 7.5-minute gradients, SWAPS achieves increases of 46.3%, 86.2%, and 112.1% on precursor-level over MS2-based identifications from MaxQuant. Despite the inherent challenges in controlling false discovery rates (FDR) with MS1-based methods, SWAPS demonstrates strong efficacy in deconvoluting MS1 signals, offering powerful discrimination and deeper sequence exploration while maintaining quantitative accuracy. By building on and applying peptide property predictions in practical contexts, SWAPS reveals that current models, while advanced, are still not yet fully comparable to experimental measurements, sparking the need for further research. Additionally, its modular design allows seamless integration of future improvements, positioning SWAPS as a forward-looking tool in proteomics.","fileCount":"556","fileSizeKB":"245760408","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Three-species mixture HYE","instrument":"timsTOF HT","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"SWAPS;timsTOF;MS1-based;Match-Between-Runs;DatasetType:Proteomics","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD060140","task":"945a478c70714c5fa528ab773bd457a8","id":"1309"}, {"dataset":"MSV000096923","datasetNum":"96923","title":"Proteome-scale recombinant standard datasets for XL-MS","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737661808000","created":"Jan. 23, 2025, 11:50 AM","description":"This submission includes the complete set of raw data generated from the analytical standard, the concept of which is described in our manuscript \"Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics\". In this study, we develop a strategy to generate a well-controlled XL-MS standard by systematically mixing and cross-linking recombinant proteins. The standard can be split into independent datasets, each of which has the MS2-level complexity of a typical proteome-wide XL-MS experiment. This submission includes 5 raw datasets (batches 1-5), each comprising 64 randomly selected human proteins engaging in up to 224 allowed protein-protein interactions per dataset. The data were searched with Scout (v. 1.4.14, https:\/\/github.com\/diogobor\/Scout) and results are reported in mzIdentML 1.2.0 format. For the specific results reported in our original publication, please refer to PXD042173.","fileCount":"361","fileSizeKB":"309580401","spectra":"7325731","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Crosslinking mass spectrometry;Search engine;Bioinformatics;DatasetType:Proteomics","pi":[{"name":"Fan Liu","email":"fliu@fmp-berlin.de","institution":"Leibniz-Forschungsinstitut f\uFFFDr Molekulare Pharmakologie","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD042173","task":"b7ac8d1b8a5d498db9d20088f17e52de","id":"1310"}, {"dataset":"MSV000096917","datasetNum":"96917","title":"proteomics analaysis of mouse KP tumors with normal and western diet","user":"csun022","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737594886000","created":"Jan. 22, 2025, 5:14 PM","description":"The dataset comprises KP lung tumors derived from mice fed either a normal or Western diet, analyzed to identify changes in signaling pathways influenced by dietary differences. Protein samples underwent TMT-based labeling, fractionation, and mass spectrometry, including Orbitrap MS3 for proteome and phosphorylated peptide analyses, ensuring high-resolution data collection. Phosphorylation site localization and protein quantification were rigorously filtered with a 1% FDR threshold and corrected for isotopic impurities. These analyses aim to uncover how dietary variations modulate key signaling mechanisms in lung tumor progression.\n\n\n\n\n\n\n\n","fileCount":"30","fileSizeKB":"14744274","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse ","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"lung cancer;DatasetType:Proteomics","pi":[{"name":"ramon sun","email":"ramonsun@ufl.edu","institution":"university of florida","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD060090","task":"bb58994e5cf143e193af020c2ccd3e42","id":"1311"}, {"dataset":"MSV000096916","datasetNum":"96916","title":"Characterization of conformational dynamics and allostery of the catalytic domain of human mitochondrial YME1L protease","user":"mgoncalves","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737591946000","created":"Jan. 22, 2025, 4:25 PM","description":"Continuous labelling HDX on dN-YME1L, hexYME1L, hexYME1L_E600Q in apo, ATP-bound, ADP-bound and ATP and Ni2+-bound states. Folders are organized per state. Peptide mapping and undeuterated controls are included.","fileCount":"2490","fileSizeKB":"41781801","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Synapt G2-S HDMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HDX-MS;Allostery;YME1L;AAA+ proteases;DatasetType:Other (HDX-MS)","pi":[{"name":"Siavash Vahidi","email":"svahidi@uoguelph.ca","institution":"University of Guelph","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"84c44b51ea8245159be9c7c8aac2fe9e","id":"1312"}, {"dataset":"MSV000096915","datasetNum":"96915","title":"Machine learning reveals genes impacting oxidative stress resistance across yeasts","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737588292000","created":"Jan. 22, 2025, 3:24 PM","description":"Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection. Here, we characterized the variation in resistance to ROS across the ancient yeast subphylum Saccharomycotina and used machine learning (ML) to identify gene families whose sizes were predictive of ROS resistance. The most predictive features were enriched in gene families related to cell wall organization and included two reductase gene families. We estimated the quantitative contributions of features to each species' classification to guide experimental validation and showed that overexpression of the old yellow enzyme (OYE) reductase increased ROS resistance in Kluyveromyces lactis, while Saccharomyces cerevisiae mutants lacking multiple mannosyltransferase-encoding genes were hypersensitive to ROS. Altogether, this work provides a framework for how ML can uncover genetic mechanisms underlying trait variation across diverse species and inform trait manipulation for clinical and biotechnological applications.","fileCount":"31","fileSizeKB":"241183591","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932);Kluyveromyces lactis (NCBITaxon:28985)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Yeast;Proteomics;Artificial Intelligece;AI;Kluyveromyces lactis;Saccharomyces cerevisiae;Data Independent Acquisition;Machine Learning;Oxidative Stress;Reactive Oxygen Species;DatasetType:Proteomics","pi":[{"name":"Joshua Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f33be8793408422985c50d00e4e96b7f","id":"1313"}, {"dataset":"MSV000096914","datasetNum":"96914","title":"Phosphoproteome of RAW264.7 cells infected with quorum sensing ON and OFF Group A Strep","user":"Sfelds3","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737586730000","created":"Jan. 22, 2025, 2:58 PM","description":"Phosphoproteome of RA264.7 macrophages 30m post infection with quorum sensing ON or OFF or both Streptococcus pyogenes (Group A Strep), or uninfected. Available are peak lists, .raw files, and processed and quantified results analyzed via Comet.","fileCount":"27","fileSizeKB":"21825237","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:260 - \\\"Thiophosphorylation.\\\"","keywords":"group a strep;quorum sensing;infeciton;macrophage;immune response;inflammation;streptococcus pyogenes;DatasetType:Proteomics","pi":[{"name":"Michael Federle","email":"mfederle@uic.edu","institution":"University of Illinois - Chicago","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"d34a4792015841bb9130ca14b85a6747","id":"1314"}, {"dataset":"MSV000096913","datasetNum":"96913","title":"GNPS - Metabolomic data from a cerebral malaria case-control study in Mali","user":"jpcourneya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737580378000","created":"Jan. 22, 2025, 1:12 PM","description":"Metabolome data from cerebral malaria cases and uncomplicated malaria controls in a case-control study in Mali.","fileCount":"145","fileSizeKB":"7153589","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"untargeted metabolomics;Cerebral malaria;severe malarial anemia;DatasetType:Metabolomics","pi":[{"name":"Dr. Mark Travassos","email":"mtravass@som.umaryland.edu","institution":"University of Maryland School of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ba8df9f0096c4bf6abb946f323f153c1","id":"1315"}, {"dataset":"MSV000096912","datasetNum":"96912","title":"Oxidation of Retromer Complex controls Mitochondrial Translation","user":"hbc8","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737575705000","created":"Jan. 22, 2025, 11:55 AM","description":"Reactive oxygen species (ROS) underlie human pathologies including cancer and neurodegeneration. The mitochondrial electron transport chain is appreciated as a key regulator of ROS stoichiometry in cells. However, the pathways that sense and regulate ROS levels more broadly remain to be fully elucidated. Here, systematic base-editor and computational screens identify VPS35, a member of the Retromer trafficking complex, as a cytosolic ROS sensor. Mechanistically, we find that VPS35 C653\/C673 regulates compartmentalized mitochondrial translation by disrupting the plasma membrane localization of SLC7A1, leading to dramatic resistance against ROS-generating anti-cancer agents including cisplatin. Our study describes the regulation of compartmentalized translation and cellular ROS homeostasis by a single amino acid within vesicular trafficking machinery, supporting the long-standing hypothesis that mitochondrial ROS is implicated in cisplatin resistance. We anticipate that the approaches employed herein may template a generalizable method for the identification of functional ROS targets and sensors under various biological contexts.","fileCount":"78","fileSizeKB":"47154032","spectra":"0","psms":"326123","peptides":"75757","variants":"116083","proteins":"8859","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"TMTpro 18-plex","keywords":"K562;Plasma Membrane;Anti-cancer Agents;DatasetType:Proteomics","pi":[{"name":"Liron Bar-Peled","email":"lbar-peled@mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060069","task":"40b23f750cf14606a8a9b4ce4b3fe1e1","id":"1316"}, {"dataset":"MSV000096911","datasetNum":"96911","title":"Mass spectrometry analysis of ABHD17B partners in hepatic stellate cells","user":"mullenlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737566592000","created":"Jan. 22, 2025, 9:23 AM","description":"Primary human hepatic stellate cells were transduced with lentivirus expressing ABHD17B-FLAG or GFP-FLAG. Cells were lysed, and immunoprecipitation was performed with M2 anti-FLAG beads. Peptides were eluted with FLAG peptide and separated by gel electrophoresis prior to analysis by LC-MS\/MS\n\nSamples were analyzed at the Taplin Biological Mass Spectrometry Facility at Harvard Medical School using standard protocols for protein sequence analysis by LC-MS\/MS. Excised gel bands were cut into approximately 1 mm3 pieces. Gel pieces were then subjected to a modified in-gel trypsin digestion procedure. Gel pieces were washed and dehydrated with acetonitrile for 10 min. followed by removal of acetonitrile. Pieces were then completely dried in a speed-vac. Rehydration of the gel pieces was with 50 mM ammonium bicarbonate solution containing 12.5 ng\/ul modified sequencing-grade trypsin (Promega, Madison, WI) at 4C. After 45 min., the excess trypsin solution was removed and replaced with 50 mM ammonium bicarbonate solution to just cover the gel pieces. Samples were then placed in a 37C room overnight. Peptides were later extracted by removing the ammonium bicarbonate solution, followed by one wash with a solution containing 50% acetonitrile and 1% formic acid. The extracts were then dried in a speed-vac (~1 hr). The samples were then stored at 4C until analysis. On the day of analysis the samples were reconstituted in 5 - 10 ul of HPLC solvent A (2.5% acetonitrile, 0.1% formic acid). A nano-scale reverse-phase HPLC capillary column was created by packing 2.6 um C18 spherical silica beads into a fused silica capillary (100 um inner diameter x ~30 cm length) with a flame-drawn tip. After equilibrating the column each sample was loaded via auto sampler (LC Packings, San Francisco CA) onto the column. A gradient was formed and peptides were eluted with increasing concentrations of solvent B (97.5% acetonitrile, 0.1% formic acid). As peptides eluted they were subjected to electrospray ionization and then entered into a Velos Orbitrap Pro ion-trap mass spectrometer (Thermo Fisher Scientific, Waltham, MA). Peptides were detected, isolated, and fragmented to produce a tandem mass spectrum of specific fragment ions for each peptide.\n\nPeptide sequences (and hence protein identity) were determined by matching protein databases with the acquired fragmentation pattern by the software program, Sequest (Thermo Fisher Scientific, Waltham, MA). All databases include a reversed version of all the sequences and the data was filtered to between a one and two percent peptide false discovery rate.\n\n\n","fileCount":"42","fileSizeKB":"2441524","spectra":"0","psms":"133279","peptides":"90741","variants":"93020","proteins":"45395","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"abhd17b;hepatic stellate cell;liver fibrosis;DatasetType:Proteomics","pi":[{"name":"Alan C. Mullen","email":"mullenlabmgh@gmail.com","institution":"UMass Chan Medical School","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD060068","task":"940d9d7b84704be7b92193ca8b6aa0e1","id":"1317"}, {"dataset":"MSV000096908","datasetNum":"96908","title":"HPLC-ESI-ddMS2 analysis of extracts from three Hypericum genus plant species aimed identify xanthones and prenylated phloroglucinol derivatives","user":"Ingus","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737554987000","created":"Jan. 22, 2025, 6:09 AM","description":"Results from HPLC-ESI-ddMS2 survey of ethanolic extracts of three Hypericum genus plant species aimed to find xanthones and prenylated phloroglucinol derivatives.","fileCount":"65","fileSizeKB":"168","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hypericum inodorum;Hypericum androsaemum;Hypericum perforatum","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hypericum;xanthone;prenylated phloroglucinol derivatives;DatasetType:Metabolomics","pi":[{"name":"Ingus Perkons","email":"ingus.perkons@bior.lv","institution":"Institute of Food Safety, Animal Health and Environment \"BIOR\"","country":"Latvia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"71dfbf933857490e8c0423a890dd805e","id":"1318"}, {"dataset":"MSV000096905","datasetNum":"96905","title":"TMEM106B deficiency leads to alterations in lipid metabolism and obesity in the TDP-43Q331K knock-in mouse model ","user":"1234_Love","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737495340000","created":"Jan. 21, 2025, 1:35 PM","description":"Lipidomic analysis was performed to identify the lipid alteration in the liver of TDP-43 Q331K Tmem106b knockout mice","fileCount":"41","fileSizeKB":"22685282","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Vanquish UHPLC coupled with Q-Exactive Hybrid Quadrupole-Orbitrap system ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"TMEM106B, TDP-43;DatasetType:Other (lipidomics)","pi":[{"name":"Fenghua Hu","email":"fh87@cornell.edu","institution":"Cornell University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d06326676a694e2c820ec975816aeba6","id":"1319"}, {"dataset":"MSV000096903","datasetNum":"96903","title":"GNPS-Fe-nanoparticle Method Validation experiment 1","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737484957000","created":"Jan. 21, 2025, 10:42 AM","description":"FeNP can be utilized in enriching siderophores from pseudomonas fluorescens bacterial culture supernatant ","fileCount":"45","fileSizeKB":"903802","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"QExactive orbitrap LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Nanoparticle, Pseudomonas F, DFOB;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron","email":"allegra.aron@du.edu","institution":"University of Denver","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"87e26f49951246b6b7e85df9be532260","id":"1320"}, {"dataset":"MSV000096899","datasetNum":"96899","title":"Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Dilution Series and Single Shot Gradient comparison.","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737445892000","created":"Jan. 20, 2025, 11:51 PM","description":"Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependent and independent methods. This is achieved by pairing a Quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer that provides >200 Hz MS\/MS scanning speed, high resolving power and sensitivity, as well as low ppm-mass accuracy. Narrow window DIA enables profiling of up to 100 full yeast proteomes per day, or ~10,000 human proteins in half-an-hour. Moreover, multi-shot acquisition of fractionated samples allows comprehensive coverage of human proteomes in ~3h, showing comparable depth to next-generation RNA sequencing and with 10x higher throughput compared to current state-of-the-art MS. High quantitative precision and accuracy is demonstrated with high peptide coverage in a 3-species proteome mixture, quantifying 14,000+ proteins in a single run in half-an-hour.","fileCount":"60","fileSizeKB":"575221567","spectra":"17580163","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dia;Astral;Proteomics;DatasetType:Proteomics","pi":[{"name":"Jesper V. Olsen","email":"jesper.olsen@cprr.ku.dk","institution":"Professor, Deputy Head of Centre Center for Protein Research University of Copenhagen Denmark","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046283","task":"e4d42db46c9840b1883066bc2f9f12b3","id":"1321"}, {"dataset":"MSV000096896","datasetNum":"96896","title":"Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells","user":"tbockPCF","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737377492000","created":"Jan. 20, 2025, 4:51 AM","description":"Regulation of protein synthesis plays a central role in maintaining skeletal muscle integrity and its understanding is important for treatment of muscular and neuromuscular pathologies. eIF3f is one of the subunits of the translation initiation factor eIF3, having an important regulatory potential. Activity of eIF3f stands at the crossroads between protein synthesis associated hypertrophy and MAFbx\/atrogin-1 dependent atrophy in skeletal muscle cells. To date our mechanistic knowledge of eIF3f stems from contradictory studies highlighting its functional divergence in different cell types. To decipher the molecular mechanisms underpinning the role of eIF3f in regulating muscle mass, we established a cellular model to interrogate eIF3f functionality based on proximal interaction network identification. We generated a muscle cell line stably expressing eIF3f fused to the mutated BirA biotin ligase, allowing the irreversible labelling of the interactors of eIF3f in a nanometer range distance. Biotinylated proteins interacting with eIF3f were identified by streptavidin pulldowns and mass spectrometry. We successfully designed a functional eIF3f-BirA(BioID1) chimeric protein and validated its ability to interact with the core eIF3 complex upon transient expression in HEK293 cells. We used CRISPR-Cas9 molecular scissors to generate single cell clones of immortalized human muscle cells expressing the eIF3f-BioID1 chimera in place of the endogenous EIF3F locus. Irrespective of the proliferating or differentiated muscle cell states, we found that endogenously expressed eIF3f-BioID1 chimera mainly interacts with components of the eIF3 complex such as eIF3a\/b\/cl (c-like)\/e, and eIF4E, eIF4G, and eIF5 initiation factors, and co-sediments with ribosomal complexes in polysome profiles. Surprisingly, we identified several nuclear localized interactors of eIF3f, which, together with immunofluorescence analyses, indicates a previously unknown nuclear localization of eIF3f in both myoblasts and myotubes. Further, we identified several novel cytoplasmic binding partners of eIF3f, responsible for the maintenance of cytoplasmic skeletal muscle ultrastructure such as sarcomeric\/Z-disc (SYNPO2) bound proteins and proteins of the lysosomal compartment such as LAMP1. We describe here the establishment of an endogenous molecular tagging system for the translation initiation factor eIF3f, unravel its core proximal interactors in skeletal muscle cells, and validate LAMP1 as a new binding partner. We believe this cell line will be used to decipher eIF3f function in hypertrophic and atrophic conditions in skeletal muscle.","fileCount":"11","fileSizeKB":"2947718","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"eIF3f;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD059972","task":"dc06f1dfc112433c8cd0442eb2a823aa","id":"1322"}, {"dataset":"MSV000096891","datasetNum":"96891","title":"GNPS - mice terminal ileum mice infected with Salmonella","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737235193000","created":"Jan. 18, 2025, 1:19 PM","description":"Terminal ileum of mice infected with Salmonella run on Q-Exactive. Reversed-phase, ESI positive, polar C18 column (2.6 um particle size, 2.1 mm x 100 mm Phenomenex, Kinetex).","fileCount":"184","fileSizeKB":"13829113","spectra":"81844","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mice;Terminal ileum;Bacterial infection;Salmonella;LC-MS\/MS;Untargeted metabolomics;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"17d158e0f984483fa61286113116e22f","id":"1323"}, {"dataset":"MSV000096890","datasetNum":"96890","title":"Farnesylation in Th1 cells assessed by click chemistry","user":"JanaKoch","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737231514000","created":"Jan. 18, 2025, 12:18 PM","description":"T helper cell activation is highly regulated to ensure proper immune responses while avoiding autoimmune reactions. Cell functions are determined by regulation of various levels of gene expression including posttranslational modifications of proteins. Protein prenylation is a posttranslational modification, where either a farnesyl- or a geranylgeranyl residue is added to a protein. It was shown to play a role in the differentiation and activation of various T cell populations, including Th1 cells. However, it is largely unknown which proteins are prenylated in Th1 cells and what the effect of farnesyl transferase inhibitor treatment, which blocks farnesylation of proteins, on protein prenylation is in this context. Here, using mass spectrometry, we show the identification of farnesylated proteins in human Th1 cells. This approach additionally uncovered the farnesylation of proteins, not yet known to be prenylated. These data provide valuable insights into novel aspects of protein prenylation in Th1 cell activation and deepen our understanding of the effects of farnesyl transferase inhibitor treatment on the human immune system.","fileCount":"65","fileSizeKB":"83126988","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Farnesylation;Th1 cells;Prenylation;FTI;Click Enrichment;DatasetType:Proteomics","pi":[{"name":"Katja Baerenfaller","email":"katja.baerenfaller@siaf.uzh.ch","institution":"Swiss Institute of Allergy and Asthma Research","country":"Switzerland"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"41d78387336949239146c2bda6986669","id":"1324"}, {"dataset":"MSV000096888","datasetNum":"96888","title":"GNPS - Siderophore in fresh water microbial community","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737156066000","created":"Jan. 17, 2025, 3:21 PM","description":"Investigating siderophore presence in fresh water microbial community. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA). LC-MS\/MS data acquired in positive mode.","fileCount":"215","fileSizeKB":"10705523","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonadaceae (NCBITaxon:135621);Rhizobiaceae (NCBITaxon:82115)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Siderophores;Natural Products;Metabolomics;Microbial Community;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Orkun Soyer","email":"o.soyer@warwick.ac.uk","institution":"University of Warwick","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"20fd0c9ee48543978b96355b82097b12","id":"1325"}, {"dataset":"MSV000096887","datasetNum":"96887","title":"Chikungunya replication and infection is dependent upon and alters cellular hexosylceramide levels in Vero cells","user":"kmhines5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737151656000","created":"Jan. 17, 2025, 2:07 PM","description":"Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes significant global mor-bidity, including fever, rash, and persistent arthralgia. Utilizing untargeted lipidomics, we investi-gated how CHIKV infection alters host cell lipid metabolism in Vero cells. CHIKV infection induced marked catabolism of hexosylceramides, reducing their levels while increasing ceramide byprod-ucts. Functional studies revealed a reliance on fatty acid synthesis, ?-oxidation, and glycosphin-golipid biosynthesis. Notably, inhibition of uridine diphosphate glycosyltransferase 8 (UGT8), es-sential for galactosylceramide production, significantly impaired CHIKV replication and entry. CHIKV was also sensitive to evacetrapib, a cholesterol ester transfer protein (CETP) inhibitor, though the mechanism of inhibition appeared independent of CETP itself, suggesting an off-target effect. These findings highlight specific lipid pathways, particularly glycosphingolipid metabolism, as critical for CHIKV replication and further refine our understanding of how CHIKV exploits host lipid networks. This study provides new insights into CHIKV biology and suggests that targeted investigation of host lipid pathways may inform future therapeutic strategies.","fileCount":"3136","fileSizeKB":"68254855","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chikungunya virus (NCBITaxon:37124)","instrument":"Synapt XS;ACQUITY UPLC I-Class","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipidomics;hexosylceramide;CHIKV;chikungunya;DatasetType:Metabolomics","pi":[{"name":"Kelly M. Hines","email":"kelly.hines@uga.edu","institution":"University of Georgia","country":"USA"},{"name":"Melinda A. Brindley","email":"mbrindle@uga.edu","institution":"University of Georgia","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c3765f1663744baa82781f4fef8779fe","id":"1326"}, {"dataset":"MSV000096884","datasetNum":"96884","title":"GNPS-U19_ADRC_plasma_samples_project_41945_reupload","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737136134000","created":"Jan. 17, 2025, 9:48 AM","description":"U19 ADRC 654 plasma samples project number 41945. Reuploaded to remove sequestered NA data. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"3322","fileSizeKB":"102701360","spectra":"1814115","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plasma;adrc;u19;metabolomics;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7a35d515ea3f42039bddeb75b8d4ac1f","id":"1327"}, {"dataset":"MSV000096879","datasetNum":"96879","title":"Proteomic analysis of CYFIP2 knock-in mice","user":"yangyj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737090004000","created":"Jan. 16, 2025, 9:00 PM","description":"Proteomic analysis of CYFIP2 knock-in mice (hippocampus)","fileCount":"167","fileSizeKB":"73806397","spectra":"0","psms":"338688","peptides":"99149","variants":"136378","proteins":"7813","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"LC-MS\/MS;CYFIP2;Mouse brain;Hippocampus;Proteomics;DatasetType:Proteomics","pi":[{"name":"Jin Young Kim","email":"jinyoung@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep. of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059911","task":"55e513bfb94c4c86b981169fbc87a3bc","id":"1328"}, {"dataset":"MSV000096877","datasetNum":"96877","title":"Disulfide bonds are critical for stabilizing cell division, cell envelope biogenesis, and antibiotic resistance proteins in mycobacteria","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737072004000","created":"Jan. 16, 2025, 4:00 PM","description":"Mycobacterium, including Mycobacterium tuberculosis, the etiological agent of tuberculosis, have a unique cell envelope critical for their survival and antibacterial resistance. The cell envelope's assembly and maintenance influence permeability, making it a key target against multidrug resistant strains. Disulfide bond (SB) formation is crucial for the folding of cell envelope proteins The DSB pathway in mycobacteria includes two enzymes, DsbA and VKOR, required for survival. Using bioinformatics and cystine prfiling proteomics, we identified cell envelope proteins dependent on DSBs. We validated via in vivo alkylation, that key proteins like LamA (MmpS3, PstP, LpqW, and EmbB rely on DSBs for stability. Their stability is disrupted in the Delta VKOR mutant or by VKOR inhibition. Thus targeting DsbA and VKOR systems could compromise both cell division and mycomembrane integrity. These findings emphasize the potential of DSB inhibition as a novel strategy to combat mycobacterial infections.","fileCount":"36","fileSizeKB":"53354807","spectra":"0","psms":"348407","peptides":"42324","variants":"67787","proteins":"4387","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium smegmatis str. MC2 155 (NCBITaxon:246196)","instrument":"Orbitrap Eclipse","modification":"[c] DBIA;UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"disulfide bonds;oxidative protein folding;DsbA;VKOR;essential proteins;PstP;mycobacteria;actinobacteria;mycomembrane;PP2C;EmbB;Rv2507;MmpS3;cysteine-profiling mass spectrometry;DatasetType:Proteomics","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"},{"name":"Cristina Landeta","email":"clandeta@iu.edu","institution":"Indiana University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059898","task":"1f4ce2d6ec154273b169bd4ca6d7669a","id":"1329"}, {"dataset":"MSV000096875","datasetNum":"96875","title":"Lysosome skeletal muscle Proteomics","user":"amcuervo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737064413000","created":"Jan. 16, 2025, 1:53 PM","description":"Lysosome skeletal muscle Proteomics isolated from mice","fileCount":"7","fileSizeKB":"2038514","spectra":"0","psms":"41056","peptides":"34486","variants":"35906","proteins":"18498","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00412 - \\\"modification from UniMod artifact. OBSOLETE because UniMod entry 19 is now merged with UniMod 35 remap to MOD:00425 'monohydroxylated residue'.\\\"","keywords":"lysosomes, autophagy, proteostasis;DatasetType:Proteomics","pi":[{"name":"Ana Maria Cuervo","email":"ana-maria.cuervo@einsteinmed.edu","institution":"Albert Einstein College of Medicine","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059895","task":"05d5995964e24bbbaf86926dd905a2ab","id":"1330"}, {"dataset":"MSV000096874","datasetNum":"96874","title":"LYMTACs: Chimeric Small Molecules Repurpose Lysosomal Membrane Proteins for Target Protein Relocalization and Degradation","user":"wdeng03","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737060906000","created":"Jan. 16, 2025, 12:55 PM","description":"Proximity-inducing modalities that co-opt cellular pathways offer new opportunities to regulate oncogenic drivers. Inspired by the success of proximity-based chimeras in both intracellular and extracellular target space, here we describe the development of LYsosome Membrane TArgeting Chimeras (LYMTACs) as a novel small molecule-based platform that functions intracellularly to modulate the membrane proteome. Conceptually, LYMTACs are heterobifunctional small molecules that co-opt short-lived lysosomal membrane proteins (LMPs) as effectors to deliver targets for lysosomal degradation. We demonstrate that a promiscuous kinase inhibitor-based LYMTAC selectively targets membrane proteins for lysosomal degradation via RNF152, a short-lived LMP. To extend these findings, we show that oncogenic, membrane-associated KRASG12D protein can be tethered to RNF152, inducing KRAS relocalization to the lysosomal membrane, inhibiting downstream phospho-ERK signaling, and leading to lysosomal degradation of KRASG12D in a LYMTAC-dependent manner. Notably, potent cell killing could be attributed to the multi-pharmacology displayed by LYMTACs, which differentiates the LYMTAC technology from existing modalities. Thus, LYMTACs represent a proximity-based therapeutic approach that promises to expand the target space for challenging membrane proteins through targeted protein relocalization and degradation. The dataset is global proteomics analysis of pan kinase PROTAC or LYMTAC treated cells.","fileCount":"220","fileSizeKB":"38118744","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF HT;Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"LYMTAC;degrader;pan kinase;proteomics;DatasetType:Proteomics","pi":[{"name":"Patrick Ryan Potts","email":"rpotts01@amgen.com","institution":"Amgen Inc.","country":"united states"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"20a73984ae0749c69399b1771b5472db","id":"1331"}, {"dataset":"MSV000096872","datasetNum":"96872","title":"Human CNOT1 and CNOT4 interacting proteins bioID","user":"ReeselabPSU","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737050411000","created":"Jan. 16, 2025, 10:00 AM","description":"BioID identification of CNOT1 and CNOT4 interacting proteins","fileCount":"9","fileSizeKB":"1578154","spectra":"0","psms":"102548","peptides":"71499","variants":"77252","proteins":"17604","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Orbritrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CCR4-NOT, BioID, CNOT1, CNOT4;DatasetType:Proteomics","pi":[{"name":"Joseph Reese","email":"jcr8@psu.edu","institution":"Penn State University","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD059884","task":"82d01f987a1946af8c2ef50f24b361fe","id":"1332"}, {"dataset":"MSV000096871","datasetNum":"96871","title":"GNPS - Stingless bees propolis and geopropolis and Apis mellifera propolis from Brazil","user":"lgpf","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737049016000","created":"Jan. 16, 2025, 9:36 AM","description":"Metabolomics (LC-MS\/MS) of propolis and geopropolis samples produced by different species of stingless bees, collected in the city of Bandeirantes (Parana, Brazil). Commercial samples of green and red propolis from Appis mellifera honeybee were also analyzed.","fileCount":"26","fileSizeKB":"2047128","spectra":"31047","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Melipona quadrifasciata (NCBITaxon:166423);Tetragona clavipes (NCBITaxon:596866);Tetragonisca angustula (NCBITaxon:166442);Plebeia droryana (NCBITaxon:166444);Apis mellifera (NCBITaxon:7460)","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Stingless bee;Melipona quadrifasciata;Apis mellifera;Propolis;Geopropolis;Dehydroabietic acid;diterpene resin acids;DatasetType:Metabolomics","pi":[{"name":"Norberto Peporine Lopes","email":"npelopes@fcfrp.usp.br","institution":"Faculdade de Ciencias Farmaceuticas de Ribeirao Preto - Universidade de Sao Paulo","country":"Brasil"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"55d577db641046aea7154eb8d79904eb","id":"1333"}, {"dataset":"MSV000096868","datasetNum":"96868","title":"Quantitative proteomic analysis reveals JMJD6 and DNAJB11 as endogenous substrates of E3 ligase RFFL","user":"Narendradev_N","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737023569000","created":"Jan. 16, 2025, 2:32 AM","description":"Immunoprecipitation experiments using anti-RFFL antibody. Samples were loaded in technical duplicates in EvoTips, and chromatographic separation was done on an in-house column and the 30 samples per day (SPD) method on Evosep One system (Evosep). Peptides were detected and fragmented using timsTOF Pro 2 mass spectrometer (Bruker Daltonics) in data-dependent mode with parallel accumulation serial fragmentation (PASEF) enabled.\r\n\r\nThe raw data was analyzed using Fragpipe (v 22.0). MS\/MS spectra were searched using MSFragger (v 4.1) against forward and reversed Homo sapiens UniProt sequence database (UP000005640) supplemented with common contaminants (total 20,979 sequences excluding decoys).","fileCount":"7","fileSizeKB":"39916023","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RFFL;Interactome;E3 ligase;Substrates;DatasetType:Proteomics","pi":[{"name":"Prof. S. Murty Srinivasula","email":"sms@iisertvm.ac.in","institution":"Indian Institute of Science Education and Research Thiruvananthapuram","country":"India"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD059871","task":"3d59e4a5cb1649b89c1a638314e5f20c","id":"1334"}, {"dataset":"MSV000096866","datasetNum":"96866","title":"Phosphoproteomics of RAPTOR1 and LST8-1 PUP-IT samples (inducible expression)","user":"leonardblaschek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737020934000","created":"Jan. 16, 2025, 1:48 AM","description":"PUP-IT proximity labeling of Arabidopsis Target of Rapamycin Complex (TORC) subunits LST8-1 and RAPTOR1, compared against a GFP control, with beta-estradiol-inducible expression of FLAG::PUP(E). The FLAG-enriched samples were additionally enriched for phosphorylated peptides. The sample metadata, sequence database and fragpipe workflow are uploaded under the 'Metadata' tag.","fileCount":"155","fileSizeKB":"95625237","spectra":"2309775","psms":"202021","peptides":"12306","variants":"16465","proteins":"1837","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"timsTOF Pro 2","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:1264 - \\\"Addition of GGE.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"PUP-IT;Proximity labeling;Target of Rapamycin;TOR;Phosphoproteomics;DatasetType:Proteomics","pi":[{"name":"Staffan Persson","email":"staffan.persson@plen.ku.dk","institution":"Copenhagen University","country":"Denmmark"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD059869","task":"33739feca77f4c3aa73a182d3a36ac37","id":"1335"}, {"dataset":"MSV000096864","datasetNum":"96864","title":"PUP-IT proximity-labeling of Arabidopsis TOR via yeast FKBP (constitutive expression)","user":"leonardblaschek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737014795000","created":"Jan. 16, 2025, 12:06 AM","description":"PUP-IT proximity labeling of Arabidopsis Target of Rapamycin Complex (TORC), using the yeast FKBP protein (P20081) as a bait with and without rapamycin treatment and constitutive expression of FLAG::PUP(E). The sample metadata, sequence database and fragpipe workflow are uploaded under the 'Metadata' tag.","fileCount":"58","fileSizeKB":"36834177","spectra":"0","psms":"315031","peptides":"23195","variants":"28297","proteins":"3207","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"timsTOF Pro","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:1264 - \\\"Addition of GGE.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PUP-IT;Proximity labeling;Target of Rapamycin;TOR;DatasetType:Proteomics","pi":[{"name":"Staffan Persson","email":"staffan.persson@plen.ku.dk","institution":"Copenhagen University","country":"Denmmark"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD059865","task":"691bb7031eb74907a9d24eda6b96d59a","id":"1336"}, {"dataset":"MSV000096862","datasetNum":"96862","title":"PUP-IT proximity-labeling of LST8-1 and RAPTOR1 interactors (inducible expression)","user":"leonardblaschek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737012402000","created":"Jan. 15, 2025, 11:26 PM","description":"PUP-IT proximity labeling of Arabidopsis Target of Rapamycin Complex (TORC) subunits LST8-1 and RAPTOR1, compared against a GFP control, with beta-estradiol-inducible expression of FLAG::PUP(E). 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Cell pellets were processed as described previously (Marathe et al., 2021). Briefly, the pellet was re-solubilized in Urea-Thiourea Buffer (6M Urea, 2M Thio-urea in Tris-Cl) containing protease inhibitor cocktail (#4693159001, Roche), phosphatase Inhibitor cocktail 2 (#P5726, Sigma) and phosphatase Inhibitor cocktail 3 (#P0044, Sigma). After protein concentration estimation using BCA (#23225, Pierce), 30ug of proteins from each sample were used for subsequent steps. Samples were reduced with 15mM DTT a 40oC for 60 minutes, followed by alkylation with 15 mM iodoacetamide for 30 minutes at room temperature in the dark. The digestion mixture was then diluted 4× with 50 mM ammonium bicarbonate, and the protein was digested with 1 ?g of MS-grade trypsin (#V5280, Promega) overnight at 37°C. The resulting peptide solutions were cleaned with C18 ZipTips, quantified using the Scopes method (Scopes, 1974), and 700 ng of peptides were injected into Thermo Q-Exactive plus instrument via EasyNLC through C18 PepMap EasySpray RSLC analytical column (#ES903, Thermo). The MS instrument was set to an MS1 resolution of 70,000 and an MS2 resolution of 17,500, with acquisition experiments optimized for 120 min LC gradients.\r\nThe MS spectra were analyzed using Proteome Discoverer version 2.2 using the standard LFQ workflows by Thermo Fisher as described previously (Marathe et al., 2021). Briefly, tandem mass spectra were searched against the UniProt human database and reversed sequences, using SEQUEST (Eng, McCormack and Yates, 1994). Full tryptic search with up to 2 missed cleavages and a minimum peptide length of 6 is considered. Carbamidomethylation on cystines (+57.021) was considered as a static modification, and oxidation on methionine (+15.995 Da) was considered as a dynamic modification. Precursor mass tolerance was set to 10 PPM, and fragment mass tolerance was set to 0.02 Da. Precursor ion-based quantification was performed using only unique peptides and the samples were normalized with respect to the total peptide amount. The false discovery rate (FDR) at the protein level was set to 0.01. Three biological replicates were used for analysis, and statistical analysis of identified proteins was performed using ANOVA (background-based).\r\n\r\nWT (AN1.raw,BN1.raw,CN1.raw)\r\nKO (AN2.raw,,BN2.raw,CN2.raw)\r\nRescue (AN3.raw,BN3.raw,CN3.raw)","fileCount":"11","fileSizeKB":"15443039","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RFFL;E3 ligase;Substrates;Proteomics;Interactome;DatasetType:Proteomics","pi":[{"name":"Prof. S. Murty Srinivasula","email":"sms@iisertvm.ac.in","institution":"Indian Institute of Science Education and Research Thiruvananthapuram","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059848","task":"78e536b8fe574ce7a87e77e81c26e1fa","id":"1338"}, {"dataset":"MSV000096860","datasetNum":"96860","title":"GNPS - ESTRMN metadata Entropy Similarity Driven Transformation Reaction Molecular Networking Sartans","user":"qianyulia","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1737000914000","created":"Jan. 15, 2025, 8:15 PM","description":"These included influents and effluents collected in January 2019 at 16 WWTPs located in 16 Chinese provinces, influents and effluents collected from August 2019 to October 2019, at 15 WWTPs in 15 Chinese provinces, effluents collected at 2 WWTPs in the Wujing river in August 2020. The full process samples at a certain WWTP in Nanjing, Jiangsu were collected twice, in March and June 2023, respectively. The names of positive and negative files are one-to-one correspondence. Unless otherwise noted, those containing nxx or n-xx are in negative ion mode. Both pxx and p-xx are in positive ion mode. In represents water inflow and out represents water outflow. If there are only in and digits, it is positive ion mode.","fileCount":"421","fileSizeKB":"156271816","spectra":"3589760","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental sample wastewater","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"wastewater;DatasetType:Metabolomics","pi":[{"name":"Weisi","email":"weisi@nju.edu.cn","institution":"Nanjing University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"57c23777cae44d828239d4c60dce4e29","id":"1339"}, {"dataset":"MSV000096859","datasetNum":"96859","title":"A single point mutation on FLT3L-Fc protein increases the risk of Immunogenicity","user":"qtphung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736982441000","created":"Jan. 15, 2025, 3:07 PM","description":"Immunogenicity analysis of FLT3L-Fc biotherapeutic","fileCount":"121","fileSizeKB":"29414558","spectra":"228978","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"FLT3L;immunogenicity;MHC class II;DatasetType:Proteomics","pi":[{"name":"Qui Phung","email":"qtphung@gene.com","institution":"Genentech, Inc.","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bf2e9007a44f42ac825b946996b29e5b","id":"1340"}, {"dataset":"MSV000096858","datasetNum":"96858","title":"C-terminal tagging, transmembrane domain hydrophobicity, and an ER retention motif influence the secretory trafficking of the inner nuclear membrane protein emerin","user":"rvolk","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736981585000","created":"Jan. 15, 2025, 2:53 PM","description":"Mass spectrometry analysis of interacting partners of EMD or EMD with RXR motif mutated (RA) following FLAG-IP from FLAG-EMD U2OS, FLAG-RA U2OS, and parental U2OS.","fileCount":"2","fileSizeKB":"12768138","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Pro","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"emerin;nuclear membrane;DatasetType:Proteomics","pi":[{"name":"Abigail Buchwalter","email":"abigail.buchwalter@ucsf.edu","institution":"UCSF","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a3eba071fc934bab8a69dd9c2149f9f2","id":"1341"}, {"dataset":"MSV000096857","datasetNum":"96857","title":"Brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736979238000","created":"Jan. 15, 2025, 2:13 PM","description":"Cells regulate function by synthesizing and degrading proteins. This turnover ranges from minutes to weeks, as it varies across proteins, cellular compartments, cell types, and tissues. Current methods for tracking protein turnover lack the spatial and temporal resolution needed to investigate these processes, especially in the intact brain, which presents unique challenges. We describe a pulse-chase method (DELTA) for measuring protein turnover with high spatial and temporal resolution throughout the body, including the brain. DELTA relies on rapid covalent capture by HaloTag of fluorophores that were optimized for bioavailability in vivo. The nuclear protein MeCP2 showed brain region-and cell type-specific turnover. The synaptic protein PSD95 was destabilized in specific brain regions by behavioral enrichment. A novel variant of expansion microscopy further facilitated turnover measurements at individual synapses. DELTA enables studies of adaptive and maladaptive plasticity in brain-wide neural circuits.","fileCount":"420","fileSizeKB":"263627540","spectra":"0","psms":"1196338","peptides":"45347","variants":"45347","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Ascend","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"Brain, Synaptic protein turnover, learning;DatasetType:Proteomics","pi":[{"name":"Jeffrey N. Savas, PhD","email":"jeffrey.savas@northwestern.edu","institution":"Department of Neurology Northwestern University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059839","task":"663807690c0f4adaa0ebe47109bfcc7b","id":"1342"}, {"dataset":"MSV000096856","datasetNum":"96856","title":"GNPS - Ion Mobility Mass Spectrometry - Metallophores","user":"bugnilabgroup","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736977644000","created":"Jan. 15, 2025, 1:47 PM","description":"Raw data files regarding publication titled \"Ion Mobility-coupled Mass Spectrometry for Metallophore Detection\"\r\n[insert doi here following publication]","fileCount":"3559","fileSizeKB":"5278409","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinomadura sp. WMMA1423 (NCBITaxon:2591108);Pseudonocardia sp. WMMC193;Bacillus sp. WMMC1349;Micromonospora sp. WMMC415 (NCBITaxon:2675222)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Ion mobility;Metallophores;DatasetType:Metabolomics","pi":[{"name":"Tim Bugni","email":"tim.bugni@wisc.edu","institution":"University of Wisconsin - Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"64defb3034c74681b84d4f1532797833","id":"1343"}, {"dataset":"MSV000096854","datasetNum":"96854","title":"Hijacking intrinsic resistance in Mycobacterium abscessus","user":"sbyrum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736972538000","created":"Jan. 15, 2025, 12:22 PM","description":"We performed total quantitative proteomics on planktonic Mycobacterium abscessus ATCC19977 cells treated with 100 microM of florfenicol amine (FF-NH2 or FFA) treated or vehicle (DMSO) control for 30 minutes and 3 hours to detect unbiased FF-NH2-induced differences in the M. abscessus proteome.","fileCount":"22","fileSizeKB":"201157037","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium abscessus ATCC 19977 (NCBITaxon:561007)","instrument":"timsTOF HT","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"DIA;infectious diseases;timsTOF;Mycobacterium;DatasetType:Proteomics","pi":[{"name":"Richard E. Lee","email":"Richard.Lee@stjude.org","institution":"St. Jude Children's Research Hospital","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD059834","task":"04808136d78d4aabab8722561c2a6836","id":"1344"}, {"dataset":"MSV000096853","datasetNum":"96853","title":"Cancer-restricted cryptic antigens are targets for T cell recognition","user":"clauser","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736971251000","created":"Jan. 15, 2025, 12:00 PM","description":"Ely ZA, Kulstad ZJ, Gunaydin G, Addepalli S, Verzani EK, Casarrubios M, Clauser KR, Wang X, Lippincott IE, Louvet C, Schmitt T, Kapner KS, Agus MP, Hennessey CJ, Cleary JM, Hadrup SR, Klaeger S, Su J, Jaeger AM, Wolpin BM, Raghavan S, Smith EL, Greenberg PD, Aguirre AJ, Abelin JG, Carr SA, Jacks T, Freed-Pastor WA. 2025 \nTranslation of the non-coding genome in cancer can generate cryptic peptides capable of presentation by human leukocyte antigen class I (HLA-I); however, the cancer-specificity and immunogenicity of non-canonical HLA-I-bound peptides (ncHLAp) is not fully understood. Using personalized proteogenomics coupled with high-resolution immunopeptidomics, we found that cryptic peptides are abundant in the pancreatic cancer immunopeptidome. We developed a novel translation-centric pipeline and discovered that ~30% of ncHLAp exhibit bona fide cancer-restricted translation, with a substantial subset shared among patients. Cancer-restricted ncHLAp demonstrated immunogenic potential in a highly sensitive ex vivo T cell priming platform. ncHLAp-reactive, TCR-redirected T cells (TCR-T) exhibit robust tumoricidal activity against patient-derived pancreatic cancer organoids. These findings demonstrate that dysregulated translation in pancreatic cancer can give rise to recurrent cancer-restricted ncHLAp capable of recognition by cytotoxic T cells. We anticipate future therapeutic strategies for pancreatic cancer and other solid tumors will include targeting cryptic antigens.\n","fileCount":"314","fileSizeKB":"145044605","spectra":"4670082","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"C-cysteinylation; C-carbamidomethylation;M-oxidation;q-pyro-glutamic acid","keywords":"immunopeptidome;pancreatic ductal adenocarcinoma;non-canonical ORF;DatasetType:Proteomics","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059832","task":"a1403c8adf28494ab89e1d12570cfbc1","id":"1345"}, {"dataset":"MSV000096852","datasetNum":"96852","title":"GNPS - Improved MALDI-MS Imaging of Polar and 2H-Labeled Metabolites in Mouse Organ Tissues","user":"Kasarla04","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736971195000","created":"Jan. 15, 2025, 11:59 AM","description":"Matrix-assisted laser desorption\/ionization mass spectrometry imaging (MALDI-MSI) is an indispensable analytical tool to depict the spatial distribution of analytes such as polar metabolites, lipids, proteins, and drugs in biological specimens. Imaging small polar metabolites and analyzing their in-vivo dynamics with stable isotope labeled (SIL) tracing through various biochemical pathways, including citric acid (TCA) cycle, glycolysis, and amino acid metabolism, has gained substantial interest over the years. However, imaging these polar metabolites across different tissue types is limited due to their lower ionization efficiencies and ion suppression from other abundant biomolecules. These challenges can be further exacerbated with SIL studies, which require the improvement of sample preparation methods. Solvent pretreatments before matrix application on a tissue section have the potential to improve the sensitivity, but often challenges with validation of spatial distribution of metabolites revealed in MALDI-MSI. Here, we present a optimized 'basic hexane' wash method that improved the detection of small molecules with exceptional sensitivity up to several folds for polar and 2H labeled glycolytic metabolites across five different mouse organ tissues (kidney, heart, brain, liver, and brown adipose tissue). Further, we addressed one of the major concerns such as validation of localised polar metabolites within the tissue regions by implementing spatial validation workflow. The workflow depicts the use of region of interest guided laser capture microdissection of tissue regions followed by LC-MS\/MS. Indeed, majority of metabolites showed an excellent corroboration with distribution of metabolites in MALDI-MSI and LMD-LC-MS\/MS. Besides, we also observed the similar effect on boosting signal intensities of polar metabolites extracted from the microsampled tissues using LMD followed by LC-MS\/MS. Overall, we provided an improved MALDI sample pretreatment approach and the spatial validation workflow to understand polar metabolite distribution in mouse organs.","fileCount":"281","fileSizeKB":"36759891","spectra":"473157","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MALDI-MSI;Metabolomics;Laser capture microdissection;LC-MS\/MS;Spatial validation;DatasetType:Metabolomics","pi":[{"name":"Dr. Prasad Phapale","email":"prasad.phapale@isas.de","institution":"Leibniz-Institut fuer Analytische Wissenschaften-ISAS-e.V.","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cc12305719e6400c8a7e36ef97fccbbc","id":"1346"}, {"dataset":"MSV000096845","datasetNum":"96845","title":"GNPS - Drug metabolites 5-ASA RT matching","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736827402000","created":"Jan. 13, 2025, 8:03 PM","description":"Drug metabolites of 5-ASA, Retention time matching","fileCount":"14","fileSizeKB":"1537814","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Drug, metabolites, feces, metabolomics;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"db04ebc9952b41c8a58ff3662e72b440","id":"1347"}, {"dataset":"MSV000096839","datasetNum":"96839","title":"Structural obstruction to full DNA replication in the chromatin of terminally differentiated skeletal muscle cells","user":"serena_camerini","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736778817000","created":"Jan. 13, 2025, 6:33 AM","description":"Terminal cell differentiation is often associated with permanent withdrawal from proliferation, termed the postmitotic state. Though widespread among vertebrates and determinant for their biology, the molecular underpinnings of this state are poorly understood. Postmitotic skeletal muscle myotubes can be induced to reenter the cell cycle; however, they generally die as a result of their inability to complete DNA replication. Here, we explore the causes of such incompetence. Genomic hybridization of newly synthesized DNA showed that the replicative failure does not concern specific genomic regions, but can stochastically affect any of them. Myoblast and myotube were incubated in replicative Xenopus egg extract, which provides a full DNA replication machinery. While myoblast nuclei attained complete DNA replication, those from myotubes, even in these conditions, duplicated less than half of their genomes, strongly indicating that the very structure of myotube chromatin obstructs DNA replication. Furthermore, disassembling and disorganizing chromatin with a strong salt treatment did not modify the replicative differences between the two nucleus types, suggesting that they are rooted in the core structure of chromatin.\nProteomic methods\nCells were harvested, centrifuged, then washed once in PBS. To isolate nuclei, pellets were resuspended in Hypotonic Buffer (10mM HEPES pH 7.5, 2 mM KCl, 2 mM MgCl2, 3 mM EDTA, HALT Protease Inhibitors, 1 mM 1,4 DTT) and incubated on ice for 30 or 60 min. Myoblasts were then centrifuged again and resuspended in PBS containing 25 ug\/ml trypsin, then incubated for 2 min to release nuclei. Myotubes received a similar treatment, but were resuspended in 37.5 ug\/ml trypsin and incubated for 4 minutes. To stop digestion, PMSF was added to a final concentration of 1 mM and the solution was incubated for 5 min on ice. To permeabilize the nuclear membrane, a final concentration of 0.2 percent Triton X-100 was added to the suspension. After 5 min of incubation on ice, isolated nuclei were centrifuged as above and resuspended in Iso Buffer (10 mM HEPES pH 7.5, 25 mM KCl, 2 mM MgCl2, 75 mM sucrose, 0.5 mM PMSF, 1 mM DTT)). \nFor mass spectrometry analyses, freshly isolated nuclei were washed once in Iso Buffer, suspended in 50 mM ammonium bicarbonate, and sonicated.\nProteins extracted from nuclei treated or not with 0.5 M NaCl were analyzed by LC-MSMS after cysteine reduction with 1 mM TCEP and alkylation with 12 mM iodoacetamide, and overnight digestion with trypsin (protein ratio 1:50 w:w) at 37 degree. Peptides were then injected into an Ultimate 3000 UHPLC (Dionex, Thermo Fisher Scientific) in line with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific). After a desalting step in a trap column, analytical separations were performed on a single 45 cm long silica capillary packed in house with a C18, and heated at 45 degree in an oven (Sonation). A 90 min long HPLC gradient was used. The Data Independent Acquisition (DIA) mode was used. MS data were acquired in the 300-1200 m over z range split into 40 contiguous windows with 1 m over z overlap, fragmented by HCD 28 percent, and the MS2 spectra were acquired in the Orbitrap at 30K resolution in the 145 to 1450 m over z range.\nProtein identification was obtained using the SwissProt mouse database containing the manually curated list of histones (24,945 sequences) obtained from El Kennani. The raw data were analyzed with the DIA-NN software v. 1.8.1. Statistical analyses were performed using the Perseus software (v. 2.0.11). Data analyses regarded only nuclear proteins, based on SwissProt annotations, while contaminating non nuclear proteins were ignored. To evaluate significant changes in protein abundances between NaCl treated and untreated samples, raw intensity values were normalized to total core histone values. After normalization, all values were transformed to log2. Only proteins quantified in at least 5 of 8 samples were considered. Missing values were imputed, replacing them with values from the normal distribution (Width 0.3, Down Shift 1.8). Significance was evaluated using Students t-Test (FDR 0.05, S0 = 0.1, 250 randomization).\n","fileCount":"10","fileSizeKB":"7942181","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"cell cycle nuclei muscle skeletal cell;DatasetType:Proteomics","pi":[{"name":"Serena Camerini","email":"serena.camerini@iss.it","institution":"istituto superiore di sanita","country":"Italia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059731","task":"82a3aae083a247929273659437ddeaee","id":"1348"}, {"dataset":"MSV000096837","datasetNum":"96837","title":"A universal peptide and any peptidoform spectrum annotator for mass spectrometry-based proteomics","user":"ShelleyJager","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736774749000","created":"Jan. 13, 2025, 5:25 AM","description":"Example dataset for Annotator tool. Data includes:\n- the top-down data of Fab of Herceptin, summed and deconvoluted, measured on Eclipse;\n- the bottom-up data of O-glycosylation of human colostrum IgA, measured on ZenoTOF 7600 using EAD;\n- the bottom-up data of N-glycosylation of human plasma, measured on ZenoTOF 7600 using EACID.","fileCount":"111","fileSizeKB":"4851567","spectra":"38942","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ZenoTOF 7600;Orbitrap Eclipse","modification":"N-glycans;O-glycans","keywords":"PTMs;top-down;Glycans;Bottom-up;DatasetType:Proteomics","pi":[{"name":"Joost Snijder","email":"j.snijder@uu.nl","institution":"Utrecht University","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059727","task":"bb85d63946b444089499ab5208e71245","id":"1349"}, {"dataset":"MSV000096836","datasetNum":"96836","title":"Enhancing the efficacy in melanoma treatment: the chemosensitising role of Vipera ammodytes venom on human melanoma cell lines.","user":"Marialuisa_PX","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736765264000","created":"Jan. 13, 2025, 2:47 AM","description":"This study investigates the potential of Vipera ammodytes venom as a therapeutic agent for human melanoma, specifically evaluating its cytotoxicity and chemosensitizing effects. Proteomic analysis identified over 125 proteins in the venom, with phospholipases A2, C type lectins, and metalloproteinases among the most abundant components. These proteins are associated with cytotoxic, anti proliferative, and tumor inhibiting properties. Three melanoma cell lines (M001, Me501, and A375) were used to assess venom activity. The IC50 values demonstrated consistent venom sensitivity across cell lines. Combined treatment with venom and cisplatin significantly increased cytotoxicity compared to single agent treatments. Notably, venom enhanced cisplatin sensitivity in resistant cell lines (M001 and Me501), increasing cell mortality by up to 40 percentage. Protein sample preparation for mass spectrometry analysis was carried on following two protocols. In the first protocol, snake venom proteins were dissolved in 100 mM ammonium bicarbonate (AMBIC), subjected to cysteine reduction by 25mM TCEP for 10 min and alkylation by 10mM IAM for 30 min in the dark, precipitated by incubation with six volumes of an organic solution (methanol, acetone and ethanol; 25percent, 25 percent, and 50 percent v\/v) at minus 20C over night. Protein pellet was centrifuged at 4C, suspended in 1M urea and 25mM AMBIC and over-night digested adding trypsin, at a substrate to enzyme ratio of 50:1 (w\/w) at 37 C on a mixer heat block. In the second protocol, snake venom proteins were denatured for 10 min at 95C in 25mM AMBIC and without a protein precipitation step, directly digested after cysteine reduction and alkylation, in the previously described conditions. The peptide mixture derived from each protocol was injected four times in an Ultimate 3000 UHPLC (Thermo Fisher Scientific, CA, United States) coupled with an Orbitrap Fusion Tribrid mass spectrometer. Peptides were desalted on a trap column and then separated on a 45 cm long silica capillary .The analytical column was encased by a column oven (Sonation; 40C during data acquisition) and attached to a nanospray Flex ion source. Peptides were separated by a 120min long gradient of buffer A (95 percent water, 5 percent acetonitrile, and 0.1 percent formic acid) and buffer B (95percent acetonitrile, 5percent water, and 0,1 percent formic acid), at a flow rate of 250 nl min. The mass spectrometer was operated in positive ion mode, using a data dependent acquisition strategy. Precursor ion scanning was performed in the Orbitrap in the 350 1550 m to z range with 120K resolution. Data dependent acquisition was performed in top speed mode (3s long maximum cycle time): the most intense precursors were selected through a monoisotopic precursor selection (MIPS) filter and with charge grater than1, quadrupole isolated and fragmented by higher energy collisional dissociation (HCD) (30 percent). Product ion spectra were acquired in the ion trap with rapid scan rate. Peptide spectra were searched by the software Proteome Discoverer 2.4 using Sequest HT as search engine against two databases downloaded from UniProtKB Swiss-Prot: Vipera ammodytes ammodytes (Rev Unrev) database (Release 2024; 126 sequences) and Vipera (Rev Unrev) database (Release 2024; 1559 sequences). Spectral matches were filtered using Percolator node, with 1percent q value based false discovery rate (FDR).\nOnly master proteins were taken into account and only specific trypsin cleavages with two miscleavages were admitted. Cysteine carbamydomethylation was set as static modification, while methionine oxidation and N acetylation on protein terminus were set as variable modifications. \nPrecursor and fragment mass tolerance was set to 15 ppm and 0.6 Da, respectively. ","fileCount":"17","fileSizeKB":"34217086","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vipera ammodytes ammodytes (NCBITaxon:8705)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Proteomics, snake venom, viper venom, melanoma;DatasetType:Proteomics","pi":[{"name":"Marialuisa Casella","email":"marialuisa.casella@iss.it","institution":"Istituto Superiore Sanita","country":"Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059718","task":"ffec87f1bedb491fbdc12b5b8d6bdffb","id":"1350"}, {"dataset":"MSV000096835","datasetNum":"96835","title":"The development of a high throughput screening platform using mass spectrometry for the discovery of potential inhibitors against SARS-CoV-2 Omicron Receptor-Binding Domain and human Angiotensin-Converting Enzyme 2 binding interaction from traditional Chinese medicine","user":"cjchen_01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736759065000","created":"Jan. 13, 2025, 1:04 AM","description":"The coronavirus disease 2019 (COVID-19) pandemic, initiated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread worldwide. The entry of SARS-CoV-2 into human cells relies on the interaction between the receptor- binding domain (RBD) of the spike protein on the surface of the virus and the angiotensin-converting enzyme 2 (ACE2) receptor on the surface of human cells. Consequently, disrupting the interaction between the spike protein and ACE2 is a promising strategy for preventing SARS-CoV-2 infection and treating SARS-CoV-2 infected patients. To discover potential drugs for SARS-CoV-2 from traditional Chinese medicines (TCMs), we established a plat-form combining ACE2-conjugated magnetic particles, a spike protein, a C18 plate, and MALDI-TOF for rapid screening of potential TCM candidates for SARS-CoV-2. After screening over 100 TCMs, some were found to effectively inhibit the binding interaction between ACE2 and spike proteins. We further identified three active compounds in these TCMs that could inhibit the binding between ACE2 and the spike protein of the Omicron variant. These three compounds also showed potent activity in blocking viral entry in a SARS-CoV-2 viral pseudo-particles (Vpp) cell-based assay.","fileCount":"67931","fileSizeKB":"29223091","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"MALDI ","modification":"NA","keywords":"SARS-CoV-2, RBD, ACE2, Mass spectrometry;DatasetType:Other (protein)","pi":[{"name":"Chao-Jung Chen","email":"cjchen@mail.cmu.edu.tw","institution":"China Medical University","country":"Taiwan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cf36007b509149a7a8d4b94f6bc6b420","id":"1351"}, {"dataset":"MSV000096833","datasetNum":"96833","title":"GNPS_CMMC_Luvunga_sarmentosa_1","user":"Firman2001","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736686199000","created":"Jan. 12, 2025, 4:49 AM","description":"MS\/MS fragmentation data of acquired on Orbitrap Fusion with chromatographic seperation on a accuocore vanquish C18 Coloumn","fileCount":"4","fileSizeKB":"310045","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicaple","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coumarin;Alkaloid;Terpenoid;Fatty acid;DatasetType:Metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e8bd0cd9ad7c427e94ce50df6e90c1b4","id":"1352"}, {"dataset":"MSV000096830","datasetNum":"96830","title":"Combinatorial phosphorylation on CTD of RNA polymerase II selectively controls transcription and export of protein-coding mRNAs","user":"bfloyd","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736623955000","created":"Jan. 11, 2025, 11:32 AM","description":"C-terminal domain (CTD) of RNA polymerase II is crucial for recruiting transcription regulators via specific post-translational modifications (PTM), especially phosphorylation. The hypothesis of combination of PTMs, or CTD code, that can allow precise and dynamic recruitment of transcription machinery is highly attractive, yet the experimental evidence to support this hypothesis has been scarce. Here, despite lacking specific antibodies for combinatorial CTD phosphorylation, we developed an innovative approach that detects double phosphorylation patterns on the CTD in a whole-genomic fashion by leveraging the antibody masking effect with selectively removing the flanking interference. Using this method, we detected pT4pS5 double phosphosites occurring exclusively during the transcription of protein-coding genes. Furthermore, we showed that pT4pS5 marks recruit the Transcription and Export complex (TREX), which specifically facilitates mRNA processing and nucleocytoplasmic export of protein-coding mRNAs. The recruitment of TREX by pT4pS5 phosphosites is particularly important for the processing of lengthy neurogenesis-related genes. Our results provide experimental support for the notion that CTD coding system can function combinatorically and in a gene-specific manner, which encodes an exact information about the transcription of specific gene clusters. This method can be broadly applied to map all combinatorial PTM patterns on RNA polymerase II, paving the way for a deeper understanding of gene-specific transcription regulation at the molecular level","fileCount":"16","fileSizeKB":"9180981","spectra":"0","psms":"3399","peptides":"712","variants":"712","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Phosphorylation;PPI;DatasetType:Proteomics","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059670","task":"d553f560e3584f19a019afde234f99e1","id":"1353"}, {"dataset":"MSV000096828","datasetNum":"96828","title":"PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736553531000","created":"Jan. 10, 2025, 3:58 PM","description":"Analysis of synthetic peptide reference datasets to demonstrate the performance of PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events.","fileCount":"72","fileSizeKB":"35794412","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 5600","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Site localization;Synthetic phospho-peptides;Human;Lc-ms\/ms;DatasetType:Proteomics","pi":[{"name":"Robert Moritz","email":"rmoritz@systemsbiology.org","institution":"Institute for Systems Biology","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD013210","task":"97562b6027fe40368a3d4f1bf5e06fef","id":"1354"}, {"dataset":"MSV000096827","datasetNum":"96827","title":"Hepatic p62, a major autophagic receptor in CYP4A ALD","user":"mtrnka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736552777000","created":"Jan. 10, 2025, 3:46 PM","description":"In cell DSS crosslinking of HEK293 cells expressing His-tagged CYP4A11 and HA-tagged p62. Cells were treated with DSS, lysed, and enriched by Ni-NTA affinity chromatography. The eluate was separated by SDS-PAGE and the CYP-p62 crosslinked band identified by multi-channel western blot visualization. The crosslinked band was excised and in gel digested. Crosslinked peptides were analyzed on an Orbtrap Exploris 480 with a FAIMS source and running a 0.75 um x 50 cm c18 column with a 4-hour separation. The sample was injected twice using two different sets of compensation voltages: S20240820-04.raw: -45, -60, -70 V. S20240820-05: -40, -50, -65C.","fileCount":"8","fileSizeKB":"4583112","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1020 - \\\"Monolink of DSS\\\/BS3 crosslinker to Lys or N-terminus.\\\"","keywords":"In cell DSS crosslinking;DatasetType:Proteomics","pi":[{"name":"Maria Almira Correia","email":"almira.correia@ucsf.edu","institution":"UCSF","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6fc83099e99a416eb3933275919648e2","id":"1355"}, {"dataset":"MSV000096826","datasetNum":"96826","title":"MBTS 2019 Spring CANON Cruise P-lipid data","user":"jhwang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736550681000","created":"Jan. 10, 2025, 3:11 PM","description":"Meta-lipidomic analysis of seawater from GF\/F filters. Analysis was run with two differing chromatographic gradients to optimize for triglyceride resolution","fileCount":"969","fileSizeKB":"108694315","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"phhytoplankton;CCE;Monterey Bay;photopigment;marine lipid;DatasetType:Other (lipidomics)","pi":[{"name":"Bethanie R Edwards","email":"bethanie_edwards@berkeley.edu","institution":"University of California, Berkeley","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"22d2eeb1e10148c6910f0d8fcf716a5c","id":"1356"}, {"dataset":"MSV000096824","datasetNum":"96824","title":"The 40S ribosomal subunit recycling complex modulates mitochondrial dynamics and endoplasmic reticulum - mitochondria tethering at mitochondrial fission\/fusion hotspots","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736544554000","created":"Jan. 10, 2025, 1:29 PM","description":"Samples 939560 F1-8 are the 8 fractions for the samples A1-D3, as well as F3, G3, H1, and I1 (these 4 were included in both sets and can be used to help normalize between sets). Samples 939560 F1-8 are the 8 fractions for the samples E1-I3, as well as A2 (included in both sets to help with normalization\/comparison between sets).\n939560:\nsample TMT Label\nA1 126\nA2 127N\nA3 127C\nB1 128N\nB2 128C\nB3 129N\nC1 129C\nC2 130N\nC3 130C\nD1 131N\nD2 131C\nD3 132N\nF3 132C\nG3 133N\nH1 133C\nI1 134N\n\n939561:\nsample TMT Label\nE1 126\nE2 127N\nE3 127C\nF1 128N\nF2 128C\nF3 129N\nG1 129C\nG2 130N\nG3 130C\nH1 131N\nH2 131C\nH3 132N\nI1 132C\nI2 133N\nI3 133C\nA2 134N\n\nA1-A3: W minus- MHC> Gal4 (Control)\nB1-B3: WT- MHC-Gal4> USP10 OE\nC1-C3: WT- MHC-Gal4> USP10 Sh RNAi\nD1-D3: WT- MHC-Gal4> USP10 RNAi KK\nE1-E3: WT- MHC-Gal4> FMR1 OE\nF1-F3: WT- MHC-Gal4> FMR1 RNAi\nG1-G3: WT- MHC-Gal4> FMR1 RNAi\nH1-H3: WT- MHC-Gal4> RIN OE\nI1-I3: WT- MHC-Gal4> RIN RNAi","fileCount":"49","fileSizeKB":"28035133","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Usp10;rin;DatasetType:Proteomics","pi":[{"name":"Boxiang Lu","email":"boxiangliu@nus.edu.sg","institution":"National University of Singapore","country":"Singapore"},{"name":"Zhihao Wu","email":"zhihaowu@mail.smu.edu","institution":"Southern Methodist University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"34ef9b3985254aa9853108240bd9720d","id":"1357"}, {"dataset":"MSV000096823","datasetNum":"96823","title":"GNPS - AWP698 E coli isolate with piperacillin and tazobactam antibiotics","user":"tliebergesell","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736536814000","created":"Jan. 10, 2025, 11:20 AM","description":"AWP698 E. coli clinical isolate study with piperacillin and tazobactam antibiotics.","fileCount":"25","fileSizeKB":"668750","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"E. coli;Mass spectrometry;antibiotics;DatasetType:Metabolomics","pi":[{"name":"Aaron Puri","email":"awpuri@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1eccb8359d2c4f029bc45f2e6bb27ccf","id":"1358"}, {"dataset":"MSV000096822","datasetNum":"96822","title":"Ccdc78 and Ccdc33 AP-MS from Xenopus laevis animal caps.","user":"OpheliaP","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736526316000","created":"Jan. 10, 2025, 8:25 AM","description":"Anti GFP AP-MS of GFP-fusions for Ccdc78 and Ccdc33 from excised cultured Xenopus animal caps rich in multi-ciliated cells. Control samples were anti-GFP pull-downs from similar tissue expressing only GFP. Samples were prepared by in-gel digest, and there are 3 injections for each sample (labeled a,b,c). Filenames with dates from 8\/2024 are Ccdc33 pull-downs and matched controls. Samples with dates 6\/24 and 7\/24 are Ccdc78 pulldowns and matched controls.","fileCount":"84","fileSizeKB":"36786783","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xenopus laevis (NCBITaxon:8355)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:6 - \\\"Iodoacetic acid derivative.\\\"","keywords":"animal caps, motile cilia, Xenopus, vertebrate;DatasetType:Proteomics","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8be5bfd19c574151b8cc412803c166b4","id":"1359"}, {"dataset":"MSV000096821","datasetNum":"96821","title":"Comparative Analysis of Glycoproteomic Software Using a Tailored Glycan Database","user":"rhogan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736519712000","created":"Jan. 10, 2025, 6:35 AM","description":"Glycoproteomics is a rapidly developing field, and data analysis has been stimulated by several technological innovations. As a result, there are many software tools from which to choose; and each comes with unique features that can be difficult to compare. This work presents a head-to-head comparison of five modern analytical software: Byonic, Protein Prospector, MSFraggerGlyco, pGlyco3, and GlycoDecipher. To enable a meaningful comparison, parameter variables were minimized. One potential confounding variable is the glycan database that informs glycoproteomic searches. We performed glycomic profiling of the samples and used the output to construct matched glycan databases for each software. Up to 17,000 glycopeptide spectra were identified across three replicates of wild-type SH-SY5Y cells. There was overlap among all software for glycoproteins identified, locations of glycosites, and glycans; but there was no clear winner. Incorporation of several comparative criteria was critically important for learning the most information in this study and should be used more broadly when assessing software. A single criterion, such as number of glycopeptide spectra found, is not sufficient. We present evidence that suggests Byonic reports many spurious results at the glycoprotein and glycosite level. Overall, our results indicate that glycoproteomic searches should involve more than one software, excluding the current version of Byonic, to generate confidence by consensus. It may be useful to consider software with peptide-first approaches and with glycan-first approaches.","fileCount":"61","fileSizeKB":"18744250","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"N-glycosylation","keywords":"N-glycosylation;Glycoproteomics;Protein Prospector;pGlyco3;MSFraggerGlyco;GlycoDecipher;Byonic;DatasetType:Proteomics","pi":[{"name":"Robert Chalkley","email":"chalkley@cgl.ucsf.edu","institution":"UCSF","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059632","task":"b1fb7cd559c74536b02e1bb82a4c38cb","id":"1360"}, {"dataset":"MSV000096818","datasetNum":"96818","title":"Metabolic dysregulation contributes to the development of dysferlinopathy","user":"verizy27","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736512241000","created":"Jan. 10, 2025, 4:30 AM","description":"Dysferlin is a transmembrane protein that plays a prominent role in membrane repair of damaged muscle fibers. Accordingly, mutations of the dysferlin gene cause progressive muscular dystrophies, collectively referred to as dysferlinopathies for which no effective treatment exists. Unexpectedly, experimental approaches that successfully restore membrane repair fail to prevent a dystrophic phenotype, suggesting that additional, hitherto unknown dysferlin-dependent functions contribute to the development of the pathology. Our experiments revealed an altered metabolic phenotype in dysferlin-deficient muscles, characterized by 1) mitochondrial abnormalities and elevated death signaling and 2) increased glucose uptake, reduced glycolytic protein levels, and a pronounced glycogen accumulation. Strikingly, elevating mitochondrial volume density and muscle glycogen accelerates disease progression while improvement of mitochondrial function and recruitment of muscle glycogen with exercise ameliorated functional parameters in a mouse model of dysferlinopathy. Collectively, our results not only shed light on a metabolic function of dysferlin, but also imply new therapeutic avenues aimed at promoting mitochondrial function and normalizing muscle glycogen to ameliorate dysferlinopathies, complementing efforts that target membrane repair.","fileCount":"71","fileSizeKB":"191046285","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos;timsTOF Ultra","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"dysferlinopathy, exercise, glucose metabolism, glycogen, mitochondrial dysfunction muscular dystrophy, PGC-1alpha;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059629","task":"fcc469e73df047d4986ce6e20d7a3929","id":"1361"}, {"dataset":"MSV000096814","datasetNum":"96814","title":"Altered Cerebrospinal Fluid Proteins in Smith-Lemli-Opitz Syndrome","user":"jklwp007","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736461155000","created":"Jan. 9, 2025, 2:19 PM","description":"Smith-Lemli-Opitz Syndrome (SLOS) is a rare, autosomal recessive, neurocognitive disorder caused by mutations in the 7-dehydrocholesterol reductase gene (DHCR7), leading to impaired cholesterol biosynthesis. The biochemical results of these defects include accumulation of the cholesterol precursor, 7-dehydrocholesterol (7DHC), and reduced cholesterol. Individuals with SLOS present with a spectrum of developmental anomalies and neurocognitive impairments. Despite various therapeutic approaches being explored, no FDA-approved treatment exists, highlighting the need for reliable biomarkers to better understand the disease pathophysiology that can be used to monitor therapeutic intervention studies. Here, we utilized discovery-based mass spectrometry to perform quantitative proteomic profiling of cerebrospinal fluid (CSF) from SLOS individuals compared to unaffected controls. Our analysis identified several differentially expressed proteins that could serve as potential biomarkers for assessing therapeutic efficacy and advancing our understanding of SLOS. Notably, we observed significant alterations in the reelin signaling pathway and a decrease in catecholamine release, implicating these processes in the development and progression of the disease.","fileCount":"1620","fileSizeKB":"21413916","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"UNIMOD:730 - \\\"Representative mass and accurate mass for 113, 114, 116 & 117.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"rare neurocognitive disease;isobaric labeling;protein biomarker;reelin;granin family;DatasetType:Proteomics","pi":[{"name":"Stephanie Cologna","email":"cologna@uic.edu","institution":"University of Illinois at Chicago","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"","task":"f61258d6dce84915a2880ba31bbf34f3","id":"1362"}, {"dataset":"MSV000096813","datasetNum":"96813","title":"Rational design of potent small molecule SMARCA2\/A4 (BRM\/BRG1) degraders","user":"budayevh","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736459756000","created":"Jan. 9, 2025, 1:55 PM","description":"Target-anchored monovalent degraders are more drug-like than their bivalent counterparts, Proteolysis Targeting Chimeras (PROTACs), while offering greater target specificity control than the E3 ligase anchored monovalent degraders, also known as molecular glues.","fileCount":"110","fileSizeKB":"51108357","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"ubiquitinomics, global proteome profiling, degrader;DatasetType:Proteomics","pi":[{"name":"Hanna Budayeva","email":"budayeva.hanna@gene.com","institution":"Genentech, Inc.","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"05414868d654453fa3e106ad1f9b7d83","id":"1363"}, {"dataset":"MSV000096811","datasetNum":"96811","title":"Differential protein expression analysis of western flower thrips +\/- TSWV","user":"es3064","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736437125000","created":"Jan. 9, 2025, 7:38 AM","description":"Quantitative LC\/MS\/MS was performed on 4 uL of each sample, using a nanoAcquity UPLC system (Waters Corp) coupled to a Thermo Orbitrap Fusion Lumos high resolution accurate mass tandem mass spectrometer (Thermo) equipped with a FAIMSPro device via a nanoelectrospray ionization source. Briefly, the sample was first trapped on a Symmetry C18 20 mm x 180 um trapping column (5 ul\/min at 99.9\/0.1 v\/v water\/acetonitrile), after which the analytical separation was performed using a 1.8 um Acquity HSS T3 C18 75 um x 250 mm column (Waters Corp.) with a 90-min linear gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 400 nanoliters\/minute (nL\/min) with a column temperature of 55C. Data collection on the Fusion Lumos mass spectrometer was performed for three difference compensation voltages (-40v, -60v, -80v). Within each CV, a data-dependent acquisition (DDA) mode of acquisition with a r=120,000 (m\/z 200) full MS scan from m\/z 375 - 1500 with a target AGC value of 4e5 ions was performed. MS\/MS scans were acquired in the linear ion trap in rapid mode with a target AGC value of 1e4 and max fill time of 35 ms. The total cycle time for each CV was 0.66s, with total cycle times of 2 sec between like full MS scans. A 20s dynamic exclusion was employed to increase depth of coverage. The total analysis cycle time for each sample injection was approximately 2 hours","fileCount":"33","fileSizeKB":"117819890","spectra":"1399728","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Thysanoptera (NCBITaxon:30262)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Thrips, proteomics, TSWV;DatasetType:Proteomics","pi":[{"name":"Dorith Rotenberg","email":"drotenb@ncsu.edu","institution":"North Carolina State University","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059595","task":"fa05dd9d44414029b3123cdeae2f3a77","id":"1364"}, {"dataset":"MSV000096807","datasetNum":"96807","title":" Local growth hormone facilitates the aging colon epithelial microenvironment","user":"Arminja","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736373385000","created":"Jan. 8, 2025, 1:56 PM","description":"Aging is associated with appearance of senescent cells secreting the senescence-associated secretome facilitating a milieu favoring age-related changes in microenvironment. Previously, we showed accumulation and secretion of local non-pituitary growth hormone (npGH) in senescent colon epithelial cells. Here, we elucidate mechanisms underlying npGH action in the non-tumorous colon tissue microenvironment. We demonstrate autocrine npGH action in normal human colon cells (hNCC) infected with lentivirus expressing hGH (lentiGH), as well as paracrine npGH action in hNCC cocultured with lentiGH hNCC and in intact human 3-dimensional intestinal organoids co-cultured with organoids infected with lentiGH. Enriched gene ontology and pathway analysis of intact organoids exposed to paracrine npGH identified distorted extracellular matrix (ECM) and focal adhesion pathways concurrent with altered expression of ECM and cytoskeletal proteins. Significant phosphoprotein changes associated with cytoskeleton and cell migration pathway occurred in GH-exposed hNCC. Paracrine npGH triggers these changes by activating epithelial-mesenchymal transition, as shown by suppression of E-cadherin and induction of Twist2 in cellular models, as well as in the colon of nude mice harboring GH-secreting xenografts. These changes are consistent with observed increased migration of hNCC overexpressing lentiGH, or in those co-cultured with GH-secreting hNCC or with GH-secreting normal colon fibroblasts. Furthermore, whole exome sequencing detected increased cell copy number alterations in intact organoids co-cultured with lentiGH-infected organoids, likely as a consequence of GH-mediated suppressed DNA damage repair thereby favoring cell transformation. Our results indicate that accumulated npGH in aging tissue enables a microenvironment landscape favoring age-associated pro-proliferative changes.","fileCount":"232","fileSizeKB":"32881028","spectra":"0","psms":"1290909","peptides":"820174","variants":"1066871","proteins":"20105","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Growth hormone, aging, extracellular matrix, epithelial-mesenchymal transition;DatasetType:Proteomics","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"Geisel School of Medicine at Dartmouth College","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059561","task":"3b9f8fbd15634f21910182eed72a7958","id":"1365"}, {"dataset":"MSV000096806","datasetNum":"96806","title":"GNPS - LC-MS raw spectra for a metabolomics study on colorectal cancer","user":"Xrrrr98784","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736371383000","created":"Jan. 8, 2025, 1:23 PM","description":"All the samples were analyzed by the Thermo Vanquish UPLC system coupled with a Q-Exactive Orbitrap mass spectrometer equipped with a heated electro-spray ionization probe (Thermo Fisher, CA, USA) as well as a XBridge BEH Amide XP column (130A, 2.5 um, 2.1 mm X 150 mm, 2.5 um particle size; Waters Corporation, Milford, MA). For the chromatographic analysis, mobile phase A comprised a mixture of 5 mM ammonium acetate in acetonitrile \/water (10:90, v\/v) with 0.1% acetic acid, while mobile phase B was composed of 5 mM ammonium acetate in acetonitrile \/water (90:10, v\/v) with 0.1% acetic acid. A linear gradient elution program was implemented, initiating with 70% B and gradually decreasing to 30% B within 5 minutes. Subsequently, the mobile-phase composition was sustained at 30% B for 4 minutes, after which it was reverted to 70% B within 2 minutes and maintained for an additional 2 minutes. The entire run duration lasted 13 minutes. The flow rate was set to 0.3 mL\/min, and the column temperature was maintained at 40 C.","fileCount":"2832","fileSizeKB":"476347217","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"NA","keywords":"Metabolomics;Colorectal Cancer;DatasetType:Proteomics","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9a52b4480ed34cb2b5ac9da0333105f6","id":"1366"}, {"dataset":"MSV000096805","datasetNum":"96805","title":"A deep XL-proteomic dataset of intact HEK293T cells using DSBSO","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736364378000","created":"Jan. 8, 2025, 11:26 AM","description":"Cross-linking mass spectrometry is an emerging method to study protein-protein interactions (PPIs) in intact biological systems. Here, we optimized a workflow for gnerating high coverage maps of PPIs using the enrichable cross-linker Azide-A-DSBSO. This created one of the largest to-date XL-MS datasets, enabling structural characterization of thousands of PPIs in their intact subcellular environment. ","fileCount":"52","fileSizeKB":"71219921","spectra":"1097315","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\"","keywords":"Human;Deep xl-ms;Cell culture;DatasetType:Proteomics","pi":[{"name":"Fan Liu","email":"fliu@fmp-berlin.de","institution":"Leibniz-Institute for Molecular Pharmacology (FMP)","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD043531","task":"4570aed32363416996adb38b4e04173d","id":"1367"}, {"dataset":"MSV000096804","datasetNum":"96804","title":"GNPS - Chesneau_et_al_MetaFlowTrain_Exometabolites","user":"sperin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736357090000","created":"Jan. 8, 2025, 9:24 AM","description":"Bacterial and fungal exometabolites were harvested from the MetaFlowTrain system, where bacteria and fungi were cultivated in various peat washes. Two milliliters of exometabolites were collected from the MetaFlowTrain output at two distinct time points: 24 hours and 62 hours. These exometabolites were subsequently extracted (for detailed methods, refer to the associated publication).\r\nData Overview:\r\n221208 Folders: Data were used to create Figures 3 and 4 and were acquired in Full-MS\/ddMS2 (Top10).\r\n230530 Folders: Data contributed to Figure 2 and were acquired in Full-MS.\r\nFile Naming Convention:\r\nSample number_Microbial inoculum in the first chamber_Microbial inoculum in the second chamber_Peat wash used\r\nFor example, 01_F_B_Peat1 refers to sample 1, fungi in the first chamber, bacteria in the second chamber, and peat wash 1.\r\nAbbreviations: F: Fungi, B: Bacteria, X: Mock\r\nAdditional Files:\r\nTraceFinder Raw Tables\r\nThese tables are provided for the four files (221208_Guillaume_Chambers_AA, 221208_Guillaume_Chambers_TCA&Gly, 230530_Guillaume_Chambers, 230530_Guillaume_Chambers_AA) and include key parameters for all samples, pools, and standards:\r\n- Retention Time (Actual RT)\r\n- Accurate Mass Measurements (m\/z Apex \/ m\/z Delta)\r\n- Ion Abundance (Area)\r\n- Ion Height (Height)\r\nSummary Table (Level 1 identification):\r\nA summary table is also included, detailing targeted retention times for all metabolites and the spectra for the TCA&Gly identification:\r\n- RT Sample Average: The average retention time for samples in the set.\r\n- RT Sample %RSD: The percentage relative standard deviation (%RSD) of sample retention times, indicating variability.\r\n- RT Pool Average: The average retention time for pooled samples.\r\n- RT Pool %RSD: The %RSD for pooled samples, showing variability.\r\n- RT Std Average: The average retention time for standard samples.\r\n- RT Std %RSD: The %RSD for standard retention times.\r\n- RT Difference Pool-Std: The difference in retention times between pooled and standard samples.\r\n","fileCount":"631","fileSizeKB":"73316985","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Communities of Bacterial and Fungal strains","instrument":"QExactive","modification":"none","keywords":"Microbial Exometabolites;DatasetType:Metabolomics","pi":[{"name":"Guillaume Chesneau","email":"gchesneau@mpipz.mpg.de","institution":"Max Planck for Plant Breeding","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"eee2cd8a61ba4879b9d846c5f3e348db","id":"1368"}, {"dataset":"MSV000096803","datasetNum":"96803","title":"Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses","user":"rubenjjframos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736347932000","created":"Jan. 8, 2025, 6:52 AM","description":"The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors (ICI), such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. By functionally analyzing fecal metagenomes from 112 melanoma patients, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumor mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumor immune responses, and LPS-binding antibiotics and a small molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumor immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.","fileCount":"50","fileSizeKB":"6381980","spectra":"39477","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Klebsiella pneumoniae (NCBITaxon:573)","instrument":"6546 Q-TOF LC\\\/MS (Agilent Instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cancer, Checkpoint blockade immunotherapy, Microbiome, LPS, Gram-negative bacteria, melanoma;DatasetType:Metabolomics","pi":[{"name":"Virginia A. Pedicord","email":"vap33@cam.ac.uk","institution":"Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7d97dfb1c2834a2ea0b9d2c9a224cc8e","id":"1369"}, {"dataset":"MSV000096802","datasetNum":"96802","title":"GNPS - Serum metabolomics-based study of Alzheimer's disease and Mild cognitive impairment patients.","user":"olgampeg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736345889000","created":"Jan. 8, 2025, 6:18 AM","description":"The study recruited 158 participants from the Greek Association of Alzheimer s Disease and Related Disorders (GAADRD) Day Centers between 2016 and 2021. The cohort included 45 individuals with Mild Cognitive Impairment (MCI), 91 with Alzheimer s Disease (AD), and 22 Healthy Controls (HC), diagnosed per DSM V criteria. Comprehensive medical, laboratory, and neuropsychological evaluations were performed to confirm diagnoses. \r\nThe analysis was performed using a Waters Xevo G3 QToF Mass Spectrometer coupled with a Waters ACQUITY Premier UPLC. Separation was achieved using a Waters ACQUITY Premier HSS T3 column, with 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B) as mobile phases.\r\n","fileCount":"2863","fileSizeKB":"2887641913","spectra":"2488133","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Xevo G3 QTof","modification":"-","keywords":"Untargeted metabolomics, Alzheimer's disease, MCI, QTOF MS;DatasetType:Metabolomics","pi":[{"name":"Helen Gika","email":"gkikae@auth.gr","institution":"Aristotle University of Thessaloniki","country":"Greece"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e373a807c9384db886d4b436ea24456d","id":"1370"}, {"dataset":"MSV000096801","datasetNum":"96801","title":"Homozygous loss-of-function mutation in SIT1 leads to combined immunodeficiency due to dysregulated TCR signaling","user":"XIOLIU","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736340015000","created":"Jan. 8, 2025, 4:40 AM","description":"Through BioID and mass spectrometry, we investigated SIT1 interactome in a patient with a homozygous SIT1 splice-site variant leading to immunodeficiency and lymphoma. SIT1, previously identified as a negative regulator of T-cell activation, was found to interact with vesicle trafficking proteins, including components of the SCAR\/WAVE complex, TRAPP complex, and clathrin-coated pits.","fileCount":"335","fileSizeKB":"11677661","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"SIT1, protein protein interaction;DatasetType:Other (interactomics)","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"471089a6eb484454afc1aaccef53bbfe","id":"1371"}, {"dataset":"MSV000096799","datasetNum":"96799","title":"Dataset used to guide the development of Scout and bechmark XL-MS search engines","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736329101000","created":"Jan. 8, 2025, 1:38 AM","description":"This submission includes the raw data analyzed and search results described in our manuscript \u201CProteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics\u201D. In this study, we develop a strategy to generate a well-controlled XL-MS standard by systematically mixing and cross-linking recombinant proteins. The standard can be split into independent datasets, each of which has the MS2-level complexity of a typical proteome-wide XL-MS experiment. The raw datasets included in this submission were used to (1) guide the development of Scout, a machine learning-based search engine for XL-MS with MS-cleavable cross-linkers (batch 1), test different LC-MS acquisition methods (batch 2), and directly compare Scout to widely used XL-MS search engines (batches 3 and 4).","fileCount":"295","fileSizeKB":"209756829","spectra":"5436130","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Search engine;Cross-linking;Ppi;Benchmarking;Xl-ms;Fdr;DatasetType:Proteomics","pi":[{"name":"Fan Liu","email":"Fliu@fmp-berlin.de","institution":"Leibniz-Forschungsinstitut fuer Molekulare Pharmakologie","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052022","task":"0d9a7814fdf54d2e908a4b2d5f4cfdcb","id":"1372"}, {"dataset":"MSV000096798","datasetNum":"96798","title":"Mechanisms of P. aeruginosa resistance to Type VI Secretion System attacks","user":"trendsetter","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736322673000","created":"Jan. 7, 2025, 11:51 PM","description":"The Type VI Secretion System (T6SS) is a molecular nanomachine that injects toxic effector proteins into the environment or neighbouring cells, playing an important role in interbacterial competition and host antagonism during infection. Pseudomonas aeruginosa encodes three different T6SSs. The H1-T6SS delivers toxins into aggressive bacteria in response to attacks mediated by their own T6SS. This suggests that P. aeruginosa has the ability to survive T6SS assaults. However, the resistance mechanisms are poorly characterized. In this work, we performed a CRISPRi screen to identify pathways involved in resistance to T6SS effectors of Acinetobacter baylyi and Vibrio cholerae. We show that members of the GacA\/GacS regulon, such as the mag operon, and GacA-independent factors, such as the outer membrane protein OprF, confer resistance to T6SS toxins. Specifically, MagD protects mainly against PG-targeting effectors, whereas OprF confers general protection against multiple effector types. We show that these mechanisms are crucial for resistance against T6SS attacks, as well as for resistance to certain antibiotics. Interestingly, some of these mechanisms also lead to higher antibiotic susceptibility, suggesting more complex links between general T6SS and antibiotic resistance.","fileCount":"10","fileSizeKB":"9371087","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa (NCBITaxon:287)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"T6SS;Infection;Resistance;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD059537","task":"784337a371e54e42b7a0fc0e53f7ecd9","id":"1373"}, {"dataset":"MSV000096797","datasetNum":"96797","title":"GNPS - LC-MS and MSMS dataset for the heterologous expression of threopeptin in S. albus","user":"yuey15","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736301602000","created":"Jan. 7, 2025, 6:00 PM","description":"dataset for the heterologous expression of threopeptin in S. albus. 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Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA). LC-MS\/MS data acquired in positive mode.","fileCount":"115","fileSizeKB":"4049219","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not specified","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;Natural Products;DatasetType:Metabolomics","pi":[{"name":"Jehad Almaliti","email":"jalmaliti@ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e9ddeb4289314283a5b00aa677ae3dbb","id":"1375"}, {"dataset":"MSV000096795","datasetNum":"96795","title":"The embryonic DPPA3 gene stimulates the expression of pregnancy-related genes in bovine endometrial cells","user":"naproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736289938000","created":"Jan. 7, 2025, 2:45 PM","description":"Extracellular vesicles (EVs) released by cells contain mRNAs, miRNAs, lncRNAs, lipids, and proteins, playing crucial roles in cell-cell communication. While full-length mRNA transcripts have been documented in EVs secreted by cancer cells, there are no reports on full transcripts secreted by embryos. Our study aimed to identify EV mRNAs in the culture media of bovine embryos and investigate their roles in embryo-mother communication. Following the isolation of EVs from in-vitro fertilization media samples and RNA sequencing, we identified a full mRNA transcript of DPPA3, known to play an essential role in embryo development. To examine the role of DPPA3 in embryo-mother communication, an in vitro transcribed mRNA of DPPA3 was transfected into bovine endometrial epithelial cells. Transfected and control cells were subsequently analyzed with RNA sequencing and proteomics to assess the effects of DPPA3 on gene expression. A total of 24 genes were found to be upregulated, and one gene was downregulated (FDR < 0.01) following DPPA3 transfection, many with known functions in pregnancy recognition. Proteomic analysis revealed 28 differentially expressed, with 19 upregulated and 15 downregulated. Two proteins, ISG15 and MX1, overlapped with the differentially expressed mRNAs. To mimic the natural transfer of EVs from embryos to endometrial cells, we performed co-culture with day-8 blastocysts or supplemented the cells with embryo-conditioned culture media. DPPA3 presence was detected in endometrial cells exposed to embryo-conditioned media after just 30 minutes. 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Although PRVB is a well-characterized protein in many bony fishes, little is known about the hilsa, an anadromous fish with great economic importance and mostly found in Southeast Asia. In this study, we have characterized the hilsa PRV utilizing various proteomic approaches in response to two major riverine habitats and developmental stages. Unique peptide sets correspond to three different PRV isoforms were identified in hilsa muscle tissues. Label-free quantitative proteomic analysis coupled with ELISA revealed higher levels of PRVB in young fish comparative to the adult, irrespective of their riverine habitats. A comparative quantitative analysis of PRVB further demonstrated that hilsa had less PRVB than other commonly consumed freshwater fish species. Multiple reaction monitoring (MRM)-based targeted proteomic approach showed the potential of PRV as a marker protein for allergen quantitation and authenticating the presence of hilsa in a complex freshwater fish mixture. Our findings collectively offer fundamental knowledge on hilsa parvalbumins for further investigation on the food safety and quality evaluation of hilsa fish.","fileCount":"28","fileSizeKB":"4600220","spectra":"0","psms":"165043","peptides":"3931","variants":"5677","proteins":"646","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Tenualosa ilisha (NCBITaxon:373995)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Allergens, developmental stage, Clupeidae, Food safety, Targeted Proteomics;DatasetType:Proteomics","pi":[{"name":"Nagib Ahsan","email":"nahsan@ou.edu","institution":"University of Oklahoma","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"b4c3af629df142cf810e0cb419595cff","id":"1377"}, {"dataset":"MSV000096792","datasetNum":"96792","title":"Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736282304000","created":"Jan. 7, 2025, 12:38 PM","description":"Mass spectrometry analysis of lipids in early-stage embryos across various lineages of Astyanax mexicanus.","fileCount":"49","fileSizeKB":"22382550","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Astyanax mexicanus (NCBITaxon:7994)","instrument":"Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"cavefish;surface fish;Reproductive Adaptation;Astyanax mexicanus;Nutrient Limitation;lipidomics;DatasetType:Metabolomics","pi":[{"name":"Rohner, Nicolas","email":"nro@stowers.org","institution":"Stowers Institute for Medical Research","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"410e39dba1804166b4fa75295613f7bd","id":"1378"}, {"dataset":"MSV000096791","datasetNum":"96791","title":"Modulation of hepatic transcription factor EB activity during cold exposure uncovers direct regulation of bis(monoacylglycero)phosphate lipids by Pla2g15","user":"Simcox_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736278611000","created":"Jan. 7, 2025, 11:36 AM","description":"Targeted lipidomic analyses of: acycarnitines in mouse plasma and liver; ceramides in lysosomes isolated from mouse liver; and bis(monoacylglycero)phosphate lipids in mouse liver and 293t cells. 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A knowledge gap is presented by the need to directly measure these modifications, especially for unannotated organisms with unknown primary histone sequences. In the present work, we developed and applied a novel workflow for identifying and annotating histone proteoforms directly from mass spectrometry-based measurements for the endangered Caribbean coral Acropora cervicornis. Combining high accuracy de novo top-down and bottom-up analysis based on tandem liquid chromatography, trapped ion mobility spectrometry, non-ergodic electron-based fragmentation, and high-resolution mass spectrometry, near complete primary sequence (up to 99%) and over 86 post-translational modification annotations were obtained from pull-down histone fractions. In the absence of reliable genome annotations, H2A, H2B and H4 histone sequences and the annotation of the post-translational modifications of the stressed A. cervicornis coral allow for a better understanding of chromatin remodeling and new strategies for target intervention and restoration of endangered reef corals.","fileCount":"82","fileSizeKB":"403462596","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Acropora cervicornis (NCBITaxon:6130)","instrument":"maXis II;timsTOF Pro 2","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"nLC-TIMS-PASEF-ToF MS\/MS;nESI-TIMS-ToF MS\/MS;coral;top-down;bottom-up;DatasetType:Proteomics","pi":[{"name":"Francisco A Fernandez-Lima","email":"fernandf@fiu.edu","institution":"Florida International University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059506","task":"f04dc188850043f59fae4f00e17ce8f0","id":"1381"}, {"dataset":"MSV000096787","datasetNum":"96787","title":"GNPS - Sequential Target and Non-target for Global (STANG) metabolomics in a Single Injection to Discover Prognostic Biomarkers of Acute Ischemic Stroke","user":"cjchen_01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736241856000","created":"Jan. 7, 2025, 1:24 AM","description":"Non-targeted metabolomics by an LC-MS system offers the advantage of wide signal coverage, enabling the discovery of novel biomarkers. However, it suffers from a low identification rate and limitations due to incomplete databases and reliable bioinformatics software to handle large data sets. On the other hand, targeted metabolomics focuses on specific biomarkers, allowing for a more directed search but potentially limiting the exploration of other potential biomarkers. To address these challenges, we developed a novel method called Sequential Target And Non-target for Global metabolomics (STANG metabolomics) using the functionality of the triple quadrupole-linear ion trap mass spectrometer (Q-Trap MS). This method combines the capabilities of a triple quadrupole for a wide linear range of MRM scans and an ion trap for fast full-scan acquisition. Our approach enables the direct analysis of known metabolites while simultaneously recording mass spectrometry signals of non-targeted substances in the full-scan spectra, facilitating comprehensive biomarker identification. Currently, 448 metabolite targets have been built, and the STANG metabolomics approach was applied to discover prognostic biomarkers of acute ischemic stroke. We identified 32 biomarkers through targeted metabolomics and 83 candidates through non-targeted metabolomics. The top four markers with the highest AUC values are lithocholic acid (AUC=0.999), ursodeoxycholic acid (AUC=0.985), 3,4-Dihydroxyphenylglycol (AUC=0.836), and 4-Hydroxybenzaldehyde (AUC=0.807). This approach shortens sample analysis time, reduces data conversion, increases metabolite coverage, and improves analytical sensitivity and accuracy. The potential of the STANG metabolomics approach was evaluated in discovering prognostic biomarkers of stroke, demonstrating its value as a comprehensive tool for biomarker discovery and disease mechanism elucidation.","fileCount":"566","fileSizeKB":"5127178","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QTRAP 6500+","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sequential Target and Non-target for Global metabolomics, Stroke, STANG;DatasetType:Metabolomics","pi":[{"name":"Chen, chao-jung","email":"cjchen@mail.cmu.edu.tw","institution":"Graduate Institute of Integrated Medicine","country":"Taiwan, ROC."}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"25db4c7383c04de9a72fa82fae8c9efc","id":"1382"}, {"dataset":"MSV000096786","datasetNum":"96786","title":"Wang_Yemelyanov_BioID_alpha_catenin_2024","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736212807000","created":"Jan. 6, 2025, 5:20 PM","description":"This dataset consists of 12 raw MS files and associated peak lists and result files, acquired on Orbitrap Elite mass spectrometer operated in Data Dependent Acquisition mode. All samples are BioID experiments, performed in HEK293 Flp-In T-REx cells. Christopher Go performed sample preparation and mass spectrometric acquisition. The files are associated with a manuscript by Yuou Wang, Alex Yemelyanov, and Cara J. Gottardi. Cara Gottardi is the author of the study (c-gottardi@northwestern.edu). Anne-Claude Gingras can be contacted for questions on this dataset (gingras@lunenfeld.ca).","fileCount":"82","fileSizeKB":"27031022","spectra":"552368","psms":"21976","peptides":"13938","variants":"16109","proteins":"8329","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;Proximity-dependent biotinylation;catenin;DatasetType:Proteomics","pi":[{"name":"Dr. Anne Claude Gingras","email":"gingras@lunenfeld.ca","institution":"University of Toronto \/ Sinai Health System","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059476","task":"05f553e484304a129f7aa9e4c974a30f","id":"1383"}, {"dataset":"MSV000096785","datasetNum":"96785","title":"Global Proteoform Alterations Across Multiple Cellular Compartments Underlie Obstructive Hypertrophic Cardiomyopathy","user":"zgao269","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736208985000","created":"Jan. 6, 2025, 4:16 PM","description":"Background: Hypertrophic cardiomyopathy (HCM) has traditionally been regarded as a disease of the sarcomere, however it is in the midst of a paradigm shift with growing recognition of contributions beyond the sarcomere to the heterogeneity of HCM phenotypes. Innovative approaches are essential to uncover novel determinants and mechanisms underlying this heterogeneity. Top-down proteomics has emerged as a powerful method for analysis of proteoforms the myriad protein products arising from genetic variants, post-translational modifications (PTMs), and splicing isoforms from a single gene offering a more precise lens to understand the disease heterogeneity in HCM. Yet, how proteoforms are altered on the global scale in HCM has not been investigated. \nMethods: Global top-down proteomics was performed on myocardial samples from patients with advanced obstructive HCM and nonfailing controls. Specifically, serial protein extraction enabled by the photocleavable surfactant, Azo was employed to solubilize diverse categories of proteins from minimal tissue, including membrane proteins. Subsequently, high-sensitivity top-down mass spectrometry was utilized to detect and quantify proteoforms across various cellular compartments.\nResults: Using this global top-down approach, we detected ~2000 proteoforms across disparate cellular compartments, including the sarcoplasmic reticulum (SR), cytoskeleton, mitochondria, and nucleus, in advanced obstructive HCM tissues compared to non-failing controls. Quantitative analysis uncovered significant alterations not only in sarcomeric but also cytoskeletal, mitochondrial, nucleosome, and SR proteoforms. Notably, we discovered a significant proteoform crosstalk among the sarcomere, SR, and cytoskeleton. Moreover, we identified a previously unrecognized decrease in succinylated mitochondrial proteoforms as a critical feature of advanced obstructive HCM proteoform landscape, alongside a marked reduction in acetylation of nucleosome proteins. \nConclusions: This study represents the most comprehensive analysis of proteoform landscape in HCM to date. We have identified broad proteoform alterations spanning multiple cellular compartments in advanced obstructive HCM, indicating that a complex network of perturbations underlie HCM. These findings highlight pathways beyond the sarcomere that may contribute to HCM pathophysiology, offering potential targets for development of therapeutic interventions.\n","fileCount":"7699","fileSizeKB":"113983040","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"maXis II","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:64 - \\\"Succinic anhydride labeling reagent light form (N-term & K).\\\";UNIMOD:1253 - \\\"S-(2-monomethylsuccinyl) cysteine.\\\";UNIMOD:1363 - \\\"Crotonylation.\\\"","keywords":"Hypertrophic cardiomyopathy, proteoform, top-down proteomics, posttranslational modification, phosphorylation, succinylation;DatasetType:Proteomics","pi":[{"name":"Ying Ge","email":"ge2@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059475","task":"92741f4a3ba44bf5b931f01f55535081","id":"1384"}, {"dataset":"MSV000096784","datasetNum":"96784","title":"Iron-restricted Mycobacterium tuberculosis exports pathogenicity factors packed in extracellular vesicles","user":"haiyanzheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736195276000","created":"Jan. 6, 2025, 12:27 PM","description":"Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, responds to iron limitation by upregulating extracellular vesicle (EV) production. This study examined the protein composition of induced Mtb vesicles using chromatography coupled with mass spectrometry. The findings revealed vesicle packaging of critical pathogenicity effectors, including proteins that promote bacterial survival, immune evasion, and inflammation. The results are relevant to the fundamental understanding of Mtb-host interactions and can guide efforts to develop vesicle-based TB biomarkers.","fileCount":"9","fileSizeKB":"12352313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium tuberculosis","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Iron limitation;Mycobacterium tuberculosis;extracellular vesicles;DatasetType:Proteomics","pi":[{"name":"Rodriguez, Gloria","email":"rodrigg2@njms.rutgers.edu","institution":"Rutgers University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"85abd0122a5547d980c55ca3a2012841","id":"1385"}, {"dataset":"MSV000096780","datasetNum":"96780","title":"Dual Roles of hABCB1 in Drug Resistance and Immune Evasion: Implications for Lung Cancer Therapy","user":"bangree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736156117000","created":"Jan. 6, 2025, 1:35 AM","description":"Standard chemotherapy for lung cancer often leads to drug resistance, posing a significant clinical challenge. A major mechanism of resistance is overexpression of P-glycoprotein (P-gp), encoded by the human ATP-binding cassette subfamily B member 1 (hABCB1) gene, functioning as a drug efflux transporter. In this study, we aimed to investigate the dual role of hABCB1 overexpression in mediating resistance to chemotherapy and natural killer (NK) cell-mediated cytotoxicity in lung cancer.","fileCount":"25","fileSizeKB":"25131730","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"drug resistance;DatasetType:Proteomics","pi":[{"name":"Geul Bang","email":"bangree@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Korea"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD059457","task":"9c7c5dbaaa434d959316e8df252a8f89","id":"1386"}, {"dataset":"MSV000096779","datasetNum":"96779","title":"Identification of disulfide bond-linking sites in biosynthesized platelet factor 4 by establishing a partial reduction method without alkylation","user":"13856359339","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1736107905000","created":"Jan. 5, 2025, 12:11 PM","description":"In this research, a bacterial expression system was established to efficiently generate recombinant human PF4 (rhPF4), and the accuracy of the sequence was validated by liquid chromatography-high-resolution mass spectrometry. 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The external metabolome of thirty-one strains of freshwater algae were collected to better understand the drivers of interactions between phytoplankton hosts and bacteria.\r\n\r\nTo collect the metabolite profile, sterile monocultures of the 31 phytoplankton strains were grown under identical conditions. When each strain reached carrying capacity, the culture was filtered through a 0.22um filter, removing all phytoplankton cells. This filtrate was then acidified to a pH of 2.5 and stored at 4C for 2-29 hours, until it could be processed through the solid phase extraction column. To prep the column, 1 cartridge volume (1mL) of 100% methanol was passed through the column. Once the column was prepped, 50mL of cell-free, acidified culture was passed through the column to collect the organic material. The column was cleaned with 2 cartridge volume of 0.01M HCl and air dried for 5 minutes. The sample was eluted into a deep-well plate over dry ice with 1mL of 100% methanol. 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Erastin (ER), a ferroptosis inducer, kills\r\ntumor cells by generating and accumulating reactive oxygen species (ROS)\r\nwithin the cell, resulting in an iron-dependent oxidative damage-mediated\r\nferroptotic cell death. We have utilized human ovarian cancer cell lines, OVCAR-\r\n8 and its adriamycin-selected, multi-drug resistance protein (MDR1)-expressing\r\nNCI\/ADR-RES, both equally sensitive to ER, to identify metabolic biomarkers\r\nof ferroptosis. Our studies showed that ER treatment rapidly depleted cellular\r\nglutathione and cysteine and enhanced formation of ophthalamate (OPH) in\r\nboth cells. Opthalalmate has been proposed to be a biomarker of oxidative\r\nstress in cells. Our study also found significant decreases in cellular taurine, a\r\nnatural antioxidant in cells. Additionally, we found that ER treatment decreased\r\ncellular levels of NAD+\/NADP+, carnitines and glutamine\/glutamate in both\r\ncells, suggesting significant oxidative stress, decrease in energy production,\r\nand cellular and mitochondrial disfunctions, leading to cell death. Our studies\r\nidentified several potential biomarkers of ER-induced ferroptosis including OPH,\r\ntaurine, NAD+, NADP+ and glutamate in ovarian cancer cells. Identifying specific\r\nmetabolic biomarkers that are predictive of whether a cancer is susceptible to\r\nferroptosis will help us devise more successful treatment modalities.","fileCount":"231","fileSizeKB":"35282998","spectra":"237151","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;ferroptosis;DatasetType:Metabolomics","pi":[{"name":"Alan K. 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Here, for the first time, we present an on-filter in-cell (OFIC) processing approach, which can digest C. elegans proteins directly in the cells of the organism after methanol fixation. With OFIC processing and single-shot LCMS analysis, we identified over 9,400 proteins from a sample of only 200 worms, the largest C. elegans proteome reported to date that did not require fractionation or enrichment. We systematically evaluated the performance of the OFIC approach by comparing it with conventional lysis-based methods. Our data suggest equivalent and unbiased performance of OFIC processing for C. elegans proteome identification and quantitation. We further evaluated the OFIC approach with even lower input samples, then used this method to determine how the proteome is impacted by loss of superoxide dismutase sod-1, the ortholog of human SOD-1, a gene associated with amyotrophic lateral sclerosis (ALS). Analysis of 8,800 proteins from only 50 worms as the initial input showed that loss of sod-1 affects the abundance of proteins required for stress response, ribosome biogenesis, and metabolism. In conclusion, our streamlined OFIC approach, which can be broadly applied to other systems, minimizes sample loss while offering the simplest workflow reported to date for C. elegans proteomics analysis.","fileCount":"55","fileSizeKB":"95193179","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"In-cell digestion;OFIC;E4technology;Caenorhabditis elegans;Quantitative proteomics;superoxide dismutase sod-1;DatasetType:Proteomics","pi":[{"name":"Yanbao Yu","email":"yybyu@udel.edu","institution":"Department of Chemistry and Biochemsitry, University of Delaware","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e9aa2818b71a4497ba8cfa6c536b02b2","id":"1396"}, {"dataset":"MSV000096751","datasetNum":"96751","title":"psilocybin production in E. coli ","user":"wangx98","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1735784807000","created":"Jan. 1, 2025, 6:26 PM","description":"comparative proteomics on psilocybin-producing E. coli during log and stationary phase growth.","fileCount":"242","fileSizeKB":"12031993","spectra":"0","psms":"477908","peptides":"171404","variants":"262101","proteins":"8476","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli BL21(DE3) (NCBITaxon:469008)","instrument":"LTQ Orbitrap XL","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"psilocybin;DatasetType:Proteomics","pi":[{"name":"Xin Wang","email":"wangx3@ufl.edu","institution":"University of Florida","country":"US"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059355","task":"5dcbf9aa8ae8408fa8b844770b6466ce","id":"1397"}, {"dataset":"MSV000096747","datasetNum":"96747","title":"Microtubule doublets from T. vaginalis","user":"awsteven","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1735669414000","created":"Dec. 31, 2024, 10:23 AM","description":"microtubule doublets isolated from locomotive flagella of T. vaginalis, P5 fraction.","fileCount":"17","fileSizeKB":"1449362","spectra":"0","psms":"9108","peptides":"4550","variants":"5357","proteins":"925","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichomonas vaginalis G3 (NCBITaxon:412133)","instrument":"Q Exactive Plus (Thermo Scientific instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"trichomonas vaginalis;microtubule doublet;DatasetType:Proteomics","pi":[{"name":"hong zhou","email":"hong.zhou@ucla.edu","institution":"University of California, Los Angeles","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD059340","task":"e9f44c8d76fd4728b38f2230febfe9e4","id":"1398"}, {"dataset":"MSV000096745","datasetNum":"96745","title":"GNPS - Mineralocorticoid Receptor Phase Separation Modulates Cardiac Preservation - Metabolomic Data","user":"mcwilson5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1735589928000","created":"Dec. 30, 2024, 12:18 PM","description":"Human and swine cardiac tissue samples collected from healthy controls treated with popular transplant organ preservative (Histidine-tryptophan-ketoglutarate, HTK) OR an experimental transplant organ preservative (cocktail of HTK and canrenone) to compare preservative effectiveness. 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Comprehensive hit validation and structure-degradation relationship analyses guided by global proteomics, identifies highly selective and potent phenyl glutarimide-based degraders of novel neosubstrates, including KDM4B, G3BP2 and VCL, none of which contain the classical CRBN degron motif. 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Our results show both that ferulic acid (mimicking the plant environment) influences the content of EVs released by Azospirillum sp. B510 and that bacterial EVs also impact plant physiology at a systemic level according to their cargoes. This research provides the first evidence of a global effect of bacterial EVs on the plant and highlights the dynamics of plant-bacteria interactions mediated by EVs.","fileCount":"16","fileSizeKB":"6728372","spectra":"0","psms":"212023","peptides":"21374","variants":"30265","proteins":"3020","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Azospirillum sp. 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H6PD is involved in essential physiological processes, including energy and redox metabolism as well as redox and hormonal regulation. H6PD sole reported interacting partner is 11b-hydroxysteroid dehydrogenase 1 (11b-HSD1), utilizing NADPH for its well-known role in glucocorticoid activation. Increasing evidence suggests that H6PD contributes to breast cancer progression. However, H6PD interactions with other proteins besides 11b-HSD1 and the mechanisms and by which this protein participates in breast cancer progression are not yet well understood. Therefore, to unravel pathways and mechanisms by which H6PD promotes breast cancer progression, it is essential to first identify the interactome of this protein.\nResults: We adapted the proximity-dependent Biotin Identification (BioID) method to identify novel H6PD interacting partners within the endoplasmic reticulum. First, we validated the method and confirmed the known interaction between H6PD and 11b-HSD1. Next, we constructed a triple-negative breast cancer (TNBC) MDA-MB-231 cell clone stably expressing a H6PD-biotin ligase fusion protein. Enriched biotinylated proteins were analyzed by mass spectrometry and potential candidates assessed by co-immunoprecipitation and functional assays. The resulting interactome revealed luminal protein disulfide isomerases (PDI), chaperones and calcium binding proteins. Due to its association with breast cancer, we examined the PDI Anterior gradient protein 2 (AGR2) as H6PD interacting partner. Gene enrichment analysis indicated multiple overlapping pathways being enriched in breast cancer tissue with relatively high H6PD or AGR2 expression. Co-immunoprecipitation (Co-IP) from MCF7 cells confirmed a physical interaction between the two proteins. Downregulation of ARG2 increased H6PD protein levels but decreased activity. Furthermore, co-expression with AGR2 in HEK-293 cells enhanced H6PD activity.\nConclusion: BioID identified AGR2 to interact with H6PD, which was confirmed using Co-IP from MCF7 cells expressing endogenous levels of the two proteins. The results indicate that AGR2 controls H6PD protein expression and enhances its enzymatic activity. Whether a higher H6PD activity due to increased AGR2 expression promotes a more aggressive cancer cell phenotype warrants further investigations.","fileCount":"67","fileSizeKB":"30206626","spectra":"851073","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"H6PD;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD059039","task":"c8cfc182dff7465fad50c8688401e605","id":"1418"}, {"dataset":"MSV000096695","datasetNum":"96695","title":"GNPS - AGB Stomach Lystates Metabolomics Dataset ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734546590000","created":"Dec. 18, 2024, 10:29 AM","description":"Metabolomics dataset of human stomach lysate samples. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"342","fileSizeKB":"15319640","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"tissue;stomach;gut;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Andres Gottfried Blackmore","email":"andresg@health.ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"47968bfbb94546e8a6564b698d21ed7f","id":"1419"}, {"dataset":"MSV000096694","datasetNum":"96694","title":"GNPS - Pierce ASD Stool Metabolomics Dataset ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734546117000","created":"Dec. 18, 2024, 10:21 AM","description":"ASD Fecal metabolomics dataset for Karen Pierce. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"347","fileSizeKB":"14343059","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"stool;fecal;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Karen Pierce","email":"kpierce@health.ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8ab020f43b114f66a4d9580293c27f52","id":"1420"}, {"dataset":"MSV000096690","datasetNum":"96690","title":"Boni_FGFR1mutations_P127_TripleTOF6600","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734528272000","created":"Dec. 18, 2024, 5:24 AM","description":"This dataset consists of 44 raw MS files and associated peak lists and result files, acquired on AB SCIEX 6600 TripleTOF mass spectrometer operated in Data Dependent Acquisition mode. Controls are shared with MassIVE dataset MSV000083695. \nSamples were generated by Cassandra Wong. Affinity purification and mass spectrometry acquisition was performed by Cassandra J. Wong. Analysis was performed by Cassandra J. Wong, HyeRim Han, Jonathan Boulais, Jacopo Boni, and Anne-Claude Gingras. \nThe files are associated with a manuscript submitted for publication by Jacopo Boni et al. The main goal of this paper was to identify how FGFR1 mutations in low-grade glioneuronal tumors contribute to tumorigenicity. \nBarbara Rivera is the corresponding author of the manuscript (brivera@idibell.cat); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca).\n\nThis submission is associated with 2 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence (as per iProphet)\n","fileCount":"140","fileSizeKB":"65329102","spectra":"0","psms":"520367","peptides":"79864","variants":"94509","proteins":"44927","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"FGFR1;BioID;Proximity-dependent biotinylation;low-grade glioneuronal tumors (LGGNT);DatasetType:Proteomics","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058982","task":"289d6943b0684f428978d36bbe0793ca","id":"1421"}, {"dataset":"MSV000096686","datasetNum":"96686","title":"GNPS - Differential transport pathways of saturated and unsaturated fatty acid esters in male mouse hepatocytes","user":"fengwu_chen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734509085000","created":"Dec. 18, 2024, 12:04 AM","description":"Forty medium and long-chain fatty acids and fatty acid esters in the mouse livers\/plasma\/VLDL were ethylated and analyzed by UHPLC-MS\/MS. ","fileCount":"77","fileSizeKB":"126989","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6470A Triple Quadrupole LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Saturated fatty acid;Unsaturated fatty acid;DatasetType:Other (Fatty Acid Targeted Quantitative Mass Spectrometry)","pi":[{"name":"Fengwu Chen","email":"fengwu_chen@126.com","institution":"Tsinghua University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"172d7183e3074dcea96d82890fba2532","id":"1422"}, {"dataset":"MSV000096680","datasetNum":"96680","title":"GNPS - Lahaina Fire Coastal Water HLB solid phase extraction ","user":"seanos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734478445000","created":"Dec. 17, 2024, 3:34 PM","description":"This project includes water samples that were collected in West Maui, Hawaii, USA following the August 2023 wildfires. The majority of samples were collected along the shoreline, both inside and outside of the burn zone. A subset of samples were collected along an offshore transect. Another subset of samples were collected in or at the mouth of streams within the burn zone. All water samples consisted of 200 ml of water, pre-filtered with 0.2 um sterivex, run over Agilent HLB columns, and eluted with methanol. ","fileCount":"805","fileSizeKB":"26866489","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coastal;Water;Marine;Stream;Fire;HLB;DatasetType:Metabolomics","pi":[{"name":"Craig Nelson","email":"craig.nelson@hawaii.edu","institution":"University of Hawaii","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8d83ddbbc37a40a59c0f74073d1fbf57","id":"1423"}, {"dataset":"MSV000096679","datasetNum":"96679","title":"FeNP Titration Experiment_12172024","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734477346000","created":"Dec. 17, 2024, 3:15 PM","description":"Fe nanoparticles are effective in enriching siderophore and other secondary metabolites present in pseudomonas fluorescence ","fileCount":"41","fileSizeKB":"747385","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"pseudomonas","instrument":"QExactive orbitrap LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fenanoparticle;Titration;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3222e1366fba470c85d656ba042c937c","id":"1424"}, {"dataset":"MSV000096678","datasetNum":"96678","title":"GNPS - Fission yeast metabolome dynamics during phosphate starvation and replenishment","user":"rubenjjframos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734467960000","created":"Dec. 17, 2024, 12:39 PM","description":"Inorganic phosphate is an essential nutrient acquired by cells from their environment and assimilated into myriad intracellular metabolites and macromolecules. Here we characterize the metabolic responses of fission yeast to a 24-h interval of phosphate starvation, during which cells enter a state of G0 quiescence. Time-resolved profiling revealed that many key phosphometabolites were progressively depleted, including: (i) NTPs, NDPs, and dNTPs; (ii) coenzyme A, NAD+, NADP+, NADH, and ADP-ribose; (iii) glycolysis pathway intermediates upstream of pyruvate; (iv) pentose phosphate pathway intermediates from 6-phosphogluconate to sedoheptulose-7-phosphate; (v) nucleotide sugars GDP-glucose\/mannose, UDP-glucose\/galactose, and UDP-GalNAc\/GluNAc; and (vi) phospholipid precursors glycerol-3-phosphate, CDP-choline, and glycerophosphocholine. By contrast, early Krebs cycle intermediates accumulated during phosphate starvation. Other metabolic changes included: (i) interdiction of de novo pyrimidine synthesis; (ii) depletion of S-adenosylmethionine and S-adenosylhomocysteine; (iii) transient accumulation of polyamine biosynthetic intermediates putrescine, S-adenosylmethioninamine and 5-methylthioadenosine; (iv) accumulation of betaine (correlating with an increase in expression of atd1 mRNA encoding aldehyde dehydrogenase); and (v) depletion of aminoadipate pathway intermediates 2-oxoadipate, 2-aminoadipate and saccharopine. Replenishing phosphate after 24 h of starvation resulted in restoration of the metabolite levels to similar levels as non-starved controls (over 2 to 12 h) as cells exited quiescence and resumed growth. ","fileCount":"505","fileSizeKB":"21117357","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Schizosaccharomyces pombe (NCBITaxon:4896)","instrument":"6545 Q-TOF LC\\\/MS;6230A Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"phosphate metabolism;phosphate starvation;Schizosaccharomyces pombe;DatasetType:Metabolomics","pi":[{"name":"Stewart Shuman","email":"shumans@mskcc.org","institution":"Memorial Sloan Kettering Cancer Center","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"11b4626b276246319fb412b8d669992f","id":"1425"}, {"dataset":"MSV000096676","datasetNum":"96676","title":"Extracellular vesicles of a phytobeneficial bacterium trigger distinct systemic response in plant","user":"Timefaciens","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734454311000","created":"Dec. 17, 2024, 8:51 AM","description":"Bacterial extracellular vesicles (EVs) are lipidic shuttles that play roles in virulence, inter-species competition, and in the induction of the host immune response. While they have primarily been investigated in animal-bacteria interactions, knowledge regarding phytobacterial EVs remains limited. Recent findings revealed that various biotic factors like hydroxycinnamic acids can regulate EVs production. Hydroxycinnamic acids, such as ferulic acid, are lignin components abundantly released in the plant environment, where they impact the ecology of numerous phytobacteria. Azospirillum sp. B510, a phytobeneficial bacterium, induces the accumulation of hydroxycinnamic acid derivatives in the plant and can metabolize them as carbon sources. We hypothesized that the presence of ferulic acid in the environment of Azospirillum sp. B510 would influence its EVs production in terms of size, quantity, and cargo. Conversely, we also proposed that EVs from this phytobacterium would influence plant metabolites and defense gene expression. Our results show both that ferulic acid (mimicking the plant environment) influences the content of EVs released by Azospirillum sp. B510 and that bacterial EVs also impact plant physiology at a systemic level according to their cargoes. This research provides the first evidence of a global effect of bacterial EVs on the plant and highlights the dynamics of plant-bacteria interactions mediated by EVs.","fileCount":"145","fileSizeKB":"14483099","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Solanum lycopersicum (NCBITaxon:4081)","instrument":"6546 Q-TOF LC\\\/MS (Agilent instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Extracellular vesicles, Azospirillum, Solanum lycopersicum, multi-omics, PGPR, plant physiology;DatasetType:Metabolomics","pi":[{"name":"Ludovic Vial","email":"ludovic.vial@univ-lyon1.fr","institution":"Universite Claude Bernard Lyon 1, UMR 5557 Ecologie Microbienne, CNRS, INRAE, VetAgro Sup, UCBL, F-69622, Villeurbanne, Lyon, France","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ec694e7cff3046be82eaf81c53d9a2db","id":"1426"}, {"dataset":"MSV000096675","datasetNum":"96675","title":"GNPS - Metabolomics - blended juice - MEF - SS","user":"gimercali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734453414000","created":"Dec. 17, 2024, 8:36 AM","description":"MS\/MS data of the study that investigated the impact of moderate electric field (MEF) and shear stress (SS) on the chemical profile of a blended fruit and vegetable juice using untargeted metabolomics. ","fileCount":"764","fileSizeKB":"1618093","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Blended juice, composed of apples (58%), leaves of red kale (10%), blackberries (11%), lime juice (7%), ginger (1%) and water (13%)","instrument":"Agilent 6546, QTOF-MS","modification":"none","keywords":"moderate electric field;shear stress;anthocyanins, phenolic componds;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Giovana Domeneghini Mercali","email":"giovana.mercali@ufrgs.br","institution":"Federal University of Rio Grande do Sul","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"750b6bb59b6f4331b8ab540793d846a5","id":"1427"}, {"dataset":"MSV000096674","datasetNum":"96674","title":"TMT-based Multiplexed (Chemo)proteomics on the Orbitrap Astral Mass Spectrometer","user":"Yuchen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734451224000","created":"Dec. 17, 2024, 8:00 AM","description":"This dataset contains an evaluation of TMT-based multiplexed proteomics on the Orbitrap Astral mass spectrometer.","fileCount":"237","fileSizeKB":"568149870","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral;Orbitrap Eclipse;Orbitrap Ascend","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Orbitrap Astral;TMT;DDA;DIA;DatasetType:Proteomics","pi":[{"name":"Joao A. Paulo","email":"joao_paulo@post.harvard.edu","institution":"Cell Biology, Harvard Medical School","country":"N\/A"},{"name":"Qing Yu","email":"qing.yu@umassmed.edu","institution":"University of Massachusetts Chan Medical School","country":"USA"},{"name":"Steven P Gygi","email":"steven_gygi@hms.harvard.edu","institution":"Department of Cell Biology, Harvard Medical School, Boston, USA","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3e02d1cfe2ac4b1cb2676c9952642d35","id":"1428"}, {"dataset":"MSV000096671","datasetNum":"96671","title":"Dynamic Expression of the Zebrafish (Danio rerio) Proteome Across Early Larval Development ","user":"henkea","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734401522000","created":"Dec. 16, 2024, 6:12 PM","description":"Here, we characterize proteome expression patterns in larval zebrafish at 4-, 7- and 10 dpf using bottom-up shotgun proteomics","fileCount":"348","fileSizeKB":"105386301","spectra":"65050","psms":"62627","peptides":"22810","variants":"36130","proteins":"22148","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"ACQUITY UPLC;Synapt G2-S HDMS","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Zebrafish;Development;early life stage;Danio rerio;DatasetType:Proteomics","pi":[{"name":"Bryan W. Brooks","email":"Bryan_Brooks@Baylor.edu","institution":"Baylor University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058917","task":"6d03a9fa49a04e85b98406a8bb3bbde7","id":"1429"}, {"dataset":"MSV000096669","datasetNum":"96669","title":"GNPS - Dietary isoleucine content defines the metabolic and molecular response to a Western diet","user":"Simcox_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734367451000","created":"Dec. 16, 2024, 8:44 AM","description":"Untargeted lipidomics of liver samples from female and male DBA\/2J or C57BL\/6J mice fed a control diet, Western diet, or high- or low-isoleucine Western diet. Both positive and negative mode are included. 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TMEM106B has been identified as a risk factor for several neurodegenerative diseases characterized by aggregation of the RNA-binding protein TDP-43, including frontotemporal lobar degeneration (FTLD) and limbic-predominant age-related TDP-43 encephalopathy (LATE). To investigate the role of TMEM106B in TDP-43 proteinopathy, we ablated TMEM106B in the TDP-43Q331K knock-in mouse line, which expresses an ALS-linked TDP-43 mutation at endogenous levels. We found that TMEM106B deficiency leads to glial activation, Purkinje cell loss, and behavioral deficits in TDP-43Q331K mice without inducing typical TDP-43 pathology. Interestingly, ablation of TMEM106B results in significant body weight gain, increased fat deposition, and hepatic triglyceride (TG) accumulation in TDP-43Q331K mice. In addition, lipidomic and transcriptome analysis shows a profound alteration in lipid metabolism in the liver of TDP-43Q331KTmem106b-\/- mice. Our studies reveal a novel function of TMEM106B and TDP-43 in lipid metabolism and provide new insights into their roles in neurodegeneration.","fileCount":"77","fileSizeKB":"64528621","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"TMEM106B;TDP-43;Purkinje cells obesity;lipid metabolism;DatasetType:Proteomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Fenghua Hu","email":"fh87@cornell.edu","institution":"Cornell University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0ed906be94b341d19acc1f07daa80ade","id":"1434"}, {"dataset":"MSV000096662","datasetNum":"96662","title":"GNPS - Daphnia dentifera - Metschnikowia bicuspidata host-pathogen system","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734128606000","created":"Dec. 13, 2024, 2:23 PM","description":"The unexplained variation in susceptibility in several Daphnia species to multiple pathogens indicates that much remains to be learned about the Daphnia immune system. The goal of this experiment is to identify potentially important metabolites that contribute to the susceptibility or resistance of the host Daphnia dentifera to the fungal pathogen Metschnikowia bicuspidata. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). Data acquired in positive mode.","fileCount":"709","fileSizeKB":"33620044","spectra":"957904","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Daphnia dentifera (NCBITaxon:42852);Metschnikowia bicuspidata (NCBITaxon:27322)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Carla Caceres","email":"cecacere@illinois.edu","institution":"University of Illinois","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9efb43c1cd564124926543bc85702706","id":"1435"}, {"dataset":"MSV000096661","datasetNum":"96661","title":"GNPS - Pilot Bile Salt Hydrolase Screening with different substrates","user":"Dpattynama","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734124622000","created":"Dec. 13, 2024, 1:17 PM","description":"Bile Salt Hydrolases (BSH) and Penicillin V Acylase (PVA) enzymes from various microbial strains were overexpressed in E. coli and purified using nickel affinity chromatography. Enzyme assays were performed by incubating the purified enzymes with bile acids and amines. Following incubation, the reactions were quenched, and the extracts were dried and reconstituted in 50% methanol containing an internal standard. MS\/MS data acquisition was carried out on a Q Exactive mass spectrometer in positive ionization mode, with chromatographic separation achieved using a Phenomenex Polar C18 column. 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Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0038b9852e9f42358b9530da0c8b206b","id":"1436"}, {"dataset":"MSV000096660","datasetNum":"96660","title":"Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734123872000","created":"Dec. 13, 2024, 1:04 PM","description":"Proteins were extracted from forty 2-cell-embryos each from Surface, Pachon, and Molino cavefish in six biological replicates using a Lipid Extraction Kit (ab211044) and 1.5ml BioMasher II Micro Tissue Homogenizers (749625-0010) according to manufacture protocols. Briefly, embryos were homogenized in 500ul Extraction Buffer on ice for one minute, then incubated at room temperature for 20 minutes at 1000g. After centrifugation at 10,000g for 5 minutes at 4C, pellets as non-polar coproduct was saved for proteomic analysis. Three biological replicate pellets were resuspended in 100ul of 8M Urea with 100mM of Tris, pH8.5 and reduced with 5mM tris(2-carboxyethyl) phosphine (TCEP) and alkylated with 10mM 2-chloroacetamide (CAM) for 30 minutes protected from light at room temperature. Endoproteinase Lys-C (Promega) was added at 1:1000 w\/w at 37C overnight. The reactions were diluted to 2M Urea by adding 100mM of Tris, pH8.5, then Trypsin (Promega Gold) was added at 1:200 w\/w at 37C overnight. The digested samples were centrifuged at 16,000g for 30 minutes and transferred supernatant to new tubes. All samples were cleaned up by Pierce Peptide Desalting Spin Columns (89851) before a colorimetric peptide assay (Pierce). \nTo each of the TMT10plex (Thermo Fisher, 90110) 0.8mg vials, 20 ul of anhydrous acetonitrile were added, then mixed with 30ug peptides and incubated 1 hr at RT. The differentially labeled samples (40ul each) were combined, and the resulting volume was reduced using a SpeedVac (Savant) to less than 10ul. The dried TMT-labeled peptide mixture was resuspended in 300ul of 0.1% trifluoroacetic acid (TFA). One high pH fractionation cartridge (Pierce, cat. 84868) was placed on a new 2.0ml sample tube and 300ul of the TMT-labeled peptide mixture were loaded onto the column. A total of 8 HpH RP fractions were collected by sequential elution in new sample tubes using 300ul of 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25% and 50% acetonitrile in 0.1% TFA. The solvents were evaporated to dryness using vacuum centrifugation. Dried samples were resolubilized in 44ul of buffer A (5% acetonitrile in 0.1% formic acid, FA) before LC-MS analysis.\nTMT-labeled peptides were analyzed on Orbitrap Eclipse Tribrid Mass Spectrometer (Thermo Scientific), equipped with a Nanospray Flex Ion Source, and coupled to a Vanquish Neo System. Peptides (22ul for each HpH RP fraction) were loaded on an Acclaim PepMap 100 C18 trap cartridge (0.3mm inner diameter (i.d.), 5mm length; Thermo Fisher Scientific) with the Neo loading pump at 2ul\/minute via the autosampler. \nA 75um i.d. analytical microcapillary column was packed in-house with 25mm of 1.9um ReproSil-Pur C18-AQ resin (Dr. Masch). AgileSLEEVE (Analytical Sales & Products) was used to maintain column temperature at 40C. The organic solvent solutions were water:acetonitrile:formic acid at 95:5:0.1 (volume ratio) for buffer A (pH 2.6) and 20:80:0.1 (volume ratio) for buffer B. The chromatography gradient was a 5 minutes column equilibration step in 1% B; a 74 minutes ramp to reach 30% B; 20 minutes from 30% to 60% B; 3 minutes to reach 90% B; a 10 minutes wash at 90% B; 0.1 minutes to 1% B; followed by a 12 minutes column re-equilibration step in 1% B. The Neo pump flow rate was set to 0.180ul\/minute. \nThe Orbitrap Eclipse was set up to run the TMTpro-SPS-MS3 method. Briefly, peptides were scanned from 400-1600 m\/z in the Orbitrap at 120,000 resolving power before MS2 fragmentation by CID at 35% NCE and detection in the ion trap set to turbo detection. Dynamic exclusion was enabled for 45s. Carbamidomethyl (57.0215 Da on Cys) and TMT10plex (229.163 Da on Kn) were searched statically, while methionine oxidation (15.9949 Da) was searched as a variable modification. Synchronous precursor scanning (SPS) selected the top 10 MS2 peptides for TMT reporter ion detection in the Orbitrap using HCD fragmentation at 65% NCE at 50,000 resolving power. \nThe LC\/MSn dataset was processed using Proteome Discoverer 3.1 (Thermo Fisher Scientific). MS\/MS spectra were searched against a mexicanus protein database (NCBI 2022-07) complemented with common contaminants. SEQUEST-HT implemented through Proteome Discoverer was set up as: precursor ion mass tolerance 10 ppm, fragment mass tolerance 0.6 Dalton, up to two missed cleavage sites, static modification of cysteine (+57.021 Da), and lysine and peptide N-termini with TMT tag (+229.163 Da) and dynamic oxidation of methionine (+15.995 Da). Results were filtered to a 1% FDR at peptides levels using Percolator through Proteome Discoverer. MS3 spectra were processed to extract intensity for each reporter ion. Proteins were quantified by summing reporter ion intensities across all matching PSMs. Differentially enriched proteins were identified using ANOVA.\n","fileCount":"29","fileSizeKB":"6062676","spectra":"0","psms":"18649","peptides":"8739","variants":"9654","proteins":"2050","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Astyanax mexicanus (NCBITaxon:7994)","instrument":"Orbitrap Eclipse","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01722 - \\\"A protein modification that effectively replaces the N6'-hydrogen atom of a lysine residue with the Proteome Sciences TMT6plex-126 reporter+balance group.\\\";MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\"","keywords":"TMT;DatasetType:Proteomics","pi":[{"name":"Laurence Florens","email":"laf@stowers.org","institution":"The Stowers Institute for Medical Research","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058862","task":"fd30a5e7fd364f689442be4940e805c2","id":"1437"}, {"dataset":"MSV000096658","datasetNum":"96658","title":"Mouse Muscle Proteome Profiling and Secretome Profiling of MRC2 E990G Heterozygous Mice","user":"syjung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734109202000","created":"Dec. 13, 2024, 9:00 AM","description":"The wild-type and heterozygous MRC2 E990G loss-of-function variant mice proteomics profiling and secretome profiling was performed. Secretomic samples were obtained from isolated mouse atrial fibroblasts, while proteomic samples were taken from whole atrial pairs excised from the mice.","fileCount":"74","fileSizeKB":"68289358","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Muscle Proteome Profiling;Secretome Profiling;MRC2 E990G Heterozygous Mice;DatasetType:Proteomics","pi":[{"name":"Sung Jung","email":"syjung@bcm.edu","institution":"Baylor College of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058860","task":"b8bf7f038bab44bc84120be92727d8f5","id":"1438"}, {"dataset":"MSV000096657","datasetNum":"96657","title":"PUP-IT proximity-labeling of LST8-1 and RAPTOR1 interactors (transient expression in N. benthamiana)","user":"leonardblaschek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734108559000","created":"Dec. 13, 2024, 8:49 AM","description":"PUP-IT proximity labeling of Arabidopsis Target of Rapamycin Complex (TORC) subunits LST8-1 and RAPTOR1, compared against a GFP control, via transient expression in Nicotiana benthamiana. The sample metadata, sequence database and FragPipe workflow are uploaded under the 'Metadata' tag. A short R script to format FragPipe TSV output for mzTab conversion is under 'Supplementary Files'.","fileCount":"47","fileSizeKB":"23792659","spectra":"0","psms":"336209","peptides":"28947","variants":"41482","proteins":"4563","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702);Nicotiana benthamiana (NCBITaxon:4100)","instrument":"timsTOF Pro","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:1264 - \\\"Addition of GGE.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PUP-IT;Proximity labeling;Target of Rapamycin;TOR;DatasetType:Proteomics","pi":[{"name":"Staffan Persson","email":"staffan.persson@plen.ku.dk","institution":"Copenhagen University","country":"Denmmark"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD058859","task":"fe2d03e20a4a445d8bfdcb202623aa2e","id":"1439"}, {"dataset":"MSV000096656","datasetNum":"96656","title":"Dessauer_AKAP7_TripleTOF6600_P124","user":"LTRI_proteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734096047000","created":"Dec. 13, 2024, 5:20 AM","description":"This dataset consists of 20 raw BioID MS and associated peak lists and results files, acquired on an ABSciex TripleTOF6600 operated in Data Dependent Acquisition mode. All control samples (untransfected and eGFP) are deposited with MSV000096100. \r\nSamples were generated by Taeyeop Park. Streptavidin affinity purification was performed by Zhen-Yuan Lin. Mass spectrometry acquisition was performed by Zhen-Yuan Lin and Cassandra Wong. Analysis was performed by Taeyeop Park, Cassandra Wong, Karen Colwill, and Carmen Dessauer. \r\nThe files are associated with a manuscript submitted for publication by Taeyeop Park et al. The main goal of this dataset was to identify near neighbors of AKAP7-gamma in neonatal cardiomyocytes. \r\nCarmen W. Dessauer (Carmen.W.Dessauer@uth.tmc.edu) is the corresponding author of the proteomics data; John Scott is the corresponding author of the manuscript; Karen Colwill should be contacted for questions on this dataset (colwill@lunenfeld.ca)\r\n\r\nThis submission is associated with 6 Supplementary Files (in addition to this README file)\r\nTable 1 BioID describes the composition of the BioID dataset\r\nTable 2 BioID lists all the peptide identification evidence of the BioID dataset\r\nTable 3 BioID lists the SAINTexpress interactions for BioID dataset\r\n","fileCount":"43","fileSizeKB":"12979876","spectra":"0","psms":"114840","peptides":"24287","variants":"28094","proteins":"37844","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;proximal protein interactions;AKAP7;cardiomyocytes;DatasetType:Proteomics","pi":[{"name":"Karen Colwill","email":"colwill@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058849","task":"612242937f05478296346b11bb7139a7","id":"1440"}, {"dataset":"MSV000096655","datasetNum":"96655","title":"Resistance to anti-EGFR targeted therapy in head and neck squamous cell carcinoma","user":"anwouters","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1734080633000","created":"Dec. 13, 2024, 1:03 AM","description":"Total proteins were extracted in triplicate from cetuximab-sensitive and -resistant SC263 and SCC22b HNSCC cells. The LC system was coupled to a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Fisher Scientific) programmed to acquire in data-dependent mode. A target of 1.7 x103 ions and a maximum injection time of 80 ms were used for MS\/MS. The method was set to analyze the top 20 most intense ions from the survey scan and dynamic exclusion was enabled for 20 s. Tandem mass spectra were processed using MaxQuant software version 1.6.7.0. Proteins were identified using the Andromeda search engine and using the Homo sapiens proteome reference database (UniProt, release 20200130, 20366 entries). The parameters chosen for the identification include: digestion enzyme used was trypsin, maximum number of allowed missed cleavages was two. Oxidation of methionine, N-terminal acetylation, and phosphorylation of serine, threonine and tyrosine were set as variable modifications, while carbamidomethylation of cysteine was set as a fixed modification. A maximum number of 5 modifications per peptide was set. The precursor mass tolerance was set to 4.5 ppm and the fragmentation mass tolerance to 20 ppm. The peptide-to-spectrum match (PSM) and protein false discovery rates (FDR) were set at 1%. The match-between-runs and the label-free quantification (LFQ) methods were enabled using default parameters. After data treatment using MaxQuant, statistical analysis was done using Perseus software (version 1.6.7.0). The data matrix was filtered by removing the potential contaminants and decoy reverse sequences. The LFQ intensities were then log2-transformed and missing values were replaced by imputation based on the normal distribution. This resulted in the quantification of the expression of 2,741 unique proteins. 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Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). 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Here we use organelle-specific proteomics in iPSC derived neurons (i3Neuron) and an in vitro lysosome damaging assay to demonstrate that lysosome damage, caused by the aggregation of Ceroid Lipofuscinosis Neuronal 4 (CLN4) linked DNAJC5 mutants on lysosomal membranes, serves as a critical pathogenic linchpin in CLN4 associated neurodegeneration. Intriguingly, in non neuronal cells, a ubiquitin dependent microautophagy mechanism downregulates CLN4 aggregates to counteract CLN4 associated lysotoxicity. Genome wide CRISPR screens identify the ubiquitin ligase CHIP as a central microautophagy regulator that confers ubiquitin dependent lysosome protection. Importantly, CHIP lysosome protection function is transferrable, as ectopic CHIP improves lysosomal function in CLN4 i3Neurons, and effectively alleviates lipofuscin accumulation and neurodegeneration in a Drosophila CLN4 disease model. Our study establishes CHIP mediated microautophagy as a key organelle damage guardian that preserves lysosome integrity, offering new insights into therapeutic development for CLN4 and other lysosome related neurodegenerative diseases. 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Enzyme assays were performed by incubating the purified enzymes with bile acids and amines. Following incubation, the reactions were quenched, and the extracts were dried and reconstituted in 50% methanol containing an internal standard. 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The abbreviations that name the raw files are:\n\nT7 - Fermented feed.\nPOLEN - Fermented pollen.\nCTRL - Bran.\nFALSA - False organic solvent used (HPLC grade MeOH) and equipment system (UHPLC-HRMS).\n","fileCount":"35","fileSizeKB":"1033256","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Melipona quadrifasciata fermented pollen","instrument":"microTOF LC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"pollen;fermented pollen;fermented feed;bran;DatasetType:Metabolomics","pi":[{"name":"Jullio Kennedy Castro Soares","email":"julliokennedy1998@gmail.com","institution":"Universidade Federal de Sao Paulo","country":"Brasil"},{"name":"Patricia Miranda-Pinto","email":"miranda.patricia@unifesp.br","institution":"Universidade Federal de Sao Paulo","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5966c07d88f34482b9fef2f60259aaf3","id":"1449"}, {"dataset":"MSV000096640","datasetNum":"96640","title":"A multi factor comparison of seven reversed-phase C18 separation media for proteomic applications","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733941718000","created":"Dec. 11, 2024, 10:28 AM","description":"This study examines the differences in separation selectivity and carryover characteristics for seven popular C18 columns used in bottom-up proteomics. Identical linear water:acetonitrile gradients (0.48 %ACN per minute) were applied to all separations at 300 nL\/min flow rate. Both buffers A (water) and B (80:20 acetonitrile:water) contained 0.1 % formic acid. 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Data acquired in positive mode.","fileCount":"378","fileSizeKB":"19922864","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Surfing;Metabolomics;DOM;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Mauricio Caraballo","email":"acaraballorodriguez@health.ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"36c90f6ae0d64e538fc7198c007c1415","id":"1451"}, {"dataset":"MSV000096638","datasetNum":"96638","title":"Phosphoproteomics on cisplatin or LPS treated on HEI OC1 cells","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733939642000","created":"Dec. 11, 2024, 9:54 AM","description":"HEI-OC1 cells were treated with cisplatin, LPS or PB and lysed with 8 M guanidine hydrochloride. 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The clinical features of OA exhibit significant sexual dimorphism. However, the specific metabolic characteristics underlying this difference remain incompletely understood, with a notable lack of molecular risk factors related to OA. In this study, we established a cohort of 60 OA cases comprising different genders. Employing liquid chromatography-tandem mass spectrometry (LC-MS\/MS), we performed untargeted metabolomic analyses on synovial membrane, synovial fluid, urine, and serum samples, obtained simultaneously from each patient. Following rigorous quality control, we successfully constructed and annotated a metabolic profile of OA encompassing multiple sample types. Moreover, we identified metabolites associated with clinical risk factors and delineated a sex-specific subset of metabolites based on sample type. This dataset provides a foundation for further investigation into the impact of sex on OA at metabolic level. Additionally, these findings are expected to enhance the study of potential sex-related biomarkers in OA and offer novel insights into clinical gender-specific management strategies.","fileCount":"421","fileSizeKB":"53691231","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"LC-MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Untargeted Metebolomics;osteoarthritis;DatasetType:Metabolomics","pi":[{"name":"Wei Zhang","email":"weizhang80s@126.com","institution":"Shandong Provincial Hospital","country":"China"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f0d075c627d244d8941398243748d31c","id":"1453"}, {"dataset":"MSV000096635","datasetNum":"96635","title":"Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein","user":"sbaboo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733882813000","created":"Dec. 10, 2024, 6:06 PM","description":"The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigated how mutations and a deletion in the KP.3.1.1 spike protein (S) affect ACE2 binding and antibody escape. Mass spectrometry revealed a new glycan site at residue N30 and altered glycoforms at neighboring N61. Cryo-EM structures showed that the N30 glycan and rearrangement of adjacent residues did not significantly change the overall spike structure, up-down ratio of the receptor-binding domains (RBDs), or ACE2 binding. Furthermore, a KP.3.1.1 S structure with hACE2 further confirmed an epistatic effect between F456L and Q493E on ACE2 binding. Our analysis shows SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.","fileCount":"199","fileSizeKB":"33671951","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);SARS coronavirus (NCBITaxon:227859)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:43 - \\\"N-Acetylhexosamine.\\\";UNIMOD:366 - \\\"Deamidation in presence of O18.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\"","keywords":"SARS-CoV-2;COVID-19;KP.3.1.1;hACE2;N-glycosylation;DeGlyPHER;DatasetType:Proteomics","pi":[{"name":"John R. 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This analysis a test to determine the minimum required biomass to successfully perform untargeted LC-MS\/MS on juvenile squid, as well as establish a baseline metabolome for whole squid (both SYM and APO). Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). 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This data was collected from symbiotic (SYM; Vibrio fischeri ES114 colonized) and aposymbiotic (APO; no symbiont exposure) squid, flash frozen 24 hours post hatch. This analysis a test to determine the minimum required biomass to successfully perform untargeted LC-MS\/MS on juvenile squid, as well as establish a baseline metabolome for whole squid (both SYM and APO). Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA). LC-MS\/MS data acquired in positive mode.","fileCount":"270","fileSizeKB":"17449228","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Euprymna scolopes (NCBITaxon:6613)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Squid;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Margareth McFall-Ngai","email":"mcfallng@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0bb1c05791ab4d6883bde889d0461c60","id":"1456"}, {"dataset":"MSV000096629","datasetNum":"96629","title":"Nitrogen Substrate Impacts Microcystis Aeruginosa Exometabolome Composition","user":"cmpeck2001","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733857724000","created":"Dec. 10, 2024, 11:08 AM","description":"Metabolomics data from Peck et al. 2024 - Nitrogen Substrate Impacts Microcystis aeruginosa Exometabolome Composition","fileCount":"7","fileSizeKB":"467","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Microcystis aeruginosa (NCBITaxon:1126)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Microcystis;Exometabolome;Nitrogen;DatasetType:Metabolomics","pi":[{"name":"Jenan Kharbush","email":"jenanjk@umich.edu","institution":"University of Michigan","country":"United States of America"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ad0a46b8dcea48aaaf57d06f7e4b6ed4","id":"1457"}, {"dataset":"MSV000096627","datasetNum":"96627","title":"Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis","user":"marion_H","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733822476000","created":"Dec. 10, 2024, 1:21 AM","description":"Faced with nutritional stress, some bacteria form endospores that can survive extreme conditions for long periods of time; yet the function of many proteins expressed during sporulation remains a mystery. We show that one such protein, KapD, is a 3 prime exoribonuclease expressed under control of the mother cell-specific transcription factors SigE and SigK in B. subtilis. KapD assembles dynamically over the spore surface through a direct interaction with the major crust protein CotY. KapD catalytic activity is required for the normal adhesiveness of spore surface layers. We identify the sigK mRNA as a key substrate for KapD and show that its sequestration by CotY controls the stability of the sigK transcript. SigK is controlled through excision of a prophage-like element, transcriptional regulation, and removal of an inhibitory pro-sequence. We reveal a fourth, posttranscriptional layer of control of sigK expression that couples late-stage gene expression in the mother cell to spore morphogenesis.","fileCount":"46","fileSizeKB":"25568619","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis (NCBITaxon:1423)","instrument":"QExactive plus","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Post-transcriptional regulation;Cell development;Sporulation;RNA degradation;Q-Exactive plus;Maxquant;DatasetType:Proteomics","pi":[{"name":"Alexandre D'Halluin","email":"alexandre.dhalluin@ibpc.fr","institution":"Institut de Biologie Physico-Chimique","country":"FRANCE"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD058725","task":"b60fef4d292e4220acecbffd8fdc3eb2","id":"1458"}, {"dataset":"MSV000096625","datasetNum":"96625","title":"PLK1 inhibition induces synthetic lethality in Fanconi anemia pathway-deficient acute myeloid leukemia","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733777013000","created":"Dec. 9, 2024, 12:43 PM","description":"Overall survival of acute myeloid leukemia (AML) remains limited. Inhibitors of the master mitotic kinase PLK1 have emerged as promising therapeutics, demonstrating efficacy in an undefined subset of AML patients. However, the clinical success of PLK1 inhibitors remains hindered by a lack of predictive biomarkers. The Fanconi anemia (FA) pathway, a tumor-suppressive network comprised of at least 22 genes, is frequently mutated in sporadic AML. Here, we demonstrate that FA pathway disruption sensitizes AML cells to PLK1 inhibition. Mechanistically, we identify novel interactions between PLK1 and both FANCA and FANCD2 at mitotic centromeres. We demonstrate that PLK1 inhibition impairs recruitment of FANCD2 to mitotic centromeres, induces damage to mitotic chromosomes, and triggers mitotic collapse in FANCA-deficient cells. Our findings indicate that PLK1 inhibition targets mitotic vulnerabilities specific to FA pathway-deficient cells and implicate FA pathway mutations as potential biomarkers for the identification of patients likely to benefit from PLK1 inhibitors.","fileCount":"43","fileSizeKB":"74381521","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse;Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"acute myeloid leukemia;PLK1;Fanconi anemia (FA) pathway;mitotic collapse;DatasetType:Proteomics","pi":[{"name":"Amber Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD058705","task":"810dcf191a94401fb57a477bdbb7068f","id":"1459"}, {"dataset":"MSV000096622","datasetNum":"96622","title":"In-depth Characterization of S-Glutathionylation of Ventricular Myosin Light Chain 1 Across Species by Top-Down Proteomics ","user":"eachapman2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733774338000","created":"Dec. 9, 2024, 11:58 AM","description":"S-glutathionylation (SSG) is increasingly recognized as a critical signaling mechanism in the heart, yet SSG modifications in cardiac sarcomeric proteins remain understudied. Here we identified SSG of the ventricular isoform of myosin light chain 1 (MLC-1v) in human, swine, and mouse cardiac tissues using top-down mass spectrometry (MS)-based proteomics. Our results enabled the accurate identification, quantification, and site-specific localization of SSG in MLC-1v across different species. Notably, the endogenous SSG of MLC-1v was observed in human and swine cardiac tissues but not in mice. Treating non-reduced cardiac tissue lysates with GSSG elevated MLC-1v SSG levels across all three species. ","fileCount":"3243","fileSizeKB":"89731083","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Sus scrofa (NCBITaxon:9823);Mus musculus (NCBITaxon:10090)","instrument":"maXis II;impact II;solariX","modification":"S-glutathionylation","keywords":"top-down proteomics;s-glutathionylation;sarcomere;myosin light chain;PTM;DatasetType:Proteomics","pi":[{"name":"Ying Ge","email":"ying.ge@wisc.edu","institution":"University of Wisconsin - Madison","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058703","task":"b5a97a703ebc450db4dfd730e91b3505","id":"1460"}, {"dataset":"MSV000096620","datasetNum":"96620","title":"The integrated stress response regulates 18S nonfunctional rRNA decay in mammals","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733760275000","created":"Dec. 9, 2024, 8:04 AM","description":"Abstract - 18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.","fileCount":"3","fileSizeKB":"2331717","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"18S NRD, ribosomes, GCN2, ISR, RNF10, RIOK3;DatasetType:Proteomics","pi":[{"name":"Colin Wu","email":"colin.wu2@nih.gov","institution":"NCI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7b377ac7c3ed49a88c239b519bbe381b","id":"1461"}, {"dataset":"MSV000096618","datasetNum":"96618","title":"Multi-modal comparison of molecular programs driving nurse cell death and clearance in Drosophila melanogaster oogenesis ","user":"srphanse","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733760142000","created":"Dec. 9, 2024, 8:02 AM","description":"Project_description:\r\nWe adapted proximity labeling to identify proteins trafficked through the endoplasmic reticulum in Drosophila follicle cells. To identify these proteins, we biochemically tagged and enriched proteins in the ER by expressing a genetically tagged fusion construct carrying horseradish peroxidase (HRP) fused to the ER-retention signal KDEL, along with secretion signal IgK leader sequence (ss). We expressed ss-HRP-KDEL-V5 in follicle cells, where it localized to the ER. We exposed dissected ovaries to biotin-phenol substrate and a brief pulse of H2O2, which catalyzed the biotinylation of the proteins in the vicinity of HRP. We identified 50 differentially abundant proteins in follicle cells in different states.\r\n\r\n\r\nSample_processing_protocol:\r\nFreshly dissected ovaries were incubated in 300 uL of 500 uM biotin phenol for 30 minutes at room temperature rotating. Samples were then rinsed with 1X PBS twice and the biotinylation reaction was initiated by adding 1 mM H2O2 in PBS to the samples for 1 minute and rotating at room temperature. Ovaries were quickly washed with quencher solution (10 mM sodium ascorbate, 5 mM Trolox (Sigma-Aldrich), 10 mM sodium azide, then lysed in 100 uL RIPA buffer with quencher solution for 5 min on ice. RIPA buffer was composed of: 50 uL 1M Tris-HCl, 150 uL 5M NaCl, 50 uL of 10% SDS, 250 uL of 10% Sodium Deoxycholate, 500 uL of 10% TritonX-100, 50 uL of 100X Protease Inhibitor (Sigma-Aldrich - P8849), 50 uL of 100 mM PMSF, 3.550 mL of diH20. Tissue was homogenized by motorized pestle and centrifuged at 16.1g for 10 min at 4 deg. C. Clarified sample (clear middle layer) was transferred to a new tube and snap frozen in liquid nitrogen. Frozen protein samples were thawed on ice. Meanwhile, 50 uL streptavidin magnetic beads (Pierce 88817) were washed with 1 mL of RIPA lysis buffer twice. The beads were subsequently incubated with 90 uL of protein lysate (about 550 ug of protein) and an additional 500 uL of RIPA buffer was added to facilitate rotation for 1 hour at room temperature. Beads were pelleted on a magnetic rack and the supernatant (flow-through) was collected on ice. After each wash, the magnetic beads were transferred into new tubes and washed twice with 1 mL RIPA buffer, once with 1 mL KCl, once with 1 mL 0.1 M Na2CO3, once with 1 mL 2 M Urea in 10 mM Tris-HCl (pH 8), and twice with 1 mL RIPA buffer. RIPA buffer was removed, and the beads snap frozen in liquid nitrogen and stored at -80 deg. C. Beads from biotinylated protein pull-down were washed with 100 mM triethylammonium bicarbonate. Peptides were eluted from beads by on-bead trypsin digestion with 1ug Trypsin (Pierce) in 100 mM triethylammonium bicarbonate overnight rotating at 37 deg. C. Peptides were desalted using C18 ZipTip (Millipore) and subjected liquid chromatography coupled to tandem mass spectrometry on a Q Exactive HF-X (Thermo Fisher Scientific). Data-dependent fragmentation used collision-induced dissociation. \r\n\r\n\r\nData_processing_protocol:\r\nRAW files were searched using MaxQuant under standard settings using the UniProt Drosophila melanogaster database, allowing for two missed trypsin cleavage sites, variable modifications for N-terminal acetylation, and methionine oxidation. Candidate peptides and protein identifications were filtered on the basis of a 1% false discovery rate. Raw intensities from the MaxQuant spectral database search engine were imported into R for downstream analysis. QC metrics such as number of unique peptides identified, percent of contaminants and reverse decoys detected, and total sum of intensities at the replicate level and condition level were computed and visualized using artMS v1.12.0. Spurious hits such as reverse decoys and potential contaminants were removed. R package DEP v1.16.0 was used to remove proteins not identified in both replicates simultaneously and variance stabilizing transformation was applied to normalize the intensities. Missing values were imputed using the k-nearest neighbors imputation method, followed by differential abundance estimation and multiple hypothesis testing correction in limma, all of which were implemented in DEP.\r\n","fileCount":"54","fileSizeKB":"52009646","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Proximity labeling, Endoplasmic reticulum, Drosophila, Ovary;DatasetType:Proteomics","pi":[{"name":"Kim McCall","email":"kmccall@bu.edu","institution":"Boston University","country":"USA"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"","task":"269c03defad0435ca3cb1b2a14f7a5c6","id":"1462"}, {"dataset":"MSV000096617","datasetNum":"96617","title":"Zhang et al - 2024 - Systems analysis of long-term heat stress responses in the C4 grass Setaria viridis","user":"AdamJCarroll","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733733415000","created":"Dec. 9, 2024, 12:36 AM","description":"These data are associated with the following peer-reviewed scientific paper:\n\nPeng Zhang, Robert Sharwood, Adam Carroll, Gonzalo M Estavillo, Susanne von Caemmerer and Robert T Furbank (2024) Systems analysis of long-term heat stress responses in the C4 grass Setaria viridis, The Plant Cell\n\nCorresponding Author: Robert Sharwood (R.Sharwood@westernsydney.edu.au)\n\nAbstract\nA substantial number of C4 plants are utilized as food and fodder crops and often display improved resource use efficiency compared to C3 plants. However, the response of C4 plants to future extreme conditions such as heatwaves is less understood. Here, Setaria viridis, an emerging C4 model grass closely related to important C4 crops, was grown under long-term high temperature stress for two weeks (42C, compared to 28C). High temperature resulted in stunted growth, but surprisingly had little impact on leaf thickness, leaf area-based photosynthetic rates and bundle sheath leakiness. Dark respiration rates increased significantly (p<0.05 two-tailed Student's t-test assuming equal variance) and there were major alterations in carbon and nitrogen metabolism in the heat-stressed plants, including reduced starch levels, accumulation of soluble sugars and increased leaf nitrogen content. Quantification of major phytohormones revealed a dramatic increase in abscisic acid and accumulation of IAA-amino acid conjugates in the heat-stressed plants, consistent with transcriptional changes of genes in these pathways. Leaf transcriptomics, proteomics and metabolomics analyses were carried out and mapped onto the metabolic pathways of photosynthesis, respiration, carbon\/nitrogen metabolism and phytohormone biosynthesis and signaling. While poor correlations were observed between transcript and protein log2(FoldChange) values for some photosynthetic genes, we provide an in-depth analysis of 37 hierarchical functional groups. Overall, many stress signaling pathways were upregulated, consistent with multiple potent signals leading to reduced plant growth. A systems-based model of the plant response to long-term heat stress is presented based on the oxidative stress, phytohormone and sugar signaling pathways.","fileCount":"351","fileSizeKB":"30663671","spectra":"0","psms":"43720","peptides":"9480","variants":"11169","proteins":"3292","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Setaria viridis (NCBITaxon:4556)","instrument":"Q Exactive Plus","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"plants;heat stress;Setaria viridis;C4 photosynthesis;proteomics;dimethyl labelling;photosynthesis;respiration;RNA-Seq;metabolomics;multi-omics;ribosomes;data-dependent acquisition;DatasetType:Proteomics","pi":[{"name":"Robert Sharwood","email":"R.Sharwood@westernsydney.edu.au","institution":"University of Western Sydney","country":"Australia"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058688","task":"71d50f613b844e5e932e6361e215ed04","id":"1463"}, {"dataset":"MSV000096614","datasetNum":"96614","title":"Drosophila Cardiac Myosin Isoform Expression","user":"bellk2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733610939000","created":"Dec. 7, 2024, 2:35 PM","description":"in-gel tryptic and Glu-C digestion of myosin heavy chain isolated from the cardiac tube of drosophila melanogaster to identify the series of alternative exons expressed in the cardiac myosin isoform. \n\nMass spectrometry analysis performed at the Center for Functional Genomics in Albany, NY","fileCount":"7","fileSizeKB":"811","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster sigma virus Derby (NCBITaxon:671496)","instrument":"QSTAR XL","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Drosophila;cardiac;myosin;MASCOT;mascot.dll;DatasetType:Other (Single protein expression analysis)","pi":[{"name":"Kaylyn Bell","email":"kaylynmbell@gmail.com","institution":"Rensselaer Polytechnic Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"158ca6bc638c4f8abb99949bcd32f822","id":"1464"}, {"dataset":"MSV000096613","datasetNum":"96613","title":"GNPS_WBJ_BA_Microbiota_20241207","user":"chg4001","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733608760000","created":"Dec. 7, 2024, 1:59 PM","description":"Raw LCMS spectra data showing the activity of genetically engineered E. coli expressing bile acid metabolic enzymes when fed with specific bile acid substrates.","fileCount":"667","fileSizeKB":"1259666","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli","instrument":"6530B Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbiota, bile acid, Escherichia coli;DatasetType:Metabolomics","pi":[{"name":"Chun-Jun Guo","email":"cj@guo-group.org","institution":"Weill Cornell Medicine","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"072d12a80a194411b7dfdbf8a586e741","id":"1465"}, {"dataset":"MSV000096611","datasetNum":"96611","title":"GNPS - Corn-Bacillus interaction - N-acyl amino acids","user":"fernanda1987","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733539837000","created":"Dec. 6, 2024, 6:50 PM","description":"MS\/MS profiling of N-acyl amino acids synthetized.","fileCount":"22","fileSizeKB":"1188636","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacilus subtillis;Zea mays (NCBITaxon:4577)","instrument":"Orbitrap","modification":"NA","keywords":"N-acyl amino acids;corn-microbe interaction;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras ","email":"danie.petras@uni-tuebingen.de","institution":"University of Tuebigen ","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6ea7142a67164ab385106ea08148971d","id":"1466"}, {"dataset":"MSV000096610","datasetNum":"96610","title":"MFRP in the retina is a molecular hub that organizes the apical membrane of RPE cells by engaging in interactions with specific protein and lipid molecules","user":"gabrig","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733532241000","created":"Dec. 6, 2024, 4:44 PM","description":"Membrane frizzled-related protein (MFRP) is an integral membrane protein present in the retinal pigment epithelium (RPE) and is essential for ocular development and the physiology of the retina. Mutations in MFRP are associated with autosomal recessive non-syndromic nanophthalmos, leading to severe hyperopia and early-onset retinitis pigmentosa. While several preclinical gene augmentation and gene editing trials hold promise for future therapies aimed at stopping degeneration and restoring retinal function, the molecular mechanisms underlying MFRP biology remain largely undefined. Here, we studied the biochemical properties of MFRP and the molecular consequences of its loss in a mouse model. Using transcriptomic and lipidomic approaches, we observed that DHA accumulation constitutes a primary defect in the MFRP-deficient RPE. In biochemical assays, we showed that MFRP undergoes extensive glycosylation and preferentially binds several classes of lipids, including phosphatidylserine and phosphatidylinositol 4-phosphate, as well as several other transmembrane proteins, notably adiponectin receptor 1 (ADIPOR1) and inward rectifier potassium channel 13 (KCNJ13). Moreover, MFRP determines ADIPOR1 and KCNJ13 subcellular localization in the RPE in vivo. This feature is affected upon MFRP deficiency and can be restored by gene therapy approaches. Overall, our observations suggest that MFRP constitutes an important interaction hub within the apical membrane of RPE cells, essential for protein trafficking and subcellular localization within the RPE and lipid homeostasis within the entire retina.","fileCount":"3","fileSizeKB":"18665638","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913)","instrument":"timsTOF Pro","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Membrane frizzled-related protein;DatasetType:Proteomics","pi":[{"name":"Krzysztof Palczewski","email":"kpalczew@uci.edu","institution":"University of California, Irvine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058662","task":"0f68af781a054c6ab804dffa65aa1681","id":"1467"}, {"dataset":"MSV000096609","datasetNum":"96609","title":"GNPS - NASTE DOM and coral tissue nutrient dosing experiment","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733530830000","created":"Dec. 6, 2024, 4:20 PM","description":"Dissolved organic matter and coral tissue metabolites from a three, three week nutrient dosing experiment using an inorganic nutrient mixture, bird guano, or effluent. DOM and tissue metabolites were from either Porites or Montipora coral treatments. The first three weeks just dosed the corals with nutrients, the following increased temperatures to simulate future warming conditions, and the last three were a recovery period. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"3247","fileSizeKB":"186695449","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Montipora (NCBITaxon:46703);Porites rus (NCBITaxon:262591)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dissolved organic matter (DOM);coral tissue;Porites;Montipora;Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Craig Nelson","email":"craig.nelson@hawaii.edu","institution":"University of Hawaii","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3b560004163a4d0f9474e278dcbcd841","id":"1468"}, {"dataset":"MSV000096608","datasetNum":"96608","title":"Open-source electrophilic fragment screening platform for UCHL1 covalent inhibitors","user":"Martolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733529015000","created":"Dec. 6, 2024, 3:50 PM","description":"Data in support of the manuscript \"Open-source electrophilic fragment screening platform for UCHL1 covalent inhibitors\"","fileCount":"519","fileSizeKB":"88400138","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"ABPP;ion mobility;DIA;DatasetType:Proteomics","pi":[{"name":"Jarrod Marto","email":"jarrod_marto@dfci.harvard.edu","institution":"DFCI","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fb1c517496c44aeaaf0fcbdb4d8203e4","id":"1469"}, {"dataset":"MSV000096605","datasetNum":"96605","title":"GNPS - FluoroMatch IM: An Interactive Software Leveraging Homologous Series and CCS Matching for PFAS Analysis by Ion Mobility Spectrometry","user":"jeremykoelmel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733516794000","created":"Dec. 6, 2024, 12:26 PM","description":"This is a dataset that containing raw .d files analyzed in the following manuscript. FluoroMatch IM An Interactive Software for PFAS Analysis by Ion Mobility Spectrometry Abstract. Per- and polyfluoroalkyl substances (PFASs) are often present as complex mixtures at trace levels in environmental samples, posing difficulties for analytical chemists. Ion mobility offers highly replicable identifiers, enabling the use of community-based libraries for PFAS annotation in non-targeted analysis. Currently, limited software exists to leverage the capabilities of liquid chromatography ion mobility high resolution mass spectrometry (LC-IM-HRMS) for non-targeted PFAS analysis. FluoroMatch IM is a vendor neutral tool for rapid annotation of LC-IM-HRMS datasets. Annotation algorithms include CCS matching, formula prediction, homologous series detection, mass defect filtering, and accurate mass matching with a database of 194 PFAS ions which can continuously be expanded by the community. Results from FluoroMatch IM were compared to a targeted approach with a laboratory-prepared mix of 63 PFASs and real wastewater samples. FluoroMatch IM revealed additional likely PFASs (n is 3) while confirming most targeted annotations (9\/10). Validation of the standard mix showed a low false negative rate of 5 percent and a 0 percent false positive rate for features included in the CCS library. This study demonstrates the promise of FluoroMatch IM for streamlining PFAS analysis workflows and maintaining accuracy in non-targeted analysis. 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The proteome coverage is, on average, over 50%. Additionally, we acquired further datasets for bacterial identification algorithm validation: i) 303 species at a 30-minute gradient (38 samples per day throughput), ii) 303 species at a 10-minute gradient (80 samples per day throughput), iii) reproducibility dataset, iv) genus-specific Pseudomonas spp. dataset (94 Pseudomonas spp. strains), v) genus-specific Bacillus spp. dataset (28 Bacillus cereus s.l. strains), vi) food routine dataset (60 dairy product isolates), and vii) clinical routine dataset (570 clinical isolates). 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Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size PolarC18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"389","fileSizeKB":"12754413","spectra":"503173","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Loxodonta africana (NCBITaxon:9785);Ceratotherium simum simum (NCBITaxon:73337)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Rhinocero;Elephant;Milk;Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Candance Williams","email":"candacewilliams07@gmail.com","institution":"San Diego Zoo Wildlife Alliance","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c9269a84a6b54602a243d21a502db0e1","id":"1474"}, {"dataset":"MSV000096599","datasetNum":"96599","title":"GNPS - SDZWA Elephant and Rhino Milk Untargeted LC-MSMS POS","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733442125000","created":"Dec. 5, 2024, 3:42 PM","description":"Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). 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Rapid analysis, high sensitivity, and maximization of sample utilization is paramount for single-cell analysis. Some challenges of coupling CZE analysis with mass spectrometry analysis (MS) of complex mixtures include 1. sensitivity due to volume loading limitations of CZE and 2. incompatibility of MS duty cycles with electropherographic timescales, especially for rapid (<20 min) analyses. Here, we address these two challenges as applied to single-cell equivalent phosphoproteomics experiments by interfacing a microchip-based CZE device integrated with a solid-phase-extraction (SPE) bed with the Orbitrap Astral mass spectrometer. The SPE bed theoretically circumvents the volume limitations that thwart detection sensitivity of classical CZE by allowing analyte capture and concentration before electrokinetic focusing and separation. Further, we leverage the high sampling rates of the Orbitrap Astral mass spectrometer to take full advantage of the fast and high-resolution SPE-CZE separations which historically pose challenges for typical MS scan speeds. Using 225 phosphorylated peptide standards and phosphorylated peptide-enriched mouse brain tissue, we investigate microchip-based SPE-CZE functionality, quantitative performance, and complementarity to nano-LC-MS analysis. We characterize important device characteristics such as volume and mass loading tolerances as well as compatibility with state-of-the-art mass spectrometry methods. Finally, we highlight unique SPE-CZE separation mechanisms that can empower fit-for-purpose applications in single-cell-equivalent phosphoproteomics. ","fileCount":"76","fileSizeKB":"59478983","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Phosphoproteomics;SPE-CZE;DatasetType:Proteomics","pi":[{"name":"Joshua Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058591","task":"92843358b2c34d5a929b116f2f8533e8","id":"1478"}, {"dataset":"MSV000096594","datasetNum":"96594","title":"HHIP protein interactions in lung cells provide insight into COPD pathogenesis","user":"hinuzuka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733346130000","created":"Dec. 4, 2024, 1:02 PM","description":"Affinity purification mass spectrometry (AP-MS) was performed to identify protein interactions with HHIP, a well-established COPD GWAS gene. 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","fileCount":"178","fileSizeKB":"125892631","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Junctophilin 2;Ryanodine receptor 2;FKBP12 deficient mice;DatasetType:Proteomics","pi":[{"name":"Sung Yun Jung","email":"syjung@bcm.edu","institution":"Baylor College of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058583","task":"f3a25880f7ba477da65cf40dca6630a8","id":"1480"}, {"dataset":"MSV000096592","datasetNum":"96592","title":"Improved Proteome-wide Succinylome Analysis by Data-Independent Acquisition Using High-Quality Succinyl Spectral Libraries","user":"JoannaBons","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733338588000","created":"Dec. 4, 2024, 10:56 AM","description":"Protein post-translational modifications (PTMs) are crucial and dynamic modulators of protein functions, interactions, and localizations as well as biological pathways and cellular signaling. Lysine succinylation analysis remains challenging, but sophisticated workflows combining succinylated peptide enrichments and quantitative mass spectrometry approaches have revolutionized proteome-wide succinylome analysis. The implementation of data-independent acquisition (DIA)-mass spectrometry has greatly advanced the detection of low abundance succinylated peptides, succinylome coverage, identification reproducibility, and quantification accuracy. However, the complexity of DIA data requires dedicated data processing algorithms and tools, that typically rely on spectral libraries. These reference libraries can be generated from experimental data-dependent acquisition (DDA) acquisitions of representative study samples submitted to DDA database search engines for confident succinylated peptide identification and precise PTM site localization. Here, we describe how to build DDA PTM spectral libraries using various software tools, specifically Spectronaut (Biognosys), SpectroMine (Biognosys), and MSFragger (Nesvizhskii Lab). The generated libraries were imported into Skyline for the previously published DIA succinylome analysis of Sirtuin-5 knocked-out vs wild-type mouse brains in order to accurately quantify and visualize PTM-containing peptides.","fileCount":"26","fileSizeKB":"27329698","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:64 - \\\"Succinic anhydride labeling reagent light form (N-term & K).\\\"","keywords":"Spectral library;Succinylation;Data-dependent acquisition (DDA);Post-translational modifications;Data-independent acquisition (DIA);Quantitative proteomics;DatasetType:Proteomics","pi":[{"name":"Birgit Schilling","email":"bschilling@buckinstitute.org","institution":"Buck Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058580","task":"f5b458da067e403cac0e84bd61704eec","id":"1481"}, {"dataset":"MSV000096591","datasetNum":"96591","title":"Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733336361000","created":"Dec. 4, 2024, 10:19 AM","description":"Ctrl = control; R = replicate; en = endogenously tagged; mNG = mNeonGreen\r\n\r\nLUM1_1034603:\tCtrl_U2OS_R1\r\n\r\nLUM1_1034604:\tCtrl_U2OS_R2\r\nLUM1_1034605\tCtrl_U2OS_R3\r\nLUM1_1034613\tU2OS_RTN4en_TurboID_mNG_R1\r\nLUM1_1034614\tU2OS_RTN4en_TurboID_mNG_R2\r\nLUM1_1034615\tU2OS_RTN4en_TurboID_mNG_R3\r\nLUM1_1034621\tU2OS_mNG_TurboID_CLIMP63en_R1\r\nLUM1_1034622\tU2OS_mNG_TurboID_CLIMP63en_R2\r\nLUM1_1034623\tU2OS_mNG_TurboID_CLIMP63en_R3\r\nLUM1_1034628\tU2OS_CANXen_TurboID_mNG_R1\r\nLUM1_1034629\tU2OS_CANXen_TurboID_mNG_R2\r\nLUM1_1034630\tU2OS_CANXen_TurboID_mNG_R3\r\nLUM1_1034632\tU2OS_mNG_TurboID_LBRen_R1\r\nLUM1_1034633\tU2OS_mNG_TurboID_LBRen_R2\r\nLUM1_1034634\tU2OS_mNG_TurboID_LBRen_R3\r\nLUM1_1034636\tU2OS_mNG_TurboID_Nesprin4_R1\r\nLUM1_1034637\tU2OS_mNG_TurboID_Nesprin4_R2\r\nLUM1_1034638\tU2OS_mNG_TurboID_Nesprin4_R3","fileCount":"73","fileSizeKB":"113881171","spectra":"1563879","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"spatial proteomics;TurboID;endoplasmic reticulum;DatasetType:Proteomics","pi":[{"name":"W. Mike Henne","email":"mike.henne@utsouthwestern.edu","institution":"UT Southwestern","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8d97dcf2cd6b4b8fbd2356870a515c59","id":"1482"}, {"dataset":"MSV000096589","datasetNum":"96589","title":"GNPS - Drug metabolism by gut community","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733331485000","created":"Dec. 4, 2024, 8:58 AM","description":"Bacterial community culture with drugs acquired on Exploris 240 with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 100 x 2.1 mm). Reversed-phase, ESI positive.","fileCount":"1197","fileSizeKB":"77681099","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Drugs;Gut microbes;Untargeted metabolomics;Community;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1ab5cea1a134430a9b0899fe50a278aa","id":"1483"}, {"dataset":"MSV000096588","datasetNum":"96588","title":"LC-MS data of trypsin-digested urinary proteins of clinical cases of diabetic nephropathy.","user":"deepakk1812","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733311467000","created":"Dec. 4, 2024, 3:24 AM","description":"The LC-MS study was carried out to identify the proteins in urine samples of clinical cases of diabetic nephropathy (Healthy control, Diabetic group, Microalbuminuria, Overt albuminuria group). \n\nStudy design\nThe urine samples (10 ml) of patients with HbA1c greater than 6.5 percent were collected in a sterile container from the endocrinology OPD, PGIMER, Chandigarh, India, after obtaining informed consent. The study was carried out following the Helsinki Declaration. The Institute Ethics Committee approved the study protocol via (IEC) vide No INT\/IEC\/2020\/SPL-1031.\nThe spot dipstick method was used to screen urine samples for the presence of blood (haematuria) and pus cells (leucocytes). Samples showing the presence of both blood and leucocytes were further excluded from the study. After screening, 90 patient samples (30 diabetic controls, 30 microalbuminuria, and 30 overt albuminuria) were included in the study. For control, urine samples of 30 healthy controls were also included in the study.\nThe albumin excretion rate parameters (Albumin to creatinine ratio (ACR)) was measured in Alere Afinion TM AS100 Analyser with ACR test kits. The ACR was expressed in mg per gram. Based on the obtained ACR, the patient groups were categorized following criteria as detailed under inclusion criteria. The inclusion and exclusion criteria are mentioned below.\nInclusion criteria \nMicroalbuminuria (meant as diabetic microalbuminuria)- Established case of Diabetes Mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin excretion rate 30 to 300 mg per gram of creatinine in a spot urine sample.\nOvert albuminuria (meant as diabetic overt albuminuria): Established case of Diabetes Mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin concentration more than or equal to 300 mg per gram of creatinine in a spot urine sample.\nDiabetic Control- Established case of diabetes mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin excretion rate of less than 30 mg per gram of creatinine in a spot urine.\nExclusion criteria\nPatients with any evidence of urine tract infection or haematuria by dipstick test. \n\nSeparation of urinary proteins\nThe urinary proteins are separated from the urine matrix through centrifugation (15000 g for 1 hour at 4 degrees Celsius. The pellet obtained was expected to contain the proteins. For this, a 2 ml urine sample was subjected to centrifugation for each participant. After centrifugation (1ml in different aliquots), 2 pellets from the same sample were obtained. The pellets were suspended in PB (200 microlitres, pH 7.38, 0.1 M) and mixed well with a vortex. The pellets obtained from the same group were pooled. A similar treatment was provided to all the samples to obtain pellets. Protein quantification was done using the BCA method.\n\nLC-MS protocol: For this, 100 micrograms of urinary protein in 10 mM Tris HCl buffer, pH 7.38 was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degrees Celsius. These were then subjected to trypsin digestion (2 micrograms, Promega, MS grade, prepared in acetic acid) and kept overnight at 37 degrees Celsius. The reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LC-MS grade). The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition (PMID 39216816).\nThe different raw files obtained are named as follows and uploaded.\n1- Healthy Control\n2- Diabetic Controls\n3- Microalbuminuria \n4- Overt albuminuria \n\nProf Dibyajyoti Banerjee, Dr. Rajasri Bhattacharyya, Dr. Sheemona Chowdhary, Dr. Deepak Kumar, and Ms Monu Kumari acknowledge ICMR, New Delhi, India, sanctioned project titled Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits for financial support. \n\n","fileCount":"17","fileSizeKB":"14230441","spectra":"297005","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"All types","keywords":"Urinary proteins, Diabetic nephropathy, Diabetes, Microalbuminuria, Overt albuminuria, LC-MS, Trypsin digestion;Clinical samples;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"01e4880f62974b5d82a3000ae5d21b71","id":"1484"}, {"dataset":"MSV000096587","datasetNum":"96587","title":"To study the acetylation of human serum albumin (HSA) with 2 Naphthyl Acetate (2NA) after digestion with Trypsin and Pepsin","user":"SumanKaur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733311205000","created":"Dec. 4, 2024, 3:20 AM","description":"This is study done for academic purpose and funded by ICMR, New Delhi, India, sanctioned project titled:- Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits. Project File No. 5\/4\/1-25\/2020-NCD-1.\n Sample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with and without 2NA (prepared in Acetonitrile) for 45 mins at 37 degree Celsius. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to trypsin digestion (2 microgram, Promega, MS grade, prepared in acetic acid) and Pepsin digestion (2 microgram, Promega, MS grade, prepared in acidic water).Further the samples with Trypsin digestion were incubated for overnight, whereas samples to be digested by pepsin were incubated for 2 hours at 37 degree Celsius. The Trypsin digested reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LC-MS grade), whereas pepsin digestion was stopped by heating samples at 95 degree Celsius. The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition. Data Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, trypsin\/P type was selected with all other parameters considered as default. In case of Pepsin digestion, Pepsin enzyme was added to MaxQuant enzyme file. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. \nDescription of the raw files is as follow. Control_Trypsin is HSA digested with Trypsin, Control_Pepsin is HSA digested with Pepsin, HSA_2NA_Trypsin is HSA incubated with 2NA and then digested by Trypsin and HSA_2NA_Pepsin is HSA incubated with 2NA & digested by Pepsin.\n","fileCount":"17","fileSizeKB":"10319428","spectra":"147697","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Human serum albumin, Acetylation, 2Naphthyl acetate, Trypsin, Pepsin;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6113850b1c3e405ba5ad2dc0004c5e48","id":"1485"}, {"dataset":"MSV000096584","datasetNum":"96584","title":"GNPS-Food_ingredients_food_simple_food","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733276195000","created":"Dec. 3, 2024, 5:36 PM","description":"MS\/MS fragmentation data of food ingredients samples acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"1331","fileSizeKB":"145250835","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No Species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Food, ingredients;DatasetType:Metabolomics","pi":[{"name":"Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c1fbc48e70ff4fb3b2de29cb70da80b7","id":"1486"}, {"dataset":"MSV000096583","datasetNum":"96583","title":"Proteomic analysis of PELP1 (RIX1) interactome.","user":"Sseu_Pei_1632","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733274853000","created":"Dec. 3, 2024, 5:14 PM","description":"A mass spectrometry-based proteomic analysis of the Rix1 60S biogenesis complex\nthrough immunoprecipitation of endogenous PELP1 from HEK293T cells.","fileCount":"103","fileSizeKB":"136292","spectra":"0","psms":"6501","peptides":"2663","variants":"3105","proteins":"12016","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pelp1 interactome;RIX1 complex;Ribosome Biogenesis;rRNA processing;DatasetType:Proteomics","pi":[{"name":"Catherine Denicourt","email":"catherine.denicourt@uth.tmc.edu","institution":"McGovern Medical School","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"","task":"f6a56a337156409fa0aedfd257c124ef","id":"1487"}, {"dataset":"MSV000096582","datasetNum":"96582","title":"GNPS - Population wide metabolomic analysis identifies peptide polymers as markers of coral stress independent of genotype","user":"enchiles","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733259181000","created":"Dec. 3, 2024, 12:53 PM","description":"Effective coral conservation depends on understanding how stress impacts reef biology and health. Coral bleaching varies widely across individuals, yet its dependence on the genetic background of coral animals is poorly understood. Given this knowledge gap, we strove to identify genotype-independent metabolite markers of stress in two Hawaiian coral species, Montipora capitata and Pocillopora acuta. After exposure to thermal and pH stress, we used untargeted metabolomic profiling to investigate the physiological response of different coral genotypes (and ploidies) of each species. Our previous studies showed that dipeptides correlate with stress, and we found these metabolites showed a consistent response across different genotypes and ploidies. We further explored dark metabolites that are stress-responsive, and our tandem mass spectrometry (LC-MS2) results suggest that these candidates are larger tri- and tetrapeptides. Our results identify short peptides as critical intermediates in the coral stress response which provide diagnostic biomarkers for field applications.","fileCount":"311","fileSizeKB":"25074677","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Montipora capitata (NCBITaxon:46704);Pocillopora acuta (NCBITaxon:1491507)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dipeptides;Tripeptides;Tetrapeptides;Stress response;Holobiont;Montipora capitata;Pocillopora acuta;DatasetType:Metabolomics","pi":[{"name":"Xiaoyang Su","email":"xs137@rwjms.rutgers.edu","institution":"Rutgers Cancer Institute of New Jersey","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"cf242b11e0114fe4aab2a8bddc51d00d","id":"1488"}, {"dataset":"MSV000096580","datasetNum":"96580","title":"Spaceflight alters protein levels and gene expression associated with cell survival and metabolic characteristics in human cardiac spheroids","user":"Zeyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733245086000","created":"Dec. 3, 2024, 8:58 AM","description":"Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) possess tremendous advantage for cardiac regeneration. However, cell survival is challenging upon cell transplantation. Since microgravity can profoundly affect cellular properties, we investigated the effect of spaceflight on hiPSC-CMs. Cardiac spheroids derived from hiPSCs were transported to the International Space Station (ISS) via the SpaceX Crew-8 mission and cultured under space microgravity for 8 days. Beating cardiac spheroids were observed on the ISS and upon successful experimentation by the astronauts in space, the live cultures were returned to Earth. These cells had normal displacement (an indicator of contraction) and Ca2+ transient parameters in 3D live cell imaging. Proteomics analysis revealed that spaceflight upregulated many proteins involved in metabolism (n=90), cellular component of mitochondrion (n=62) and regulation of proliferation (n=10). Specific metabolic pathways enriched by spaceflight included glutathione metabolism, biosynthesis of amino acids, and pyruvate metabolism. In addition, spaceflight upregulated proteins in cellular stress response, cell survival, and the AMPK signaling pathway, a master regulator of metabolism. ","fileCount":"37","fileSizeKB":"29872537","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Microgravity;Human induced pluripotent stem cells;hiPSCs;Proteomics;Metabolic pathways;AMPK signaling pathway;Cell survival;Cellular stress response;DatasetType:Proteomics","pi":[{"name":"Chunhui Xu","email":"chunhui.xu@emory.edu","institution":"Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"78670ec1147f4c74afee777f4a39aa2f","id":"1489"}, {"dataset":"MSV000096579","datasetNum":"96579","title":"Reconstructing Medieval Diets (TRI-DENTUM project, H2020-MSCA-IF-2020 No. 891511)","user":"apeder","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733229577000","created":"Dec. 3, 2024, 4:39 AM","description":"Historical (medieval) dental calculus was analyzed. This dataset is associated to the paper entitled \"Reconstructing medieval diets through the integration of stable isotope and proteomic analyses from two European burial sites\".","fileCount":"297","fileSizeKB":"50978265","spectra":"0","psms":"103643","peptides":"17787","variants":"19288","proteins":"112855","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";carbami","keywords":"historic dental calculus;plants;microbiome;TB;DatasetType:Proteomics","pi":[{"name":"Antonella Pedergnana","email":"antonella.pedergnana@iem.uzh.ch","institution":"Institute of Evolutionary Medicine","country":"Switzerland"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058524","task":"92df91ac70354e65be1ad47f00f344f5","id":"1490"}, {"dataset":"MSV000096575","datasetNum":"96575","title":"Proximity labeling and orthogonal nanobody pulldown (ID-oPD) approaches to map the spinophilin interactome uncover a role for spinophilin in protein regulation.","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733171568000","created":"Dec. 2, 2024, 12:32 PM","description":"The major synaptic protein phosphatase 1 (PP1) targeting protein, spinophilin can inhibit or target PP1 activity towards diverse substrates. To detail the full panoply of substrates at which spinophilin modulates PP1 activity, we have validated a novel approach that permits proximity labeling and orthogonal nanobody pulldown (ID-oPD) of spinophilin protein complexes. We identified 614 specific and 217 selective spinophilin interacting proteins in a HEK293 overexpression system, many of which are involved in mRNA translation or metabolism. We validated a subset of these interactors using neutravidin and ALFA-tag nanobody pulldowns followed by immunoblotting. Additionally, using wildtype or an F451A mutant spinophilin that limits PP1 binding, we found that the PP1 binding-deficient spinophilin mutant enhanced its own expression, but limited the expression of proteins involved in mRNA translation and metabolism Moreover, in the striatum, spinophilin mRNA is highly neuropil localized and endogenous spinophilin limits its own expression. Overall, our studies demonstrate a novel role for spinophilin in mediating synaptic protein expression and that care must be taken to not over-control when using proximity labeling to detect PP1 targeting protein interactomes.","fileCount":"46","fileSizeKB":"25773539","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse;orbitrap QE-plus","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"spinophilin;protein phosphatase 1;proximity labeling;orthogonal nanobody pulldown;proximity labeling and orthogonal nanobody pulldown (ID-oPD);ALFA-tag;TurboID;DatasetType:Proteomics","pi":[{"name":"A.J. Baucum II","email":"ajbaucum@iu.edu","institution":"Indiana University School of Medicine","country":"United States"},{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD058487","task":"3cc24139e4ec48c6a1eda66f130c96c9","id":"1491"}, {"dataset":"MSV000096571","datasetNum":"96571","title":"Pan-cancer N-glycoproteomic atlas of patient-derived xenografts uncovers FAT2 as a therapeutic target for head and neck cancers","user":"TKislinger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733157353000","created":"Dec. 2, 2024, 8:35 AM","description":"Here, we employed N-glycoproteomics to analyze 85 patient-derived xenografts (PDX), constructing Glyco PDXplorer - an in vivo pan-cancer atlas of cancer derived cell surface proteins. We developed a target discovery pipeline to prioritize proteins with favorable expression profiles for immunotherapeutic targeting and validated FAT2 as a head and neck squamous cancer (HNSC) enriched surface protein with limited expression in normal tissue. Functional studies revealed that FAT2 plays a crucial role in HNSC growth and adhesion through regulation of surface architecture and integrin-PI3K signaling. Chimeric antigen receptor (CAR) T cells targeting FAT2 demonstrated potent anti-tumor activity in HNSC models. This work lays the foundation for developing FAT2-targeted therapies and represents a pivotal resource to inform therapeutic target discovery for multiple cancers.","fileCount":"209","fileSizeKB":"186127637","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive;Q Exactive HF;Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";N-glycosylation","keywords":"Patient derived xenografts;pan-cancer atlas;N-glycoproteomics;CAR-T immunotherapy;FAT2;surfaceome;targeted therapy;DatasetType:Proteomics","pi":[{"name":"Dr. Thomas Kislinger","email":"thomas.kislinger@utoronto.ca","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a80bdff2804f46c7afcea623afb8f0cc","id":"1492"}, {"dataset":"MSV000096568","datasetNum":"96568","title":"Inhibition of Lysosomal LAMTOR1 Increases Autophagy by Suppressing the MTORC1 Pathway to Ameliorate Lipid Accumulations in MAFLD","user":"juyeon4444","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733150068000","created":"Dec. 2, 2024, 6:34 AM","description":"Metabolic dysfunction-associated fatty liver disease (MAFLD) is a serious metabolic disorder characterized by fat accumulation in the liver, which can trigger liver inflammation and fibrosis, potentially leading to cirrhosis or liver cancer. Despite many studies on MAFLD over the past decades, the development of effective treatment mechanisms for MAFLD remains unclear due to its complex etiology. Given these limitations, we have focused on the discovery of therapeutic agents and molecular targets for the treatment of MAFLD treatment. In this study, we demonstrated that the natural compound acacetin alleviates MAFLD by regulating autophagy in a rapidly induced steatohepatitis a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) mouse model. In addition, acacetin inhibited lipid accumulation in 3T3-L1 adipocytes through autophagy. To identify the target contributing to the autophagy activity of acacetin, we performed Drug Affinity Responsive Target Stability (DARTS) combined with Liquid Chromatography with Tandem Mass Spectrometry (LC-MS\/MS) proteomic analysis, which led to the identification of late endosomal\/lysosomal adapter and MAPK and MTOR activator (LAMTOR1), a lysosomal membrane adaptor protein. Binding of acacetin to LAMTOR1 induces the release from the LAMTOR complex, leading to inhibition of mammalian target of rapamycin complex 1 (MTORC1), thereby increasing autophagy and ameliorating metabolic disorders through modulation of the MTORC1\/AMPK axis. Furthermore, genetic knockdown of LAMTOR1 induced lysosomal activity and reduced lipid accumulation in cells, confirming that acacetin targets LAMTOR1. Taken together, this study identifies LAMTOR1 as a key protein target of acacetin, a natural anti-MAFLD compound, providing a novel therapeutic approach for the treatment of MAFLD by targeting LAMTOR1.","fileCount":"34","fileSizeKB":"27986294","spectra":"0","psms":"58769","peptides":"37141","variants":"45641","proteins":"4494","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DARTS;LC-MS\/MS;Lysosome;Metabolic diseases;MTORC1","pi":[{"name":"Ho Jeong Kwon","email":"kwonhj@yonsei.ac.kr","institution":"College of Life Science and Biotechnology, Yonsei University","country":"South Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058477","task":"202f883a9b294290847c29d44b62b793","id":"1493"}, {"dataset":"MSV000096565","datasetNum":"96565","title":"Ttttttttttttttttttttttttttttttttttttttteszt56","user":"KecskemetiGabor2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1733129235000","created":"Dec. 2, 2024, 12:47 AM","description":"dqsjhbckhacuasdgc zugdazucgaszdgc zudsavc kszauvxckdsa","fileCount":"5","fileSizeKB":"1332009","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"IBD, Serum, Plasma;DatasetType:Metabolomics","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f6e02685d3904466a472aa0d22d3f195","id":"1495"}, {"dataset":"MSV000096563","datasetNum":"96563","title":"Search for the Coagulogen: Identification and Characterization of Coagulation Factors in Insects","user":"egor_repkin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732988879000","created":"Nov. 30, 2024, 9:47 AM","description":"The aim of the project is to obtain information about the repertoire of proteins synthesized by differentiating hemocytes of the Madagascar cockroach Gromphadorhina portentosa in order to gain insight into the types of defense reactions carried out by these cells.","fileCount":"34","fileSizeKB":"1211257","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gromphadorhina portentosa ","instrument":"timsTOF Pro","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Coagulogen, Gromphadorhina portentosa, cockroach, gel-based proteomics, shotgun proteomics, UHPLC-MS\/MS;DatasetType:Proteomics","pi":[{"name":"Andrei Iakovlev","email":"andrey.yakovlev@spbu.ru","institution":"Saint-Petersburg State University","country":"Russia"},{"name":"Egor A. Repkin","email":"erepkin53@gmail.com","institution":"Saint-Petersburg State University","country":"Russia"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"66bbb702635240f6913d7ceb47dffe85","id":"1496"}, {"dataset":"MSV000096560","datasetNum":"96560","title":"Steroid-dependent metabolic rewiring reveals novel therapeutic and imaging approaches for glioblastoma","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732876588000","created":"Nov. 29, 2024, 2:36 AM","description":"Steroid anti-inflammatory drugs, such as dexamethasone are routinely used to manage brain tumour-associated oedema, yet their impact on brain tumour metabolism remained largely unexplored. Here, a metabolomic screen in naive glioblastoma cells treated with dexamethasone revealed the accumulation of N1-methylnicotinamide, a product of N-methyltransferase (NNMT), through the activation of the glucocorticoid receptor. Using stable isotope-assisted metabolomics in glioblastoma patients we showed that nicotinamide flux into N1-methylnicotinamide exceeds that into NAD+, leading to a ~7 fold accumulation of N1-methylnicotinamide in tumour compared to surrounding brain tissue. In orthotopic mouse models, NNMT activity was enhanced by dexamethasone selectively in glioblastoma tumours but not in the contralateral brain. Leveraging the tumour-specific activity of NNMT and the NNMT-dependent trapping of nicotinamide, we developed a novel 11C-nicotinamide-based positron emission tomography (PET) approach to visualize glioblastoma tumours in vivo. Furthermore, our findings demonstrate that the dexamethasone-induced methionine-dependent methylation of nicotinamide becomes detrimental for glioblastoma growth when combined with a methionine-restricted diet. These results show that steroids rewire methionine and nicotinamide metabolism, enabling the development of innovative PET imaging and metabolic therapies for glioblastoma patients. ","fileCount":"897","fileSizeKB":"105181619","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"glioblastoma;metabolomics;steroids;nicotinamide;DatasetType:Metabolomics","pi":[{"name":"David Sumpton","email":"d.sumpton@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Maria Francesca Allega","email":"Maria.Allega@bsd.uchicago.edu","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Saverio Tardito","email":"saverio.tardito@glasgow.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ab5e034442f242658067823f96be55fa","id":"1497"}, {"dataset":"MSV000096555","datasetNum":"96555","title":"Sensitive direct detection of cancer antigens via user-defined peptide spectral libraries","user":"cctortec","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732823821000","created":"Nov. 28, 2024, 11:57 AM","description":"Mass spectrometry (MS) enables precise identification of HLA-bound peptides, but challenges remain in achieving sensitive, accurate, and reproducible detection of rare yet clinically relevant antigens, including predicted tumor neoantigens. Reliable reporting of such rare peptides often requires confirmation with synthetic peptides, which are costly and time-intensive to produce or through prediction of chemical moieties, a strategy that has only recently been expanded to non-tryptic HLA peptides. To generate user-defined high-quality peptide libraries, containing up to 20,000 unique sequences, we introduce Pepyrus, a robust peptide expression system in E. coli. We demonstrate that Pepyrus-generated peptides exhibited close to identical fragmentation patterns, retention times and ion mobility distributions to conventional chemically synthesized peptides. With a HLA-specific data independent acquisition strategy, we recovered >75% of the expected sequences per single injection even at >10,000 peptide Pepyrus library. Pepyrus-assisted identification of rare neoantigens from 0.1 fmol in a complex background was feasible. Personalized Pepyrus libraries facilitated the identification of clinically relevant peptides from melanoma patients, several of which were previously undetected using MS. The customization of Pepyrus allows rapid generation of patient- or disease-specific peptide libraries that enable the confident identification of rare HLA peptides from immunopeptidomics data as well as the generation of large training datasets to improve spectrum, retention time, and ion mobility prediction tools.","fileCount":"4301","fileSizeKB":"1019322140","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Ultra","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"immunopeptidomics;DatasetType:Proteomics","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058389","task":"2b9ccf477fa74308af9a02c5365c72da","id":"1498"}, {"dataset":"MSV000096553","datasetNum":"96553","title":"GNPS - LC-MS\/MS metabolomic analyses in Solanum lycorpersycum seed exudates - control and MeJA priming - GNPS","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732803787000","created":"Nov. 28, 2024, 6:23 AM","description":"Solanum lycopersicum Stupicke, Criollo and Micro-Tom genotypes were used in this study. Some seeds of these accessions were subjected to priming treatment with MeJA. Seeds exudates were collected from MeJA-treated and untreated (control) seeds and subjected to LC-MS\/MS metabolomic analyses.","fileCount":"93","fileSizeKB":"21886110","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Solanum lycopersicum (NCBITaxon:4081)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Specialized metabolites;Seed exudates;Osmopriming;Priming MeJA;DatasetType:Metabolomics","pi":[{"name":"Jerome Verdier","email":"jerome.verdier@inrae.fr","institution":"INRAE","country":"France"},{"name":"Lukasz Tarkowski","email":"lukasz.tarkowski@inrae.fr","institution":"INRAE","country":"France"},{"name":"Massimiliano Corso","email":"massimiliano.corso@inrae.fr","institution":"INRAE","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ee25a07b77d74b26b59ec1e4f4f94bbf","id":"1499"}, {"dataset":"MSV000096550","datasetNum":"96550","title":"GNPS - Non-targeted Metabolomics Bigelow Algae Collection Part I","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732760682000","created":"Nov. 27, 2024, 6:24 PM","description":"GNPS - Non-targeted Metabolomics Bigelow Algae Collection Part I","fileCount":"568","fileSizeKB":"27178357","spectra":"1366329","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Unkown","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Algea;Bigelow;DatasetType:Metabolomics","pi":[{"name":"Robert Schmedicke","email":"rschmedicke@bigelow.org","institution":"Bigelow Marine Labs","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bae8ef91a6bf492ba158cd4835d6a2dd","id":"1500"}, {"dataset":"MSV000096548","datasetNum":"96548","title":"Analysis of FAIMS for the Study of Affinity-Purified Protein Complexes Using the Orbitrap Ascend Tribrid Mass Spectrometer","user":"washburn_lab_kumc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732730004000","created":"Nov. 27, 2024, 9:53 AM","description":"In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend Tribrid Mass Spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Our findings highlight the potential of FAIMS with Orbitrap Ascend Tribrid Mass Spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifiers.","fileCount":"30","fileSizeKB":"27559504","spectra":"452106","psms":"24948","peptides":"1033","variants":"1256","proteins":"398","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"FAIMS;AFFINITY PURIFICATION;QUANTITATIVE PROTEOMICS;DatasetType:Proteomics","pi":[{"name":"Michael Washburn","email":"mwashburn4@kumc.edu","institution":"University of Kansas Medical Center","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058341","task":"fda1ab59a05148d2a6aaf61cf4089ff8","id":"1501"}, {"dataset":"MSV000096546","datasetNum":"96546","title":"IL-7 promotes integrated glucose and amino acid sensing during homeostatic CD4+ T cell proliferation","user":"alejandro_metabo10","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732714745000","created":"Nov. 27, 2024, 5:39 AM","description":"Homeostatic proliferation, driven by cytokines including IL-7, maintains stable T cell populations over time and expands these during lymphopenia, for example following stem cell transplantation. Yet, impaired T cell expansion in this context is associated with diminished immune protection, whilst excessive proliferation contributes to graft versus host disease. This highlights the need to understand molecular mechanisms regulating this process. Here, we studied the metabolic basis for IL-7-driven CD4+ T cell proliferation. We observed that IL-7 promotes glucose uptake and metabolism, including usage for nucleotide synthesis and oxidation in the tricarboxylic acid (TCA) cycle. Of note, contrary to other TCA metabolites, glucose-derived citrate does not accumulate in IL-7 treated cells, indicating diversion into other processes. In agreement, IL-7 promotes glucose-dependent histone acetylation and chromatin accessibility during proliferation. This is particularly notable at gene loci of the amino acid-sensing Ragulator complex. Consistently, expression of its subunit LAMTOR5 is promoted by IL-7 in a glucose-dependent manner. Functionally, glucose availability determined amino acid-dependent mTOR activation in CD4+ T cells, confirming integrated sensing of these nutrients. LAMTOR5 deletion impaired IL-7-mediated CD4+ T cell expansion, establishing that glycolysis in absence of Ragulator activation was insufficient to initiate this process. Clinically, CD4+ T cells isolated from patients following myeloablative autologous stem cell transplantation demonstrate coordinated upregulation of genes encoding glycolytic and TCA cycle enzymes, as well as amino acid sensing machinery and mTOR targets. Our findings uncover integrated sensing of glucose and amino acid metabolism and demonstrate its relevance during homeostatic T cell proliferation.\n","fileCount":"33","fileSizeKB":"1091730","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human","instrument":"Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CD4 T-cell, homeostatic proliferation, metabolism;DatasetType:Metabolomics","pi":[{"name":"Sarah Dimeloe","email":"s.k.dimeloe@bham.ac.uk","institution":"University of Birmingham ","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"40c86652d7da4514851a856718843302","id":"1502"}, {"dataset":"MSV000096543","datasetNum":"96543","title":"RNA Pol II IP-MS and GFP-CUL3 IP-MS by DIA ","user":"yukiaoi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732692146000","created":"Nov. 26, 2024, 11:22 PM","description":"DIA MS dataset for RNA Polymerase II (Pol II) or GFP-CUL3 co-immunoprecipitants prepared from human DLD-1 SPT5-AID cells treated with +\/- NVP-2 +\/- auxin (for Pol II IP) or +\/- auxin (GFP IP).","fileCount":"56","fileSizeKB":"17617015","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RNA Polymerase II;CUL3;DIA;DatasetType:Proteomics","pi":[{"name":"Ali Shilatifard","email":"ash@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058313","task":"f3810a08f1b344a997643890475a09f3","id":"1503"}, {"dataset":"MSV000096542","datasetNum":"96542","title":"Identification of proteins that interact with Atg8 WT\/L49A-Y50A in yeast","user":"chenyuting0218","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732686248000","created":"Nov. 26, 2024, 9:44 PM","description":"Identification of proteins that interact with Atg8 WT\/L49A-Y50A in yeast","fileCount":"17","fileSizeKB":"3431497","spectra":"0","psms":"8857","peptides":"2692","variants":"3272","proteins":"457","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Atg8 WT;Atg8 L49A-Y50A;bind;DatasetType:Proteomics","pi":[{"name":"Chen","email":"12018091@zju.edu.cn","institution":"Zhejiang University","country":"China"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058307","task":"a9bf0951261e48419b047bd1e0e92b34","id":"1504"}, {"dataset":"MSV000096541","datasetNum":"96541","title":"LC-MS\/MS data of specific proteins involved 4-HNE modification in bone formation","user":"JNU_816","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732686116000","created":"Nov. 26, 2024, 9:41 PM","description":"To elucidate the specific proteins involved in bone formation that are modified by 4-HNE, we performed LC-MS-based proteomics analysis. This approach identified several candidate proteins, including MAP kinase-activated protein kinase 3 (MAPK3), plastin-3 (PLS3), and integrin-linked protein kinase (ILK), all of which are implicated in bone formation or osteoblast differentiation. Notably, 4-HNE-modified ILK was significantly elevated in the GPX4-inhibited group (RSL3 treatment) compared to the control group. 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This study identifies phospholipid peroxidation in osteoblasts as a key feature of postmenopausal osteoporosis in mice. 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Our multi-omics data shows that the data is significantly different depending on the normalization methods and our optimized normalization method showed that there were significant multi-omics profile changes even with young mice tissue samples. 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The Evosep used a 60 sample-per-day method with a Pepsep 8 cm x 150 um column (1.5 um particle size) with a PepSep Sprayer and stainless steel (30 um) emitter. The MS analysis used a 240,000 resolution precursor ion (MS1) scan from 380-980 m\/z, AGC target of 500% and maximum injection time (IT) of 50 ms, collected every 0.6 s in centroid mode. MS\/MS was performed using a DIA method with default charge state = 3, precursor mass range of 380-980, 10 m\/z isolation windows, AGC target of 500% and maximum IT of 20 ms, and a NCE of 28. An RF lens of 40% was used for MS1 and DIA scans. Raw MS data was converted to .htrms format using HTRMS converter and processed in Spectronaut 19 (Biognosys). A spectral library was built using direct-DIA searches of all DIA analyses using a Cellvibrio japonicus database, downloaded from Uniprot on 10\/29\/2024 and appended contaminant sequences using FragPipeSearch settings included N-terminal trypsin\/P specificity up to 2 missed cleavages; peptide length from 7-52 amino acids with the following modifications: acetyl (N-term) and carbamidomethyl(Cys). 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Files are named as follows: SEE for eVLPs bearing EGFR, IR for eVLPs bearing Insulin Receptor, and TM for control VLPs containing epitope-tagged protein comprised of the EGFR transmembrane region fused to the EABR sequence. For each sample sequential injections are designated as a,b,c,d.","fileCount":"157","fileSizeKB":"77959361","spectra":"2295652","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"eVLPs, VLPs, eGFR, IR, ESCRT, Strep-Tag, Strep-Tactin, EABR, Expi293, RTKs;DatasetType:Proteomics","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3faee72f935b4d01be10aeac8ec19d92","id":"1520"}, {"dataset":"MSV000096514","datasetNum":"96514","title":"Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines","user":"trendsetter","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732549258000","created":"Nov. 25, 2024, 7:40 AM","description":"Translation is the process by which genetic information from mRNA is decoded to produce proteins. 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To address this, here we report steady-state and dynamic multi-omics data from human liver cancer cell lines, specifically i) ribosome profiling of unperturbed cells and following translation initiation block to trace elongation (run-off ribosome profiling), ii) protein synthesis rates estimated by pulsed stable isotope labeled amino acids in cell culture (pSILAC), and iii) mean ribosome load on individual mRNAs determined by mRNA sequencing of polysome fractions (polysome profiling). Predicting protein output from mRNAs is crucial for applications like protein expression engineering or mRNA vaccine designing.\n","fileCount":"50","fileSizeKB":"82885944","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"SWATH;DIA;pSILAC;mRNA;polysome profiling;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD058242","task":"50bed821b68f42f6b4ddd675cd6dc933","id":"1521"}, {"dataset":"MSV000096513","datasetNum":"96513","title":"PUP-IT proximity-labeling of LST8-1 and RAPTOR1 interactors (constitutive expression)","user":"leonardblaschek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732545432000","created":"Nov. 25, 2024, 6:37 AM","description":"PUP-IT proximity labeling of Arabidopsis Target of Rapamycin Complex (TORC) subunits LST8-1 and RAPTOR1, compared against a GFP control, with constitutively expressed FLAG::PUP(E). The sample metadata, sequence database and fragpipe workflow are uploaded under the 'Metadata' tag.","fileCount":"82","fileSizeKB":"44904535","spectra":"0","psms":"143328","peptides":"10524","variants":"12373","proteins":"2165","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"timsTOF Pro","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:1264 - \\\"Addition of GGE.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PUP-IT;Proximity labeling;Target of Rapamycin;TOR;DatasetType:Proteomics","pi":[{"name":"Staffan Persson","email":"staffan.persson@plen.ku.dk","institution":"Copenhagen University","country":"Denmmark"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD058231","task":"dd18aefccc134190b7721b76514a5625","id":"1522"}, {"dataset":"MSV000096512","datasetNum":"96512","title":"GNPS - BlueVOC: An in situ method to capture and characterise volatile metabolites emitted by benthic organisms","user":"Axel_Olander","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732499366000","created":"Nov. 24, 2024, 5:49 PM","description":"Biogenic volatile organic compounds sampled from Australian benthic primary producers in situ, using a novel incubation chamber design.","fileCount":"68","fileSizeKB":"25990393","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Montipora (NCBITaxon:46703);Cladiella (NCBITaxon:205093);Halimeda (NCBITaxon:118221);Avicennia marina (NCBITaxon:82927)","instrument":"Pegasus 4D;Pegasus BT","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Volatilomics;Marine;In situ sampling;Coral;Macroalgae;Mangrove;DatasetType:Other (Volatilomics)","pi":[{"name":"Axel Olander","email":"axel.olander@uts.edu.au","institution":"University of Technology Sydney","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a9324393fa8a466e9909ba1d40ca71f5","id":"1523"}, {"dataset":"MSV000096511","datasetNum":"96511","title":"GNPS - Ethyl acetate Fraction K. cistoidea","user":"Darrieche","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732461768000","created":"Nov. 24, 2024, 7:22 AM","description":"Bioactive Fraction against bacterial from ethanolic extract from K. cistoidea","fileCount":"3","fileSizeKB":"32272","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Krameria cistoidea (NCBITaxon:228635)","instrument":"compact","modification":"none","keywords":"Krameria, QTOF, Antimicrobial activity;DatasetType:Metabolomics","pi":[{"name":"Dioni Arrieche","email":"dioni.arrieche@usm.cl","institution":"Universidad Tecnica Federico Santa Maria","country":"chile"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"13841f2211bf49aba7171f615ec9c724","id":"1524"}, {"dataset":"MSV000096510","datasetNum":"96510","title":"GNPS - Chemodiverse collection of natural extracts derived from plants","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732366655000","created":"Nov. 23, 2024, 4:57 AM","description":"\r\nUHPLC-PDA-HRMSMS data in pos and neg modes for a collection of plants derived from the Pierre-Fabre laboratories collection","fileCount":"614","fileSizeKB":"24022280","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Natural Products;plant extracts;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7d21a76ebb93467d95ff0edb0f82f0c1","id":"1525"}, {"dataset":"MSV000096509","datasetNum":"96509","title":"LC-MS data of trypsin-digested human serum albumin treated with different concentrations of Dabrafenib followed by the addition of acetyl CoA.","user":"sheemonach","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732360942000","created":"Nov. 23, 2024, 3:22 AM","description":"To study the acetylation of human serum albumin (HSA) with acetyl CoA in the presence and absence of Dabrafenib, the LC-MS study was carried out. This is a part of ICMR, New Delhi, India, sanctioned project titled:- Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits. Project File No. 5\/4\/1-25\/2020-NCD-1. \nSample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated for 1 hour with different concentrations of Dabrafenib (prepared in DMSO) followed by incubation with 495 micromolar acetyl CoA (prepared in MilliQ water) in separate aliquots for 2 hours at 37 degree Celsius. Control albumin solution was added with appropriate DMSO and MilliQ water and incubated under similar conditions. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree Celsius. These were then subjected to trypsin digestion (2 microgram, Promega, MS grade, prepared in acetic acid) and kept overnight at 37 degree Celsius. The reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LC-MS grade). The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition.\nData Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. For digestion, trypsin\/P type was selected with all other parameters considered as default. The albumin sequence file (accession: P02768) was taken as a reference for understanding the analysis. The different raw files obtained are named as follows and uploaded.\nS1= HSA plus Dabrafenib 400 micromolar plus Acetyl CoA 495 micromolar\nS2= HSA plus Dabrafenib 200 micromolar plus Acetyl CoA 495 micromolar\nS3= HS plus Dabrafenib 50 micromolar plus Acetyl CoA 495 micromolar\nS4= HSA plus Acetyl CoA 495 micromolar\nS5= HSA only\n","fileCount":"16","fileSizeKB":"11212419","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Human Serum Albumin;Acetyl CoA;LC-MS;Trypsin digestion;Pseudoesterase;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8da25d82976f4a279968c198c228ee62","id":"1526"}, {"dataset":"MSV000096508","datasetNum":"96508","title":"Midbrain extracellular matrix and microglia are associated with cognition in aging mice","user":"adarshmayank","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732320268000","created":"Nov. 22, 2024, 4:04 PM","description":"The present study combines high resolution imaging, quantitative tissue proteomics, novel goal directed behaviors, and genetic inductions of microglial depletion and accelerated aging to link microglia, synapse, and ECM status across the mesolimbic dopamine system with cognitive aging outcomes.","fileCount":"144","fileSizeKB":"257460124","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cognitive decline;synapses;Extracellular Matrix Aging Microglia Basal Ganglia;DatasetType:Proteomics","pi":[{"name":"Lindsay De Biase","email":"lmdebiase@mednet.ucla.edu","institution":"UCLA","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD070000","task":"28832eaadc894fc2b2f4d4bb393b4326","id":"1527"}, {"dataset":"MSV000096507","datasetNum":"96507","title":"GNPS-RiPP DTT reduction infusion with Copper II","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732317945000","created":"Nov. 22, 2024, 3:25 PM","description":"Bulbicupramide RiPP metal infusion with Copper II. Preliminary metal infusion data","fileCount":"17","fileSizeKB":"637936","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"pseudomonas","instrument":"QExactive LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"copper II;metal infusion;DatasetType:Metabolomics","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f8dea9e2b2b8472caa3f8073e502baa1","id":"1528"}, {"dataset":"MSV000096506","datasetNum":"96506","title":"GNPS - Lipidomics Reveals Cell Specific Changes During Pluripotent Differentiation to Neural and Mesodermal Lineages","user":"hjostes","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732310381000","created":"Nov. 22, 2024, 1:19 PM","description":"Raw .d files containing LC-DTIMS-CID-MS for the analysis of lipidomic changes during stem cell differentiation into mesodermal and neural cell lineages.","fileCount":"3361","fileSizeKB":"115567675","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NCRM-5 Human iPSC","instrument":"6560 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics, stem cells, ion mobility;DatasetType:Metabolomics","pi":[{"name":"Erin S. Baker","email":"erinmsb@unc.edu","institution":"University of North Carolina at Chapel Hill","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"814dae3c14274ae1b5dea923d0f4f9eb","id":"1529"}, {"dataset":"MSV000096505","datasetNum":"96505","title":"GNPS Ruta graveolens extracts L. from differents methods mzML","user":"anabsss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732309875000","created":"Nov. 22, 2024, 1:11 PM","description":"Extracts of Ruta graveolens obtained from different methods of extraction.","fileCount":"10","fileSizeKB":"770379","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruta graveolens (NCBITaxon:37565)","instrument":"impact HD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"R.graveolens;extracts;DatasetType:Metabolomics","pi":[{"name":"Ana Souza","email":"beatriz.ana22@unifesp.br","institution":"UNIFESP","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4430cbdfac2249e3a71d77ff254ef043","id":"1530"}, {"dataset":"MSV000096504","datasetNum":"96504","title":"Nicholson_PhageResistance_timsTOFPro2_Lumos_P124","user":"LTRI_proteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732305462000","created":"Nov. 22, 2024, 11:57 AM","description":"Mass spectrometry was used to identify which proteins encoded on the LME-1 genome are present in the purified phage-like particle. The protein products of 12 LME-1 genes were identified in the virion, including all those with homology to phage structural genes.","fileCount":"97","fileSizeKB":"2709396","spectra":"0","psms":"2920","peptides":"529","variants":"751","proteins":"106","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Legionella pneumophila (NCBITaxon:446)","instrument":"timsTOF Pro 2;Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"phage-like particle;virion;LME-1;DatasetType:Proteomics","pi":[{"name":"Alexander Ensminger","email":"alex.ensminger@utoronto.ca","institution":"University of Toronto","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058182","task":"a6120c1bd71248d89b67ea22053a3466","id":"1531"}, {"dataset":"MSV000096502","datasetNum":"96502","title":"GNPS - 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\\\"Beta-methylthiolation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Outer membrane biogenesis;Bacteroidetes;BAM complex;lipoproteins;beta-barrels;DatasetType:Proteomics","pi":[{"name":"Bert van den Berg","email":"Bert.Van-Den-Berg@newcastle.ac.uk","institution":"Newcastle University","country":"UK"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD058163","task":"1b080318c1c2436d9a8350185c0f5691","id":"1533"}, {"dataset":"MSV000096497","datasetNum":"96497","title":"GNPS - Systematic identification of allosteric effectors in Escherichia coli metabolism ","user":"chgruber","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732267321000","created":"Nov. 22, 2024, 1:22 AM","description":"We developed a mass spectrometry-based screening method for higher throughput in vitro enzyme assays and quantified the effects of 79 metabolites on the activity of 20 central Escherichia coli enzymes.","fileCount":"32914","fileSizeKB":"322213102","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli K-12 (NCBITaxon:83333)","instrument":"6520A Quadrupole Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"enzyme assays;high-throughput mass spectrometry;allosteric regulation;protein-metabolite interactions;DatasetType:Metabolomics","pi":[{"name":"Prof. Dr. Uwe Sauer","email":"sauer@imsb.biol.ethz.ch","institution":"ETH Zurich","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c3e6749b617c40c3a91c691ffdc1cb18","id":"1534"}, {"dataset":"MSV000096496","datasetNum":"96496","title":"TEST1-LIPID PEROXIDATION clinical test","user":"JNU_816","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732262012000","created":"Nov. 21, 2024, 11:53 PM","description":"The level of oxidized lipids during mouse aging was detected to elucidate the biological mechanism of aging","fileCount":"2","fileSizeKB":"18709","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"Q-EXACTIVE","modification":"no","keywords":"lipid peroxidation, age, clinical test;DatasetType:Metabolomics","pi":[{"name":"Gonghaibiao","email":"haibiaojnu@163.com","institution":"Jinan university","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"09b944991393407c90ebdc2585914b34","id":"1535"}, {"dataset":"MSV000096495","datasetNum":"96495","title":"The juxtamembrane domain of StkP is phosphorylated and influences cell division in Streptococcus pneumoniae","user":"Adeline","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732261981000","created":"Nov. 21, 2024, 11:53 PM","description":"Membrane eukaryotic-like Ser\/Thr protein-kinases play a pivotal role in different aspects of bacterial physiology. In contrast to the diversity of their extracellular domains, their cytoplasmic catalytic domains are highly conserved. However, the function of a long juxtamembrane domain (JMD), which connects the catalytic domain to the transmembrane helix, remains elusive. In this study, we investigated the function of the JMD of the Ser\/Thr protein-kinase StkP in cell division of Streptococcus pneumoniae. We observed that the deletion of the JMD did not affect StkP kinase activity. However, it impaired the ability of StkP to phosphorylate its endogenous substrates, which resulted in significant cell morphogenesis defects. Furthermore, multiple threonine residues were identified as being phosphorylated in the JMD. To investigate the functional significance of these phosphorylation sites, we conducted an integrative analysis, combining structural biology, proteomics and bacterial cell imaging. Our results revealed that the phosphorylation of the JMD did not affect the phosphorylation of StkP substrates. However, we observed that it influenced the timing of StkP localization at the division septum and the dynamics of cell constriction. We further demonstrated that phosphorylation of the JMD facilitated the recruitment of several cell division proteins, suggesting that it is required for the assembly of the division machinery at the division septum. In conclusion, this study demonstrates that the function of the JMD of StkP is modulated by phosphorylation and critical for the cell division of S. pneumoniae. These observations may serve as a model for understanding the regulatory function of other bacterial Ser\/Thr protein-kinases.","fileCount":"40","fileSizeKB":"10455295","spectra":"0","psms":"231572","peptides":"11504","variants":"14989","proteins":"1179","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptococcus pneumoniae (NCBITaxon:1313)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"StkP, Streptococcus pneumoniae, membrane protein-kinase, bacterial cell division, protein phosphorylation, juxtamembrane domain;DatasetType:Proteomics","pi":[{"name":"Christophe Grangeasse","email":"c.grangeasse@ibcp.fr","institution":"MMSB-UMR5086-CNRS","country":"France"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"5002f20efc144508bbe44ba02f3af501","id":"1536"}, {"dataset":"MSV000096494","datasetNum":"96494","title":"GNPS Ruta graveolens extracts L. from differents methods","user":"anabsss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732246836000","created":"Nov. 21, 2024, 7:40 PM","description":"MS data files about differents methods of extraction of bioactive alkaloids from Ruta graveolens L.","fileCount":"10","fileSizeKB":"1349229","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruta graveolens (NCBITaxon:37565)","instrument":"impact HD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"extracts;R.graveolens;DatasetType:Metabolomics","pi":[{"name":"Ana Beatriz","email":"beatriz.ana22@unifesp.br","institution":"UNIFESP","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"407b3f24dfe24061a052abc6e2ef40e8","id":"1537"}, {"dataset":"MSV000096493","datasetNum":"96493","title":"Mitochondrial Calcium Signaling Regulates Branched-Chain Amino Acid Catabolism in Fibrolamellar Carcinoma","user":"shaoen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732227581000","created":"Nov. 21, 2024, 2:19 PM","description":"Metabolic adaptations in response to changes in energy supply and demand are essential for survival. The mitochondrial calcium uniporter plays a key role in coordinating metabolic homeostasis by regulating TCA cycle activation, mitochondrial fatty acid oxidation and cellular calcium signaling. However, a comprehensive analysis of uniporter-regulated mitochondrial metabolic pathways has remained unexplored. Here, we investigate metabolic consequences of uniporter loss- and gain-of-function using uniporter knock out cells and the liver cancer fibrolamellar carcinoma (FLC), which we demonstrate to have elevated mitochondrial calcium levels. Our results reveal that branched chain amino acid (BCAA) catabolism and the urea cycle are uniporter-regulated metabolic pathways. Reduced uniproter function increases expression of BCAA catabolism genes, and the urea cycle enzyme ornithine transcarbamylase (OTC). In contrast, high uniporter activity in FLC suppresses their expression. This suppression happens via the transcription factor KLF15, a master regulator of liver metabolism, suggesting that calcium signaling plays a central role in FLC-associated metabolic changes, including hyperammonemia. Consistent with this, activation of BCAA catabolism in FLC cells impairs their growth. Collectively, our study identifies an important role for mitochondrial calcium signaling in metabolic adaptation through transcriptional regulation of metabolism and elucidates its importance for BCAA and ammonia metabolism in FLC.","fileCount":"15","fileSizeKB":"7470857","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MCU;DatasetType:Proteomics","pi":[{"name":"Yasemin Sancak","email":"sancak@uw.edu","institution":"University of Washington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058152","task":"aabcf44e5fa74dd8a808aeef79db85c8","id":"1538"}, {"dataset":"MSV000096492","datasetNum":"96492","title":"Mechanosensor-mediated Hsp70 phosphorylation orchestrates the landscape of the heat shock response","user":"Fornelli_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732226024000","created":"Nov. 21, 2024, 1:53 PM","description":"Yeast must respond rapidly to heat stress by activating multiple signaling pathways that preserve proteostasis. This includes induction of Hsf1 and Msn2\/4-mediated transcription, cell integrity signaling, stress-triggered phase separation of proteins and inhibition of translation. How these pathways are so rapidly activated and co-ordinated remains unclear. We show that the mechanosensor Mid2 senses heat-induced membrane stretch and leads to rapid phosphorylation of the cytosolic Hsp70 Ssa1 at a well-conserved threonine (T492). Phosphorylation of T492 leads to epichaperome rearrangement which includes altered interaction with Hsf1, multiple ribosomal subunits, the Bck1 MEK, and Edc3. Taken together these results provide a comprehensive, unified theory of the global yeast shock response that is mediated by the Hsp70 chaperone code.","fileCount":"40","fileSizeKB":"6423958","spectra":"0","psms":"38700","peptides":"2921","variants":"3552","proteins":"646","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"heat shock response;yeast;Hsp70;DatasetType:Proteomics","pi":[{"name":"Luca Fornelli","email":"luca.fornelli@ou.edu","institution":"University of Oklahoma","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058151","task":"b8f4fae46454459eb5fc54657827b25b","id":"1539"}, {"dataset":"MSV000096491","datasetNum":"96491","title":"GNPS - Project Rad Alder Metabolomes","user":"helenamrusso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732225565000","created":"Nov. 21, 2024, 1:46 PM","description":"A reciprocal transplant experiment using leaf packs composed of 10 red alder genotypes with resident presence and absence (gamma-irradiated [25 kGy]) to directly test how leaf-associated residents affect aquatic decomposer community composition and functional assembly, and metabolomic profiles over time. Samples were run in a Kinetex Polar C18 (2.6 um, 50 x 2.1 mm) in both positive and negative ionization modes.","fileCount":"3421","fileSizeKB":"149306817","spectra":"2103633","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alnus rubra (NCBITaxon:109069);Celtis occidentalis (NCBITaxon:228587)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plant;decomposer community;DatasetType:Metabolomics","pi":[{"name":"Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"},{"name":"Sara Jackrel","email":"sjackrel@ucsd.edu","institution":"University of California San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"296e062a1d0f4efe831f436cf38e8bb7","id":"1540"}, {"dataset":"MSV000096490","datasetNum":"96490","title":"CFTR in Vivo Conformation review","user":"pankows","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732218635000","created":"Nov. 21, 2024, 11:50 AM","description":"CPP data for CFTR and CFTR interactome in patient cells expressing different CFTR variants.","fileCount":"998","fileSizeKB":"204027519","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens","instrument":"timsTOF Pro;LTQ Orbitrap Elite","modification":"dimethyl, methionine oxidation, phosphorylation[S,T,Y]","keywords":"in vivo structure, covalent protein painting, foot printing;DatasetType:Proteomics","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fb68e222d14242c48bd0e28267d9d4b8","id":"1541"}, {"dataset":"MSV000096489","datasetNum":"96489","title":"Microtubule doublets from T. vaginalis","user":"awsteven","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732215750000","created":"Nov. 21, 2024, 11:02 AM","description":"microtubule doublets isolated from locomotive flagella of T. vaginalis","fileCount":"20","fileSizeKB":"1968698","spectra":"46494","psms":"9108","peptides":"4550","variants":"5357","proteins":"925","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichomonas vaginalis G3 (NCBITaxon:412133)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"trichomonas vaginalis;microtubule;DatasetType:Proteomics","pi":[{"name":"hong zhou","email":"hong.zhou@ucla.edu","institution":"UCLA","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058149","task":"cf01a62743924056bc0c3e0993b3ed6b","id":"1542"}, {"dataset":"MSV000096487","datasetNum":"96487","title":"Asymmetric Engagement of Dimeric CRL3KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1\/2 Complexes","user":"hbc8","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732212304000","created":"Nov. 21, 2024, 10:05 AM","description":"UM171 is a potent small molecule agonist of ex vivo human hematopoietic stem cell \n(HSC) self-renewal, a process that is tightly controlled by epigenetic regulation. By co\nopting KBTBD4, a substrate receptor of the CULLIN3-RING E3 ubiquitin ligase complex, \nUM171 promotes the degradation of members of the CoREST transcriptional \ncorepressor complex, thereby limiting HSC attrition. However, the direct target and \nmechanism of action of UM171 remain unclear. Here, we reveal that UM171 acts as a \nmolecular glue to induce high-affinity interactions between KBTBD4 and HDAC1\/2 to \npromote the degradation of select corepressor complexes. Through proteomics and \nchemical inhibitor studies, we discover that the principal target of UM171 is HDAC1\/2. \nCryo-electron microscopy (cryo-EM) analysis of dimeric KBTBD4 bound to UM171 and \nthe LSD1-HDAC1-CoREST complex unveils an unexpected asymmetric assembly, in \nwhich a single UM171 molecule enables a pair of KELCH-repeat propeller domains \nfrom the structurally plastic KBTBD4 dimer to recruit HDAC1 by clamping on its catalytic \ndomain. One of the KBTBD4 propellers partially masks the rim of the HDAC1 active site \npocket, which is exploited by UM171 to extend the E3-neo-substrate interface. The \nother propeller cooperatively strengthens HDAC1 binding via a separate and distinct \ninterface. The overall neomorphic interaction is further buttressed by an endogenous \ncofactor of HDAC1-CoREST, inositol hexakisphosphate, which makes direct contacts \nwith KBTBD4 and acts as a second molecular glue. The functional relevance of the \nquaternary complex interaction surfaces defined by cryo-EM is demonstrated by in situ \nbase editor scanning of KBTBD4 and HDAC1. By delineating the direct target of UM171 \nand its mechanism of action, our results reveal how the cooperativity offered by a large \ndimeric CRL E3 family can be leveraged by a small molecule degrader and establish for \nthe first time a dual molecular glue paradigm.","fileCount":"14","fileSizeKB":"18937044","spectra":"0","psms":"100917","peptides":"40201","variants":"58449","proteins":"7349","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo Sapiens","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"UM171;DatasetType:Proteomics","pi":[{"name":"Liron Bar-Peled","email":"lbar-peled@mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD058144","task":"1a6612020d934d83a8e7663db11cad80","id":"1543"}, {"dataset":"MSV000096481","datasetNum":"96481","title":"LC-MS data of trypsin-digested human serum albumin treated with different concentrations of nateglinide followed by the addition of acetyl CoA","user":"deepakk1812","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732178489000","created":"Nov. 21, 2024, 12:41 AM","description":"To study the acetylation of human serum albumin (HSA) with acetyl CoA in the presence and absence of Nateglinide, the LC-MS study was carried out. This is a part of ICMR, New Delhi, India, sanctioned project titled Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits. \n\nSample processing protocol: For this, 1 ml of 1 mg\/ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated for 1 hour with different concentrations of Nateglinide (prepared in DMSO) followed by incubation with 495 micromolar acetyl CoA (prepared in MilliQ water) in separate aliquots for 2 hours at 37 degree Celcius. Control albumin solution was added with appropriate DMSO and MilliQ water and incubated under similar conditions. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 dgree celsius. These were then subjected to trypsin digestion (2 microgram, Promega, MS grade, prepared in acetic acid) and kept overnight at 37 degree celsius. The reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LC-MS grade). The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition.\nData Processing protocol: The MaxQuant software (2.0.3.1) was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession P02768) was taken as a reference for understanding the analysis. For digestion, trypsin\/P type was selected with all other parameters considered as default. The different raw files obtained are named as follows and uploaded.\nS1 HSA plus Nateglinide 400 micromolar plus Acetyl CoA 495 micromolar\nS2 HSA plus Nateglinide 200 micromolar plus Acetyl CoA 495 micromolar\nS3 HS plus Nateglinide 50 micromolar plus Acetyl CoA 495 micromolar\nS4 HSA plus Acetyl CoA 495 micromolar\nS5 HSA only","fileCount":"21","fileSizeKB":"19191448","spectra":"276243","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Human Serum Albumin, Acetyl CoA, LC-MS, Trypsin digestion;Pseudoesterase, Nateglinide;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4f397e54bbc44b1b8702f1d0f29ba216","id":"1544"}, {"dataset":"MSV000096480","datasetNum":"96480","title":"GNPS - Sex-specific fear acquisition following early life stress is linked to amygdala and hippocampal purine and glutamate metabolism","user":"kkleigrewe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732175704000","created":"Nov. 20, 2024, 11:55 PM","description":"Early life stress (ELS) can negatively impact health, increasing the risk of stress-related disorders, such as post-traumatic stress disorder (PTSD). Importantly, PTSD disproportionately affects women, emphasizing the critical need to explore how sex differences influence the genetic and metabolic neurobiological pathways underlying trauma-related behaviors. This study uses the limited bedding and nesting (LBN) paradigm to model ELS and investigate its sex-specific effects on fear memory formation. Employing innovative unsupervised behavioral classification, the current study reveals distinct behavioral patterns associated with fear acquisition and retrieval in male and female mice following ELS. Females exposed to LBN display heightened active fear responses, contrasting with males. Furthermore, the study examined the crucial link between behavioral regulation and cellular metabolism in key brain regions involved in fear and stress processing. Sex-specific and stress-dependent alterations were observed in purine, pyrimidine, and glutamate metabolism within the basolateral amygdala, the dorsal hippocampus, and the ventral hippocampus. These findings provide crucial insights into the complex interplay between metabolic pathways, the neurobiological underpinnings of fear memory, and stress responses. Importantly, they emphasize the significance of considering sex-specific metabolic alterations when investigating stress-related disorders, opening potential avenues for the development of targeted interventions.","fileCount":"280","fileSizeKB":"20946584","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"TripleTOF 6600","modification":"Metabolomics","keywords":"early life stress;PTSD;amygdala glutamate metabolism;DatasetType:Metabolomics","pi":[{"name":"PD Dr. Mathias V. Schmidt","email":"mschmidt@psych.mpg.de","institution":"Max Planck Institute of Psychiatry","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"57a08451a4e64ebfaab6459099dd3636","id":"1545"}, {"dataset":"MSV000096479","datasetNum":"96479","title":"Iron-starvation induces photosystem I antenna remodeling in green algae","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732159979000","created":"Nov. 20, 2024, 7:32 PM","description":"Dunaliella salina and Dunaliella tertiolecta are extremophile, marine algae that can survive in very low Fe conditions. In this study, we used TMT-proteomics to compare the Fe starvation responses to the Fe replete responses. Samples were digested with trypsin, labeled with TMT 10-Plex, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.","fileCount":"176","fileSizeKB":"69947418","spectra":"1144904","psms":"1196047","peptides":"674715","variants":"766716","proteins":"75008","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Dunaliella cf. bardawil CHPD1 (NCBITaxon:1227098);Dunaliella tertiolecta (NCBITaxon:3047)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"algae;Chlorophyceae;iron homeostasis;metal deficiency;metal nutrition;photosynthesis;structural biology;DatasetType:Proteomics","pi":[{"name":"Sabeeha Merchant","email":"sabeeha@berkeley.edu","institution":"California Institute for Quantitative Biosciences, University of California, Berkeley","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD058109","task":"88964b9306fd49b39f004454658a3cde","id":"1546"}, {"dataset":"MSV000096477","datasetNum":"96477","title":"The lysosomal lipid transporter LIMP-2 forms lysosome-endoplasmic reticulum STARD3-VapB-dependent contact sites","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732157626000","created":"Nov. 20, 2024, 6:53 PM","description":"Flp-In 293 T-REx cells (Thermo Fisher Scientific) stably expressing FlagBirA alone or FlagBirA-LIMP-2 were generated. After selection , cells were incubated for 24 hours in complete media supplemented with tetracycline (Sigma) and biotin (BioShop). Cells were collected and pelleted, the pellets were washed twice with PBS and snap frozen. Cells were resuspended in 10 ml of modified RIPA lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% SDS, 1:500 protease inhibitor cocktail (Sigma-Aldrich), 1:1,000 benzonase nuclease (Novagen), incubated on an end-over-end rotator , sonicated then centrifuged. Supernatants were transferred to a fresh 15 ml conical tube. Streptavidin-sepharose beads (GE) were added and the mixture incubated. Beads were pelleted by centrifugation at 2,000 rpm for 2 minutes and transferred with 1 ml of lysis buffer to a fresh Eppendorf tube. Beads were washed once with 1 mL lysis buffer and twice with 1 ml of 50 mM ammonium bicarbonate (pH =8.3). Beads were transferred in ammonium bicarbonate to a fresh centrifuge tube and washed two more times with 1 ml ammonium bicarbonate buffer. Tryptic digestion was performed by incubating the beads with MS-grade TPCK trypsin (Promega, Madison, WI) dissolved ammonium bicarbonate (pH 8.3). The following morning, additional MS-grade TPCK trypsin was added, and beads were incubated 2 additional hours. Beads were pelleted by centrifugation at 2,000 x g for 2 min, and the supernatant was transferred to a fresh Eppendorf tube. Beads were washed twice with 50 mM ammonium bicarbonate, and these washes were pooled with the first eluate. The sample was lyophilized and resuspended in buffer A (0.1% formic acid). 1\/5th of the sample was analyzed per MS run.\n\nResuspended peptides were subjected to high performance liquid chromatography (HPLC) performed on pre-columns (150mm I.D.) and analytical columns (75mm I.D.) assembled in-house using fused silica capillary tubing (InnovaQuartz, Phoenix, AZ) packed with C18 (Magic, Michrom Bioresources, Auburn, CA). A 120min reversed-phase LC gradient (0-100% organic, 0.1% HCOOH) running at 250 nl\/min on a Proxeon EASY-nLC pump was applied in-line with a hybrid LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Waltham, MA). A parent ion scan was performed in the Orbitrap at 60,000 resolution (fwhm), with up to the 20 most intense precursors selected for MS\/MS (minimum ion count of 1000 for activation), using standard collision-induced dissociation (CDI) fragmentation. Dynamic exclusion was activated such that MS\/MS of the same m\/z (within a range of 15 ppm; exclusion list size = 500) detected twice within 15 seconds were excluded from analysis for 30 sec. For protein identification, Thermo .RAW files were converted to the .mzXML format using Proteowizard (PMID 24939128), then searched using X!Tandem (PMID 14976030) against the human database (Human RefSeq Version 45), using a parent ion mass tolerance error of 15ppm and fragment ion mass of 0.4 Da. Oxidation (M), acetylation (protein N-terminus) and deamidation (N, Q) were included as potential modifications. Each biological replicate was analyzed using two technical replicates. Data were analyzed using the trans-proteomic pipeline PMID 16729052) via the ProHits software suite (PMID 20944583). Proteins identified with a Protein Prophet cut-off of 0.9 were analyzed with the SAINT (PMID 21131968) algorithm using 14 Flag-BirA only samples as negative controls. High confidence interactors were defined as those with a SAINT score over 0.8 (bayesian false discovery rate (BFDR) lower than 0.01).","fileCount":"26","fileSizeKB":"3640106","spectra":"52911","psms":"64822","peptides":"9548","variants":"10870","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Velos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Flp-In HEK293, BioID, BirA, biotin, streptavidin, LIMP2, LC-MS, SAINT;DatasetType:Proteomics","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058107","task":"3e4c4c30167441988e242c9cfada9e45","id":"1547"}, {"dataset":"MSV000096476","datasetNum":"96476","title":"GNPS - Plasma CHARTER Biopsychosocial Phenotypes (BPSP) R01_2024","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732143491000","created":"Nov. 20, 2024, 2:58 PM","description":"600 Samples of plasma from HNRC for CHARTER Biopsychosocial Phenotypes (BPSP) R01 project. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"2513","fileSizeKB":"151760127","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plasma;BSPS;DatasetType:Metabolomics","pi":[{"name":"Robert K. Heaton","email":"rheaton@ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"999b80c5250442278aad5b16106cf481","id":"1548"}, {"dataset":"MSV000096475","datasetNum":"96475","title":"Chlamydomonas reinhardtii responses to Fe-excess, Fe-deficiency, and Fe-limitation in either photoautotrophic or mixotrophic growth","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732141302000","created":"Nov. 20, 2024, 2:21 PM","description":"A systems level analysis of Chlamydomonas reinhardtii grown photoautotrophically or mixotrophically with a reduced carbon source, acetate, under four different defined Fe stages of Fe-replete, Fe-deficient, Fe-limited, or Fe-excess. Samples were digested with trypsin, labeled with TMT 10-Plex, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.","fileCount":"439","fileSizeKB":"244753889","spectra":"0","psms":"4038307","peptides":"1689451","variants":"2022405","proteins":"65288","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chlamydomonas reinhardtii (NCBITaxon:3055)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"algae;Chlorophyceae;iron homeostasis;metal deficiency;metal nutrition;photosynthesis;acetate;DatasetType:Proteomics","pi":[{"name":"Sabeeha Merchant","email":"sabeeha@berkeley.edu","institution":"California Institute for Quantitative Biosciences, University of California, Berkeley","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD058104","task":"6ba45a96a1784bf89d794b04b9c6e5dc","id":"1549"}, {"dataset":"MSV000096474","datasetNum":"96474","title":"GNPS - Integrating Metagenomics and Metabolomics to Study the Gut Microbiome and Host Relationships in Sports Across Different Energy Systems","user":"lleonc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732138986000","created":"Nov. 20, 2024, 1:43 PM","description":"This study explores the role of the gut microbiome in modulating host metabolism among Colombian athletes, comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis using bioBakery tools identified significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation (Figure 1). Key metabolic pathways were enriched in both athlete groups, such as phenylalanine, tyrosine, and tryptophan biosynthesis, arginine biosynthesis, and folate biosynthesis. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between gut microbiota composition and metabolic responses tailored to athletic demands, laying groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.","fileCount":"119","fileSizeKB":"7787406","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6545 Q-TOF LC\\\/MS","modification":"na","keywords":"Microbiote;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Viviana Aya","email":"Jeimmy.aya@urosario.edu.co","institution":"Universidad del Rosario","country":"Colombia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"10489d5233b74268a4be7ae3c366d098","id":"1550"}, {"dataset":"MSV000096473","datasetNum":"96473","title":"GNPS - Liver-specific deletion of Agpat5 protects against liquid sucrose induced hyperinsulinemia and glucose intolerance","user":"Simcox_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732133372000","created":"Nov. 20, 2024, 12:09 PM","description":"Untargeted lipidomics of liver samples, both in positive and negative mode","fileCount":"40","fileSizeKB":"10171608","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Agilent 6546 Q-TOF MS dual AJS ESI mass spectrometer","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Agpat5;hyperinsulinemia;liver;lipidomics;glucose intolerance;DatasetType:Metabolomics","pi":[{"name":"Judith Simcox","email":"jsimcox@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6dc88caa8a764292b28184b5f48c7d67","id":"1551"}, {"dataset":"MSV000096472","datasetNum":"96472","title":"Intact Proteoforms from 10,000 Single Brain Cells ","user":"mikehollas123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732122921000","created":"Nov. 20, 2024, 9:15 AM","description":"We perform intact proteoform profiling of 10809 endogenous single cells from the rat hippocampus using single-cell Proteoform imaging Mass Spectrometry (scPiMS). scPiMS directly extracts whole proteins and demonstrates high throughput for mass spectrometry-based single cell proteomics compared to existing approaches. We develop an informatics workflow dedicated to this datatype and use it to assign neurons, astrocytes or microglia cell types according to their proteoform signatures.","fileCount":"33","fileSizeKB":"39286510","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Q Exactive Plus","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"single cell;hippocampus;neuron;astrocytes;cell markers;DatasetType:Proteomics","pi":[{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1414496353314110b391a9356119ad5d","id":"1552"}, {"dataset":"MSV000096471","datasetNum":"96471","title":"GNPS - Eelgrass rhizosphere exometabolites Exp1 LC-MS2 NEG","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732060034000","created":"Nov. 19, 2024, 3:47 PM","description":"This project was conducted in collaboration with the Stachowicz and Dorrestein labs exploring the effects of eelgrass genotypic diversity on rhizosphere exometabolome production under marine heat wave versus ambient conditions. This data was collected from cultures of eelgrass genotypes grown in various levels of poly or monoculture under marine heat wave or ambient conditions in mesocosm. After simulating a 15 week marine heat wave regime, we sampled for each culture type-treatment combination\u2019s rhizosphere metabolome and used non-targeted LC-MS\/MS to examine how root exudates at the culture-level interact with genotypic diversity and temperature stress in a marine habitat forming species. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"359","fileSizeKB":"11514832","spectra":"284218","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Zostera marina (NCBITaxon:29655)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Eelgrass;Rhizosphere;Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Jay Stachowicz","email":"jjstachowicz@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f8a981432c414897a77c07039b3dc9cf","id":"1553"}, {"dataset":"MSV000096470","datasetNum":"96470","title":"GNPS - Eelgrass rhizosphere exometabolites Exp1 LC-MS2 POS","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732059621000","created":"Nov. 19, 2024, 3:40 PM","description":"This project was conducted in collaboration with the Stachowicz and Dorrestein labs exploring the effects of eelgrass genotypic diversity on rhizosphere exometabolome production under marine heat wave versus ambient conditions. This data was collected from cultures of eelgrass genotypes grown in various levels of poly or monoculture under marine heat wave or ambient conditions in mesocosm. After simulating a 15 week marine heat wave regime, we sampled for each culture type-treatment combination\u2019s rhizosphere metabolome and used non-targeted LC-MS\/MS to examine how root exudates at the culture-level interact with genotypic diversity and temperature stress in a marine habitat forming species. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"270","fileSizeKB":"9723219","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Zostera marina (NCBITaxon:29655)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Eelgrass;Rhizosphere;Metabolomics;MSCollaboratory;DatasetType:Metabolomics","pi":[{"name":"Jay Stachowicz","email":"jjstachowicz@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e6adff180a794fac8ae6b61b5cfa6c70","id":"1554"}, {"dataset":"MSV000096467","datasetNum":"96467","title":"LC-MS data of trypsin-digested human serum albumin with and without acetyl coA.","user":"deepakk1812","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732037937000","created":"Nov. 19, 2024, 9:38 AM","description":"To study the acetylation of human serum albumin (HSA) with acetyl coA, the LC-MS study was carried out. This is a part of ICMR, New Delhi, India, sanctioned project titled Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits. \n\nSample processing protocol\nFor this 1 ml of 1 mg per ml solution of fatty acid free human albumin (SIGMA) in 10 mM Tris HCl buffer, pH 7.38 was incubated with 495, 20, and 8.04 micromolar of acetyl-CoA (prepared in MilliQ water) in separate aliquots for 2 hours at 37 degree C. Control albumin solution was added with MilliQ water and incubated under similar conditions. 100 microlitre of each aliquot was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degree C. These were then subjected to trypsin digestion (2 microgram, Promega, MS grade, prepared in acetic acid) and kept overnight at 37 degree C. The reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LCMS grade). The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition.\nData Processing protocol\nThe MaxQuant software was used for the analysis of data. Under group-specific parameters acetyl K, acetyl (N-term), and (acetyl protein N-term) were selected as variable modifications whereas the Carbamidomethyl (C) was considered a fixed modification. The label-free quantification was done and the albumin sequence file (accession P02768) was taken as a reference for understanding the analysis. For digestion, trypsin\/P type was selected with all other parameters considered as default. The different raw files obtained are named as follows and uploaded.\nS1= HSA only\nS2= HSA + AcetylCoA (495 micromolar)\nS3= HAS+ AcetylCoA (20 micromolar)\nS4= HSA + AcetylCoA (8.04 micromolar)","fileCount":"13","fileSizeKB":"7724897","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Human Serum Albumin, Acetyl CoA, LC-MS, Trypsin digestion;Pseudoesterase;DatasetType:Proteomics","pi":[{"name":"Dibyajyoti Banerjee","email":"dibyajyoti5200@yahoo.co.in","institution":"Postgraduate Institute of Medical Education and Research, Chandigarh, India","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"22201afc4f154bc382a64c1421f4c2c1","id":"1555"}, {"dataset":"MSV000096466","datasetNum":"96466","title":"TEMI: Tissue Expansion Mass Spectrometry Imaging ","user":"LangDing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732032826000","created":"Nov. 19, 2024, 8:13 AM","description":"LC-MS, lipidomics, metabolomics, proteomics, expansion, MSI","fileCount":"33","fileSizeKB":"10900859","spectra":"470471","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos;Orbitrap Ascend","modification":"NA","keywords":"LC-MS, lipidomics, metabolomics, proteomics, expansion, MSI;DatasetType:Proteomics;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Meng Wang","email":"mengwang@janelia.hhmi.org","institution":"HHMI Janelia Research Campus","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5edf8b85382b4c4bb84b56a40c012d48","id":"1556"}, {"dataset":"MSV000096465","datasetNum":"96465","title":"GNPS - msiFlow: Automated Workflows for Reproducible and Scalable Multimodal Mass Spectrometry Imaging and Microscopy Analysis","user":"Kasarla04","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732013755000","created":"Nov. 19, 2024, 2:55 AM","description":"Multimodal imaging by matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI MSI) and microscopy holds potential for understanding pathological mechanisms by mapping molecular signatures from the tissue micro environment to specific cell populations. However, existing software solutions for MALDI MSI data analysis are incomplete, require programming skills and contain laborious manual steps, hindering broadly applicable, reproducible, and high throughput analysis to generate impactful biological discoveries. Here we present msiFlow, an accessible open-source, platform-independent and vendor-neutral software for end-to-end, high-throughput, transparent and reproducible analysis of multi modal imaging data. msiFlow integrates all necessary steps from raw data import to analysis visualization along with state-of-the-art and newly developed algorithms into automated workflows. Using msiFlow, we unravel the molecular heterogeneity of leukocytes in infected tissues by spatial regulation of ether-linked phospholipids containing arachidonic acid. We anticipate that msiFlow will facilitate the broad applicability of MSI in multi modal imaging to uncover context-dependent cellular regulations in disease states.","fileCount":"25","fileSizeKB":"4040853","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"No","keywords":"Lipidomics, LC-MS\/MS;DatasetType:Other (Lipidomics)","pi":[{"name":"Dr. Prasad Phapale","email":"prasad.phapale@isas.de","institution":"Leibniz-Institut f\uFFFDr Analytische Wissenschaften-ISAS-e.V.","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"68e4ad310c8d4311903054dd2db7ebf6","id":"1557"}, {"dataset":"MSV000096464","datasetNum":"96464","title":"Gnps stage 1 molecular network training","user":"lyla","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1732001883000","created":"Nov. 18, 2024, 11:38 PM","description":"analyze the lc-ms raw data with molecular networking using gnps ","fileCount":"4","fileSizeKB":"193131","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"camellia sinensis","instrument":"lc-ms","modification":"ms","keywords":"classical molecular networking;DatasetType:Metabolomics","pi":[{"name":"ling","email":"13846159148@163.com","institution":"AAU","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da4083d1ee5843709fb017e6df64594e","id":"1558"}, {"dataset":"MSV000096463","datasetNum":"96463","title":"MS3 Spectra of AF-AcF Mutants Conjugated with p-TMBOA","user":"Yeon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731998568000","created":"Nov. 18, 2024, 10:42 PM","description":"Unnatural amino acids(AcF) were incorporated into the Affibody(AF) protein at six specific sites (F5, L9, L19, K28, D36, and L44) and conjugated with the radical initiator p-TMBOA via oxime ligation. The MS3 spectra of AF-F5AcF, AF-L9AcF, AF-L19AcF, AF-K28AcF, AF-D36AcF, and AF-L44AcF were obtained at charge states +5, +6, +7, and +8.","fileCount":"24","fileSizeKB":"46584","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"LTQ Orbitrap XL","modification":"0000398: No post-translational-modifications are included","keywords":"free radical initiated peptide sequencing (FRIPS), generic code expansion technology (GCE), radical-directed fragmentation, TEMPO, unnatural amino acid;DatasetType:Proteomics","pi":[{"name":"Han Bin Oh","email":"hanbinoh@sogang.ac.kr","institution":"Sogang University","country":"Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"85aaf2bda1db49c2b0311208f6dc2956","id":"1559"}, {"dataset":"MSV000096461","datasetNum":"96461","title":"GNPS - Rattlesnakes Venom Bacterial Cultures ","user":"kambriah246","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731973124000","created":"Nov. 18, 2024, 3:38 PM","description":"Positive Mode, Non-targeted analysis of bacterial isolates from rattlesnake venom ","fileCount":"55","fileSizeKB":"4432268","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crotalus atrox (NCBITaxon:8730)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Venom;microbiome;rattlesnake;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California, Riverside","country":"United States of American"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f0d189b8ab234bf2a553c05066507198","id":"1560"}, {"dataset":"MSV000096460","datasetNum":"96460","title":"GNPS - Sourdough Culture and Crude Non-targeted Analysis ","user":"kambriah246","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731970132000","created":"Nov. 18, 2024, 2:48 PM","description":"Positive Mode. Non-targeted analysis of sourdough crude extract and isolated bacterial cultures. ","fileCount":"271","fileSizeKB":"23750968","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lactobacillus (NCBITaxon:1578)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sourdough;LB;M9;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California, Riverside","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"88229e4acf7d45ce902157a9d3d98bdc","id":"1561"}, {"dataset":"MSV000096459","datasetNum":"96459","title":"TYMS expression regulates AMPK-mTOR signaling in pancreatic neuroendocrine tumors","user":"jinkoh","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731967635000","created":"Nov. 18, 2024, 2:07 PM","description":"AMPK serves as a regulator of metabolic homeostasis to conserve energy in tumor cells by inhibiting ATP-anabolic processes and promoting ATP-generating pathways. When activated, AMPK reprograms cellular metabolism and imposes growth checkpoints, particularly through inhibition of the mTOR signaling pathway. Since mTOR is activated in a subset of PanNET patients, the AMPK-mTOR signaling axis is a crucial target to evaluate the risk for chemotherapy drugs resistance and overall prognosis in these patients. \nWe now report that elevated TYMS levels downregulates AMPK signaling and activates mTOR signaling in PanNET tumor cells. These data suggest a new role for TYMS inhibition to modulate the AMPK-mTOR signaling axis and impact the efficacy of current mTOR inhibitory agents in the management of patients with advanced PanNET.\n","fileCount":"106","fileSizeKB":"17156912","spectra":"0","psms":"109775","peptides":"31954","variants":"47889","proteins":"8705","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion ETD","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"TYMS, AMPK-mTOR signaling, pancreatic neuroendocrine tumors, TMT;DatasetType:Proteomics","pi":[{"name":"Maria Zajac-Kaye ","email":"mzajackaye@ufl.edu","institution":"University of Florida ","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD058010","task":"ea02b48a99c143a0b53204533852eac7","id":"1562"}, {"dataset":"MSV000096457","datasetNum":"96457","title":"Effects of methionine supplementation on seminal plasma miRNAs and proteome in sheep","user":"naproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731964300000","created":"Nov. 18, 2024, 1:11 PM","description":"These studies provide information demonstrating that SP components can be altered by paternal diet, however, knowledge is greatly lacking in livestock species regarding the effects of specific dietary changes that may impact production and reproduction traits. To our knowledge, this is the first study to evaluate the effects of dietary methionine on SP composition, specifically miRNAs and proteins. ","fileCount":"38","fileSizeKB":"3641146","spectra":"0","psms":"73331","peptides":"4114","variants":"5005","proteins":"829","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ovis aries (NCBITaxon:9940)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Seminal plasma, methionine, proteome, miRNAs;DatasetType:Proteomics","pi":[{"name":"Nagib Ahsan","email":"nahsan@ou.edu","institution":"University of Oklahoma","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"ac85d8033b234f718d7374c068677294","id":"1563"}, {"dataset":"MSV000096456","datasetNum":"96456","title":"Asymmetric Engagement of Dimeric CRL3\/KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1\/2 Complexes","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731963962000","created":"Nov. 18, 2024, 1:06 PM","description":"UM171 is a potent agonist of ex vivo human hematopoietic stem cell (HSC) self-renewal1. By co-opting KBTBD4, a substrate receptor of the CULLIN3-RING E3 ubiquitin ligase (CRL3) complex, UM171 promotes the degradation of the LSD1-CoREST corepressor complex, thereby limiting HSC attrition2,3. However, the direct target and mechanism of action of UM171 remain unclear. Here, we reveal that UM171 acts as a molecular glue to induce high-affinity interactions between KBTBD4 and HDAC1\/2 to promote corepressor degradation. Through proteomics and chemical inhibitor studies, we discover that the principal target of UM171 is HDAC1\/2. Cryo-electron microscopy analysis of dimeric KBTBD4 bound to UM171 and the LSD1-HDAC1-CoREST complex unveils an asymmetric assembly, in which a single UM171 molecule enables a pair of KELCH-repeat propeller domains to recruit the HDAC1 catalytic domain. One KBTBD4 propeller partially masks the rim of the HDAC1 active site, which is exploited by UM171 to extend the E3-neo-substrate interface. The other propeller cooperatively strengthens HDAC1 binding via a distinct interface. The overall CoREST-HDAC1\/2-KBTBD4 interaction is further buttressed by an endogenous cofactor, inositol hexakisphosphate, which acts as a second molecular glue. The functional relevance of the quaternary complex interaction surfaces is demonstrated by base editor scanning of KBTBD4 and HDAC1. By delineating the direct target of UM171 and its mechanism of action, we reveal how the cooperativity offered by a dimeric CRL3 E3 can be leveraged by a small molecule degrader.","fileCount":"31","fileSizeKB":"16529739","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"K-TMT18, n-term-TMT18, C-carbamidomethylation, M-oxidation, N-term acetylation, N-term deamidation, N-term Q-pyroglutamate formation;Ubiquitin Residual GG from Tryp Cut on K","keywords":"ubiquitin,degradation,molecular glue;DatasetType:Proteomics","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"16b8c4b3eff44507a78c633e9893020a","id":"1564"}, {"dataset":"MSV000096455","datasetNum":"96455","title":"SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a mechanism for selective translational suppression upon cellular stress","user":"ak3952","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731959835000","created":"Nov. 18, 2024, 11:57 AM","description":"RNA binding proteins (RBPs) play crucial roles in regulating every stage of the mRNA life cycle and mediating non-coding RNA functions. Despite their importance, the specific roles of most RBPs remain unexplored because we do not know their specific RNA binding partners. Current methods, such as crosslinking and immunoprecipitation followed by sequencing (CLIP-seq), have expanded our knowledge of RBP-RNA interactions but are generally limited by their ability to map only one RBP at a time. To address this limitation, we developed SPIDR (Split and Pool Identification of RBP targets), a massively multiplexed method to simultaneously profile global RNA binding sites of dozens to hundreds of RBPs in a single experiment. SPIDR employs antibody-bead labeling coupled with split-pool barcoding to increase the throughput of current CLIP methods by two orders of magnitude. SPIDR identifies precise, single-nucleotide RNA binding sites for diverse classes of RBPs simultaneously. We identified several novel ribosomal RNA binders, including a novel interaction between LARP1 and 18S ribosomal RNA located within the mRNA entry site on the 40S small ribosomal subunit, and resolved this structure at 2.8 A using single-particle cryo-electron microscopy (cryo-EM). This structure provides a potential mechanistic explanation for the role of LARP1 in translational suppression. We next explored SPIDR ability to detect changes in RBP binding upon mTOR inhibition and identified that 4EBP1 acts as a dynamic RBP that selectively binds to 5-untranslated regions of translationally repressed mRNAs only upon mTOR inhibition. These observations provide a potential mechanism to explain the specificity of translational regulation controlled by mTOR signaling. SPIDR enables rapid, de novo discovery of RNA-protein interactions at an unprecedented scale and has the potential to transform our understanding of RNA biology and both transcriptional and post-transcriptional gene regulation.","fileCount":"68","fileSizeKB":"66052616","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"IP;DDA;DIA;DatasetType:Proteomics","pi":[{"name":"Marko Jovanovic","email":"mj2794@columbia.edu","institution":"Columbia University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"a45318345e4d446ab6eba4480ca31c05","id":"1565"}, {"dataset":"MSV000096453","datasetNum":"96453","title":"Depletion of Abundant Plasma Proteins in Human Serum via in situ Protein@ZIF-8 Synthesis for Integrated Proteomics","user":"rubyhjchan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731955202000","created":"Nov. 18, 2024, 10:40 AM","description":"Protein biomarkers in human serum provide critical insights into various physiological conditions and diseases, enabling early diagnosis, prognosis, and personalized treatment. However, detecting low-abundance protein biomarkers is challenging due to the presence of highly abundant proteins that make up ~99% of the plasma proteome. Here, we report for the first time the use of in situ metal-organic-framework (MOF) growth in serum to effectively deplete highly abundant serum proteins for integrated proteomic analysis. Through biomolecule-mediated nucleation of a zeolitic imidazolate framework (ZIF-8), abundant plasma proteins are selectively encapsulated within ZIF-8 and removed from serum via centrifugation, leaving a depleted protein fraction in the supernatant. Bottom-up proteomics analysis confirmed significant depletion of the topmost abundant proteins, many at depletion levels exceeding 95%. Such depletion enabled the identification of 277 total proteins in the supernatant (uncaptured) fraction in a single-shot analysis, including 54 uniquely identified proteins, 12 drug targets, and many potential disease biomarkers. Top-down proteomics characterization of the captured and uncaptured protein fractions at the proteoform-level confirmed this method is not biased toward any specific proteoform of individual proteins. These results demonstrate that in situ MOF growth can selectively and effectively deplete high-abundance proteins from serum in a simple, low-cost, one-pot synthesis to enable integrated top-down and bottom-up proteomic analysis of serum protein biomarkers.","fileCount":"975","fileSizeKB":"86847254","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro;impact II","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:00765 - \\\"A protein modification that effectively converts an L-cysteine residue to S-(L-cysteinyl)-L-cysteine, forming a disulfide bond with free cysteine.\\\";UNIMOD:1 - \\\"Acetylation.\\\";MOD:01347 - \\\"A modification produced in a non-enzymatic reaction between a carbohydrate carbonyl group (C1 of aldohexose or C2 of fructose) and an L-lysine residue to form a Schiff-base or an Amadori ketosamine lysine adduct.\\\"","keywords":"metal-organic framework;human serum proteomics;protein separation;bottom-up proteomics;top-down proteomics;biomarker discovery;depletion technology;DatasetType:Proteomics","pi":[{"name":"Ying Ge","email":"ge2@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD058001","task":"2efba3c0dbea44a4a98329c8dcd657b3","id":"1566"}, {"dataset":"MSV000096452","datasetNum":"96452","title":"GNPS - 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This model captures the histological, metabolic and immunological dysregulation seen in human MASH within 12 weeks and progression to HCC by 24 weeks. In this study we evaluated the effect of ihAEC EVs on steatosis, fibrosis, inflammation and liver regeneration and further characterized both protein and miRNA cargo to better elucidate the potential mechanisms of ihAEC EVs action in the setting of experimental MASLD\/MASH.","fileCount":"28","fileSizeKB":"31211022","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"stem cells;Extracellular vesicles;fibrosis;DatasetType:Proteomics","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057972","task":"2ca0efe78d154b8b870fcd3c0c6d7859","id":"1571"}, {"dataset":"MSV000096439","datasetNum":"96439","title":"HDX-MS of UCH37 and Nb-cS1 complex","user":"strieterlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731902640000","created":"Nov. 17, 2024, 8:04 PM","description":"Hydrogen deuterium exchange mass spectrometry data of UCH37 and Nb-cS1 complex, raw files","fileCount":"732","fileSizeKB":"49874645","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HDX-MS, UCH37, nanobody;DatasetType:Other (HDX-MS)","pi":[{"name":"Eric Strieter","email":"estrieter@umass.edu","institution":"University of Massachusetts Amherst","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"88dd30fbdf644adcbeffb105559cb6be","id":"1572"}, {"dataset":"MSV000096438","datasetNum":"96438","title":"HDX-MS of UCH37 and Nb-ncS1 complex","user":"strieterlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731902294000","created":"Nov. 17, 2024, 7:58 PM","description":"Hydrogen deuterium exchange mass spectrometry data of UCH37 and Nb-ncS1 complex, raw files","fileCount":"659","fileSizeKB":"39375492","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HDX-MS, UCH37, Nanobody;DatasetType:Other (HDX-MS)","pi":[{"name":"Eric Strieter","email":"estrieter@umass.edu","institution":"University of Massachusetts Amherst","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"14600aac079b42c6be8e3ff8c32600e5","id":"1573"}, {"dataset":"MSV000096435","datasetNum":"96435","title":"Interaction Landscape of Ancestral and Variants SCoV2-Human Protein Assemblies Revealed in Distinct Organs and Body Fluids of COVID-19 Patients ","user":"srphanse","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731788142000","created":"Nov. 16, 2024, 12:15 PM","description":"Knowledge of SARS-CoV2 (SCoV2) human protein-protein interactions (PPIs), and host response to viral infection is key to designing new antivirals to thwart COVID-19. Yet, it remains unclear how ancestral and variants SCoV2 detected in many body parts or fluids remodel virus-host protein assemblies. Here, we performed >600 affinity-purifications by tagging and expressing 28 SCoV2 proteins, and spike protein from ancestral and four variants in eight cell lines, derived from five mammalian organs or biofluid, and identified human proteins associated with each viral protein by mass spectrometry (MS). The ensuing high-quality and previously unreported SCoV2-human PPIs were largely organ or variant-specific. Besides confirming these PPIs in COVID-19 patients saliva by MS-based co-fractionation, host PPIs were altered between variants and ancestral SCoV2. We show SCoV2 NSP3 papain-like protease is a secreted protein that binds with fibrinogen to promote abnormal blood clots, and with interferon-induced proteins to evade host innate immunity. Deep-learning aided design of peptide inhibitors impeded SCoV2 and variants replication in human liver cells, and restored PPI changes by the virus to healthy state. Our results unveil new mechanisms for human-ancestral or variants SCoV2 PPIs in various organs or biofluids, offering potential host therapeutic targets and SCoV2 inhibitors for antiviral development. 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Here we used TurboID proximity-mediated biotinylation to map the protein-protein interaction networks of MEF2A, MEF2C, and MEF2D in mouse MA-10 Leydig cells. Interactions were captured under both basal (unstimulated) and forskolin-stimulated conditions to examine differences in the MEF2 interactomes in relation to steroidogenesis. This dataset provides insights into MEF2-related signalling pathways and the functional landscape of MEF2 transcription factors in Leydig cells.","fileCount":"231","fileSizeKB":"48371370","spectra":"0","psms":"703600","peptides":"238587","variants":"278269","proteins":"45669","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"protein-protein interaction, transcription factors, steroidogenesis, TurboID, proximity labelling, Leydig cells;DatasetType:Proteomics","pi":[{"name":"Jacques J Tremblay","email":"jacques-j.tremblay@crchudequebec.ulaval.ca","institution":"Universite Laval ","country":"Canada"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD057949","task":"a5045822fe574ea2afa18741fbaf24e2","id":"1575"}, {"dataset":"MSV000096431","datasetNum":"96431","title":"Identification of carcinogenesis and tumor progression processes in pancreatic ductal adenocarcinoma using high-throughput proteomics","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731704155000","created":"Nov. 15, 2024, 12:55 PM","description":"Pancreatic adenocarcinoma (PDAC) is an aggressive disease with an overall 5 year-survival rate of just 5%. A better understanding of both the carcinogenesis processes and the mechanisms of progression of PDAC disease is mandatory. For this, proteomics data from FFPE samples of 173 primary tumor, normal tissue, preneoplastic lesions (PanIN), or lymph node metastases were analyzed from a Systems Biology perspective. Protein expression data was analyzed using probabilistic graphical models, allowing functional characterization. Functional node activities were calculated as the mean of expression of those proteins related to the main function of each node. 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Correlation networks are emerging as a powerful approach to infer tumor biology and to prioritize candidate genes as biomarkers or drug targets. In this study we applied a weighted co-expression analysis to the functionally relevant proteome of 20 surgically resected patients with PDAC. We obtained twelve modules with overlapping yet distinct biology, which implicated metabolism and ECM complexes in several modules. Notably, one module enriched for metabolic processes and epithelial-mesenchymal-transition (EMT) was significantly associated with overall survival (p=0.01) and was validated in public RNA data (p=0.02). The prognostic value of three proteins (SPTBN1, KHSRP and PYGL) belonging to this module was confirmed using immunohistochemistry in a cohort of 82 radically resected patients.","fileCount":"205","fileSizeKB":"161414276","spectra":"3439946","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Co-expression;Pancreatic ductal adenocarcinoma;Fresh-frozen tissue;Label-free;Prognosis;DatasetType:Proteomics","pi":[{"name":"Connie Ramona Jimenez","email":"c.jimenez@amsterdamumc.nl","institution":"Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD015744","task":"30fe82361312474b97280a72cc3e8a11","id":"1579"}, {"dataset":"MSV000096425","datasetNum":"96425","title":"IP-TMT-MS of Nb-ncS1 and Nb-cS1 transfected HEK293FT cells","user":"strieterlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731682925000","created":"Nov. 15, 2024, 7:02 AM","description":"IP-TMT-MS of Nb-ncS1 and Nb-cS1 transfected HEK293FT cells","fileCount":"12","fileSizeKB":"1451566","spectra":"0","psms":"5284","peptides":"1100","variants":"1253","proteins":"214","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"Nb-IP-MS;DatasetType:Proteomics","pi":[{"name":"Eric Strieter","email":"estrieter@umass.edu","institution":"University of Massachusetts Amherst","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057935","task":"4f5e7e0ef6c04bc19b65b2d6c61be56e","id":"1580"}, {"dataset":"MSV000096424","datasetNum":"96424","title":"Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis","user":"verizy27","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731680853000","created":"Nov. 15, 2024, 6:27 AM","description":"Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being paramount to their evolutionary success. A prime example are the skeletogenic cells of the developing vertebrate endoskeleton. Depending on anatomical location, these cells originate from three different embryonic precursor lineages, yet they converge developmentally towards similar cellular phenotypes. Furthermore, these embryonic lineages have gained skeletogenic competency at distinct timepoints during vertebrate evolution, thus questioning to what extent different parts of the vertebrate skeleton rely on truly homologous cell types. \nHere, we investigate how lineage-specific molecular properties of the three precursor pools are integrated at the gene regulatory level, to allow for phenotypic convergence towards a skeletogenic cell fate. Using single-cell transcriptomics and chromatin accessibility profiling along the precursor-to-skeletogenic cell continuum, we examine the gene regulatory dynamics associated with this cell fate convergence. We find that distinct transcription factor profiles are inherited and integrated from the three precursor states, and that lineage-specific enhancer elements incorporate these different inputs at the cis-regulatory level. \nThis lineage-specific gene regulatory logic for skeletogenic convergence from three embryonic precursor pools suggests that early skeletal cells in different body parts are distinct cell types. Their regulatory uncoupling may render them amenable to individualized selection, to help to define distinct morphologies and biomaterial properties in the different parts of the vertebrate skeleton.\n","fileCount":"35","fileSizeKB":"40059062","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gallus gallus (NCBITaxon:9031)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cell type evolution, cell fate convergence, vertebrate skeletogenesis, gene regulatory evolution, single-cell functional genomics;DatasetType:Proteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057934","task":"5f4ce522448743eeae07ac7ff4064d5b","id":"1581"}, {"dataset":"MSV000096417","datasetNum":"96417","title":"Gut-microbiota derived N,N,N-trimethyl-5-aminovaleric acid (TMAVA) is a modulator of CNS-aGVHD","user":"joergbuescher","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731594628000","created":"Nov. 14, 2024, 6:30 AM","description":"In this study, we report that microbiota depletion results in exacerbated acute graft-vs-host disease in the central nervous system (CNS), mediated by microglia activation and T-cell infiltration. We could rescue the inflammatory changes in the CNS by administering the microbiota-derived metabolite N,N,N-trimethyl-5-aminovalerate.","fileCount":"891","fileSizeKB":"1844141","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6495B Triple Quadrupole LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Gut-microbiota;microbiome;TMAVA;GVHD;DatasetType:Metabolomics","pi":[{"name":"Prof. Dr. Robert Zeiser","email":"robert.zeiser@uniklinik-freiburg.de","institution":"University Medical Center Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a844dfbec297457c879df53bc48f44cf","id":"1582"}, {"dataset":"MSV000096415","datasetNum":"96415","title":"Distinguishing N-Terminal Methylation from Near-isobaric Modifications by Statistical Analysis of Mass Error Distributions of Fragment Ions","user":"hanklee321","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731591484000","created":"Nov. 14, 2024, 5:38 AM","description":"alpha-N-terminal methylation is an understudied post-translational modification with presumed functions involving protein-protein and\/or protein-DNA interaction. The covalent addition of mono-, di-, trimethyl groups to free alpha-amino group has proven to be difficult to profile globally by mass spectrometry due to trace endogenous amount and interference from near-isobaric modifications such as Nt-acetylation, even after N-terminome enrichment. To address this problem, we assume that in each MS2 spectrum b-ions will have a different mass error distribution compared to y-ions if the spectrum is falsely assigned to near-isobaric Nt-modification and exploit this statistically to correct the Nt-modification, a procedure we name as mass error test (MET)","fileCount":"42","fileSizeKB":"25338754","spectra":"0","psms":"368339","peptides":"253971","variants":"287337","proteins":"62702","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:122 - \\\"Formylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:56 - \\\"Acetate labeling reagent (N-term & K) (heavy form, +3amu).\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"N-terminal methylation;mass error test;post-translational modification;mass error distribution;near isobaric modification;DatasetType:Proteomics","pi":[{"name":"Cheolju lee","email":"clee270@kist.re.kr","institution":"Korea Institute of Science and Technology","country":"south korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057893","task":"cad2e5eb1557430db2899ba80c5ea1f9","id":"1583"}, {"dataset":"MSV000096414","datasetNum":"96414","title":"Tittel: 20241111_Wooden Breast Chicken MS data","user":"Nofima_SHIK2301","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731575396000","created":"Nov. 14, 2024, 1:09 AM","description":"Male Ross 308 broiler chickens (Gallus Gallus) were raised with ad libitum access to a pelleted wheat\/maize diet from the 10th day of age. Breast muscle was acquired from the chickens at 36 days post-hatching. The degree of wooden breast (non-affected, moderately affected and affected) were first sorted by palpation of individual chickens, followed by classification using near-infrared (NIR) spectroscopy of breast filet and histology of specimen. Samples were grouped into three categories: affected, moderately affected and non-affected according to WB myopathy based on the connective tissue content (fibrotic signs). For the shotgun proteomics analysis, salt soluble proteins were extracted from breast filet. Twelve biological replicates of each group were included in the analysis. The proteins were reduced and alkylated prior to digestion with Trypsin\/Lys-C. And peptides were analyzed by Dionex Ultimate 3000 UHPLC (Thermo Scientific) coupled to a Q-Exactive hybrid quadrupole Orbitrap mass spectrometer (Thermo Scientific).","fileCount":"41","fileSizeKB":"34206562","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gallus gallus (NCBITaxon:9031)","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Chicken;Wooden Breast;DatasetType:Proteomics","pi":[{"name":"Shiori Koga","email":"shiori.koga@nofima.no","institution":"Nofima AS","country":"Norway"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"2a989bc678cb4be584b9c4d73b6f02eb","id":"1584"}, {"dataset":"MSV000096410","datasetNum":"96410","title":"HOT335 15N2-tracking Metaproteomics","user":"jwal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731541087000","created":"Nov. 13, 2024, 3:38 PM","description":"Metaproteomics analyses of mixed-layer water from Hawaii Ocean Time-series Station ALOHA, incubated with 15N2 to track biosynthetic incorporation by diazotrophic microbes","fileCount":"55","fileSizeKB":"104605402","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"marine microbial community","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:994 - \\\"15N(1).\\\";UNIMOD:995 - \\\"15N(2).\\\";UNIMOD:996 - \\\"15N(3).\\\";UNIMOD:897 - \\\"SILAC 15N(4).\\\"","keywords":"15N tracking;ocean;marine;nitrogen fixation;diazotrophy;Hawaii Ocean Time-series;DatasetType:Proteomics","pi":[{"name":"Jacob Waldbauer","email":"jwal@uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4f0ff7dc25754985a7ffcc79f0f46b5b","id":"1585"}, {"dataset":"MSV000096406","datasetNum":"96406","title":"HIF Regulates Multiple Translated Endogenous Retroviruses: Implications for Cancer Immunotherapy","user":"clauser","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731522077000","created":"Nov. 13, 2024, 10:21 AM","description":"Jiang Q, Braun DA, Clauser KR, Ramesh V, Shirole NH, Duke-Cohan JE, Nabilsi N, Karmer NJ, Forman C, Lippincott IE, Klaeger S, Phulphagar KM, Chea V, Kim N, Vanasse AP, Saad E, Parsons T, Carr-Reynolds M, Carulli I, Pinjusic K, Jiang Y, Li R, Syamala S, Rachimi S, Verzani EK, Stevens JD, Lane WJ, Camp SY, Meli K, Pappalardi MB, Herbert ZT, Qiu X, Cejas P, Long HW, Shukla SA, Van Allen EM, Choueiri TK, Churchman LS, Abelin JG, Gurer C, MacBeath G, Childs RW, Carr SA, Keskin DB, Wu CJ, Kaelin WG. 2024.\nClear cell renal cell carcinoma (ccRCC), despite having a low mutational burden, is viewed as an immunogenic tumor because it occasionally undergoes spontaneous regressions and often responds to immunotherapies. The signature lesion in ccRCC is inactivation of the VHL tumor suppressor gene and consequent upregulation of the HIF transcription factor. An earlier case report described a ccRCC patient who was cured by an allogenic stem cell transplant and later found to have donor-derived T cells that recognized a ccRCC-specific peptide encoded by a HIF-responsive endogenous retrovirus (ERVE-4). We report that ERVE-4 is one of many ERVs that are induced by HIF, translated into HLA-bound peptides in ccRCCs, and capable of generating antigen-specific T cell responses. Moreover, ERV expression can be induced in non-ccRCC tumors with clinical-grade HIF stabilizers. These findings have implications for leveraging ERVs for cancer immunotherapy.\n","fileCount":"164","fileSizeKB":"39995403","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Fusion Lumos","modification":"C-carbamidomethylation;c-cysteinylation;m-oxidation;q-pyro-glutamic acid;K-TMT10","keywords":"immunopeptidomics;endogenous retrovirus;clear cell renal cell carcinoma;hypoxia inducing factor;DatasetType:Other (immunopeptidomics)","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057858","task":"771bf177ad6e4e198b0c5b73f74fed30","id":"1586"}, {"dataset":"MSV000096404","datasetNum":"96404","title":"Automation of Proteomics Sample Preparation at the Meso-scale Supplemented with 3D Printed Hardware","user":"mchampio","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731518301000","created":"Nov. 13, 2024, 9:18 AM","description":"Raw and processed datafiles in support of manuscript, \"Automation of Proteomics Sample Preparation at the Meso-scale Supplemented with 3D Printed Hardware\" ","fileCount":"3587","fileSizeKB":"186875072","spectra":"0","psms":"21577","peptides":"12443","variants":"16337","proteins":"1529","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"timsTOF Pro;timsTOF Pro 2","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:425 - \\\"Dihydroxy.\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\"","keywords":"Andrew Alliance;Automation;Meso Scale Proteomics;Sample Preparation;Robotics;Liquid Handling;3D Printing;DatasetType:Proteomics","pi":[{"name":"Matthew Champion","email":"mchampio@nd.edu","institution":"University of Notre Dame","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057853","task":"931f4d12561b4ed198de89b718118769","id":"1587"}, {"dataset":"MSV000096403","datasetNum":"96403","title":"Characterization of site-specific O- and N-glycopeptides from recombinant spike and ACE2 glycoproteins using LC-MS\/MS analysis","user":"juyeon4444","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731517814000","created":"Nov. 13, 2024, 9:10 AM","description":"The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of infections and deaths globally. Although vaccination campaigns are mitigating the pandemic, emerging viral variants continue to pose challenges. The spike (S) protein of SARS-CoV-2 plays a critical role in viral entry by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, making both proteins essential targets for therapeutic and vaccine development. Glycosylation of these proteins influences their structure and function, underscoring the need for detailed site-specific glycoproteomic analysis.\nIn this study, we characterized the N- or O-glycosylation profiles of recombinant receptor-binding domain (RBD) of spike protein and ACE2 proteins expressed from HEK293 cells, as well as S2 subunit of spike protein expressed in plants cells. Using a high-resolution Orbitrap Eclipse Tribrid mass spectrometer integrated with the Ultimate 3000 RSLCnano and IQ-GPA (Identification and Quantification of GlycoProteome Analyzer), 148 N- and 28 O-glycopeptides from RBD, 71 N-glycopeptides from the S2 subunit, and 139 N-glycopeptides from ACE2 were characterized.\nAdditionally, we report novel post-translational modifications (PTMs) in RBD glycopeptides, including mannose-6-phosphate (M6P) and GlcNAc-1-phosphate-6-O-mannose of N-glycan, and O-acetylation of O-glycan, identified for the first time. These findings provide valuable insights into the glycosylation patterns that influence protein function and immunogenicity, offering new perspectives for the development of vaccines and antibody-based therapies against COVID-19.","fileCount":"44","fileSizeKB":"17055500","spectra":"389174","psms":"26","peptides":"8","variants":"10","proteins":"4","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);SARS coronavirus (NCBITaxon:227859)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:408 - \\\"Glycosyl-L-hydroxyproline.\\\"","keywords":"Spike glycoprotein;Reaction Binding Domain;Recombinant proteins;site-specific glycopeptides;DatasetType:Proteomics","pi":[{"name":"Ju Yeon Lee","email":"jylee@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Republic of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057852","task":"40e09b020f914543b9531e9b42ed7527","id":"1588"}, {"dataset":"MSV000096402","datasetNum":"96402","title":"Mass Spectrometry confirmation of BSA peptide modifications during alkaline sequencing reactions.","user":"OpheliaP","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731517524000","created":"Nov. 13, 2024, 9:05 AM","description":"DDA analysis of samples of commercial tryptic peptides of BSA which had been either untreated (\"original\"), conjugated with the Harnimarta et al sequencing reagent (\"conj\") or conjugated and exposed to alkaline cleavage conditions (\"seq\"). Data was searched in Proteome Discoverer 2.5 using a 58.017 Da for the sequencing reagent dynamic modification. The associated BSA2 fasta includes a synthetic sequence to generate in silico tryptic peptides representing the original BSA tryptic peptides lacking a single N-terminal amino acid.","fileCount":"29","fileSizeKB":"13172021","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913)","instrument":"Orbitrap Fusion Lumos","modification":"sequencing reagent (Deol_N-term);sequencing reagent on any K (Deol_conj)","keywords":"Edman, sequencing;DatasetType:Proteomics","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1ebe51b442834849a9bc8cb98384b901","id":"1589"}, {"dataset":"MSV000096401","datasetNum":"96401","title":"Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms","user":"haolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731516235000","created":"Nov. 13, 2024, 8:43 AM","description":"Stable isotopic labeling by amino acids in cell culture (SILAC) is a powerful metabolic labeling technique with widespread applications and diverse study designs. SILAC proteomics requires the confident identification and quantification of complete isotopic versions of proteins and peptides during data acquisition and analysis. However, different SILAC workflows and data analysis platforms have not been comparatively evaluated. To fill this critical gap and provide practical user guidelines for SILAC proteomics data analysis, we designed a comprehensive benchmarking pipeline to evaluate different SILAC workflows and commonly used data analysis software. Ten different data analysis platforms were evaluated for static and dynamic SILAC labeling with both DDA and DIA methods. Both in-house generated and repository SILAC proteomics datasets were used for benchmarking with hundreds of raw data files from HeLa and neuron samples. We evaluated twelve performance metrics for SILAC proteomics including identification, quantification, accuracy, precision, reproducibility, filtering criteria, missing values, false discovery rate, protein half-life measurement, completeness, unique software features, and speed of data analysis. In summary, this study provided the first systematic evaluation of different SILAC data analysis platforms with practical guidelines to assist decision-making in SILAC proteomics study design and data analysis. 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The samples S256, S264, S269, and S273 are vector plasmid control IP samples. The samples S257, S265, S270, and S274 are TwinStrep-tagged OTULIN WT IP samples. The samples S259, S267, S272, and S276 TwinStrep-tagged OTULIN deltaPBM (1-348). The rest of the samples are not used in the manuscript. 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Current TB diagnostic assays have poor performance in children, and identifying novel non-sputum-based TB biomarkers to improve pediatric TB diagnosis is a global priority. We sought to develop a plasma biosignature for TB by probing the plasma proteome of 511 children stratified by TB diagnostic classification and HIV status from sites in four low- and middle-income countries, using high-throughput data-independent acquisition mass-spectrometry (DIA-PASEF-MS). We identified 47 proteins differentially regulated between children with microbiologically confirmed TB from children with non-TB lower respiratory tract infection (Unlikely TB). We further employed machine learning to derive three parsimonious biosignatures encompassing 4, 5, or 6 proteins that achieved AUCs of 0.86-0.88 all of which exceeded the minimum WHO target product profile accuracy thresholds (70% specificity at 90% sensitivity, PPV 0.65-0.74, NPV 0.92-0.95) for a TB screening test. 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In two recent studies, we found that in vitro beta-lactam antibiotic and nutrient stresses faced during infection selected for the genetic inactivation of the Pseudomonas aeruginosa (Pa) antibiotic efflux pump mexEFoprN. Unexpectedly, efflux pump mutations increased Pa virulence during infection; however, neither the prevalence of efflux pump inactivating mutations in real human infections, nor the mechanisms driving increased virulence of efflux pump mutants were known. We hypothesized that human infection would select for efflux pump mutations that drive increased virulence in Pa clinical isolates. Using genome sequencing of hundreds of Pa clinical isolates, we show that mexEFoprN efflux pump inactivating mutations are enriched in Pa cystic fibrosis isolates relative to Pa intensive care unit clinical isolates. Combining RNA-seq, metabolomics, genetic approaches, and infection models we show that efflux pump mutants increase expression of two key Pa virulence factors, elastase and rhamnolipids, which increased Pa virulence and lung damage during both acute and chronic infections. We show that increased virulence factor production was driven by increased Pseudomonas quinolone signal levels, and this mechanism of increased virulence held true in both a representative ICU clinical isolate and the notorious CF Pa Liverpool epidemic strain. Together, our findings suggest that mutations inactivating antibiotic resistance mechanisms could increase patient mortality and morbidity. ","fileCount":"54","fileSizeKB":"2195348","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa PAO1 (NCBITaxon:208964)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pseudomonas aeruginosa quorum sensing;cystic fibrosis;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Peter Jorth","email":"peter.jorth@cshs.org","institution":"Cedars Sinai Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"63b8c771eaba4a8288bd08825adc3c13","id":"1596"}, {"dataset":"MSV000096390","datasetNum":"96390","title":"Rare SNP in the HELB gene interferes with RPA interaction and cellular function of HELB","user":"sbyrum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731424529000","created":"Nov. 12, 2024, 7:15 AM","description":"HELB is a human helicase involved in initiation of DNA replication, the replication stress response, and regulation of double-strand DNA break repair. rs75770066 is a low-frequency single-nucleotide polymorphism (SNP) in the HELB gene that affects age at natural menopause. rs75770066 results in a D506G substitution in a HELB specific insertion in the 1A domain of the helicase that contains amino acids known to interact with RPA. We found that this amino acid change has no effect on the enzymatic activity of HELB but dramatically impairs the cellular function of HELB. D506G HELB exhibits impaired interaction with RPA, which likely results in the effects of rs75770066 as this reduces recruitment of HELB to sites of DNA damage. Reduced recruitment of D506G-HELB to double-strand DNA breaks and the concomitant increase in homologous recombination likely alters the levels of meiotic recombination, which affects the viability of gametes. Because menopause occurs when oocyte levels drop below a minimum threshold, altered repair of meiotic double-stranded DNA breaks has the potential to directly affect the age at natural menopause. 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Byrd","email":"akbyrd@uams.edu","institution":"University of Arkansas for Medical Sciences","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD057796","task":"1a35121a610c4509b3388ab1a03ca682","id":"1597"}, {"dataset":"MSV000096389","datasetNum":"96389","title":"AMPK interactome: M1-linked Ubiquitination by LUBAC Regulates AMPK Activity and the Response to Energetic Stress","user":"creel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731420528000","created":"Nov. 12, 2024, 6:08 AM","description":"This dataset is pertaining to the AMPK alpha1 (PRKAA1) interactome in Figure 1 of the manuscript. Overexpression and pulldown of AMPK alpha1 was done in HEK293T cells. The samples DEF486, DEF490, and DEF494 are vector plasmid control IP samples. The samples DEF489, DEF493, and DEF497 are TwinStrep-tagged AMPK alpha1 IP samples. The rest of the samples are not used in the manuscript.","fileCount":"42","fileSizeKB":"25744423","spectra":"0","psms":"114280","peptides":"19705","variants":"25219","proteins":"2911","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:00064 - \\\"A protein modification that effectively converts an L-lysine residue to N6-acetyl-L-lysine.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\"","keywords":"AMPK;Interactome;LUBAC;OTULIN;M1-linked Ubiquitin;DatasetType:Proteomics;IP-MS","pi":[{"name":"Rune Busk Damgaard","email":"rudam@dtu.dk","institution":"Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU)","country":"Denmark"}],"complete":"true","quant_analysis":"Quantification Results;Study Design","status":"Complete","private":"false","hash":"","px":"PXD057792","task":"f31e344ecce54eed8a9740453975a990","id":"1598"}, {"dataset":"MSV000096388","datasetNum":"96388","title":"HDAC8_SAHA_PCI-34051_HDX-MS_Luo","user":"Aro_best","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731415343000","created":"Nov. 12, 2024, 4:42 AM","description":"This dataset contains the HDX-MS raw mass spectra data in the article 'Integrating native MS, HDX-MS, and MD simulations to uncover the dynamic inhibition mechanism and distant structural changes of PCI-34051 on HDAC8'.","fileCount":"1434","fileSizeKB":"68444545","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hydrogen\/deuterium exchange, mass spectrometry (MS), molecular dynamics, histone deacetylase inhibitor (HDAC inhibitor) (HDI), epigenetics, protein dynamic, enzyme structure, drug design;DatasetType:Proteomics","pi":[{"name":"Huilin Li","email":"lihlin6@mail.sysu.edu.cn","institution":"Sun Yat-sen University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"21772e7832be474c8e1d77011e9a594d","id":"1599"}, {"dataset":"MSV000096385","datasetNum":"96385","title":"GNPS-rat blood plasma (1 to 4 days) (new candidate entity)","user":"khkee92","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731413796000","created":"Nov. 12, 2024, 4:16 AM","description":"This data was adapted from another paper that utilised orbitrap data to write a thesis.","fileCount":"7","fileSizeKB":"205485","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crl:WI(Han)","instrument":"HRMS(Orbitrab)","modification":"None","keywords":"Rattus norvegicus, plasma;DatasetType:Metabolomics","pi":[{"name":"Kyung Hwa Kee","email":"khkee9202@gmail.com","institution":"hanyang university","country":"South korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"99e868dd37ef4fd49d9688ec3b5514f4","id":"1600"}, {"dataset":"MSV000096382","datasetNum":"96382","title":"M1-linked Ubiquitination by LUBAC Regulates AMPK Activity and the Response to Energetic Stress","user":"MStumpe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731413772000","created":"Nov. 12, 2024, 4:16 AM","description":"The dataset is pertaining to the phospho proteome in figure 6 of the manuscipt. U2OS WT and HOIP-KO cells were starved of glucose for 0-120 minutes (n = 3 per time point). See supplementary file for label-to-sample match . raw files containing _P_ are phosho peptide enriched samples. raw files containing _FT_ are whole cell lysate. The dataset contains two TMT-16plex experiments each with 8 fractions. ","fileCount":"36","fileSizeKB":"56902704","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"bottom-up proteomics;phospho proteome;TMT label;DatasetType:Proteomics","pi":[{"name":"Rune Busk Damgaard","email":"rudam@dtu.dk","institution":"Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU)","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057785","task":"50fd042f3801435ebb0f4e548272d625","id":"1601"}, {"dataset":"MSV000096381","datasetNum":"96381","title":"Uncovering New Biomarkers for Prostate Cancer Through Proteomic and Network analysis","user":"Dds100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731413772000","created":"Nov. 12, 2024, 4:16 AM","description":"Two hundred microliters per protein sample, collected at the end of isolation, were concentrated to 50 microL in a vacuum concentrator at 60C and treated with RapiGestTMSF reagent (Waters Co, Milford, MA, USA) at the final concentration of 0.25% (w\/v). The resulting suspensions were incubated under stirring at 100C for 20 minutes. Subsequently the samples were cooled to room temperature and centrifuged 10 min at 2200 g. The protein concentration was assayed using the Invitrogen Qubit Protein BR Assay Kit (Life Technologies Corporation, Thermo Fisher, Eugene, ORE, USA) and 50 microg proteins from each sample were digested overnight at 37C by adding Sequencing grade Modified Trypsin (Promega Inc., Madison, WI, USA) at an enzyme substrate ratio of 1:50 (w\/w) in 0.1M NH4HCO3 pH 7.9 buffer with 10% CH3CN. An additional aliquot of trypsin (1:100 w\/w) was then added the next day, and the digestion continued for 4h. The enzymatic digestion was chemically stopped by acidification with 0.5%Trifluoroacetic Acid (TFA) (SigmaAldrich Inc., St. Louis, MO, USA), and a subsequent incubation at 37C for 45 minutes completed the RapiGest acid hydrolysis. Water immiscible degradation products were removed by centrifugation at 13,000 rpm for 10 minutes. Finally, the tryptic digest mixtures were desalted using PierceTM C 18 spin columns (Thermo Fisher Scientific,Pierce Biotechnology, Rockford, Il, USA), according to manufacturer protocol and were resuspended in 0.1% formic acid (Sigma-Aldrich Inc., St. Louis, MO, USA) in water (LC MS Ultra CHROMASOLV, Honeywell Riedelde HaenTM, Muskegon, MI, USA) at a concentration of 0.1 microg\/microL.\n\n\nThe nanoLC MS\/MS experiments were performed using the LTQ Orbitrap XL ETD mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) coupled with Eksigen nanoLC-Ultra 2D System (Eksigent, part of AB SCIEX Dublin, CA, USA) configured I trap elute mode. Briefly, samples (0.8microg injected) were first loaded on a trap (200 microm x 500 microm ChromXP C18 CL, 3 microm, 120 A) and washed with the loading pump running in isocratic mode with 0.1% formic acid in water for 10 minutes at a flow of 3 microL\/min. The automatic switching of auto-sampler ten-port valve then eluted the trapped mixture on a nano reversed phase column (75 microm x 15 cm ChromXP C18 CL, 3 microm, 120 A) through a 130 minutes gradient of eluent B (eluent A, 0.1% formic acid in water; eluent B, 0.1% formic acid in acetonitrile) at a flow rate of 300 nL\/min. In depth, gradient was: from 5 10% B in 5 min, 10 40% B in 85min, 40 95% B in 27 min and holding at 95% B for 10 min. The eluated peptides were directly analyzed into a LTQ Orbitrap XL ETD through a nano electrospray ion source (Thermo Fisher Scientific); each sample was analyzed in at least 3 technical replicates. The spray capillary voltage was set at 1.7 kV and the ion transfer capillary temperature was held at 220C. Full MS spectra were recorded over a 400 1600 m\/z range in positive ion mode, with a resolving power of 30000 (full width at half-maximum) and a scan rate of 2 spectra\/s. This step was followed by 5 low resolution MS\/MS events that were sequentially generated in a data-dependent manner on the top five ions selected from the full MS spectrum (at 35% collision energy), using dynamic exclusion of 0.5 min for MS\/MS analysis. Mass spectrometer scan functions and high-performance liquid chromatography solvent gradients were controlled by the Xcalibur data system version 1.4 (Thermo Fisher Scientific, MA, USA).\n\nFile description:\nHD > Healthy donors\nLRPCa > low risk patients (bladder cancer)\nHRPCa > high risk patients (bladder cancer)\nSub > subject\nI, II, III etc...> technical replicates\n\n\n","fileCount":"59","fileSizeKB":"6147337","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap XL ETD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Urine;Prostate cancer;DatasetType:Proteomics","pi":[{"name":"Dario Di Silvestre","email":"dario.disilvestre@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Pierluigi Mauri","email":"pierluigi.mauri@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"},{"name":"Rossana Rossi","email":"rossana.rossi@itb.cnr.it","institution":"Institute of Biomedical Technologies","country":"Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d704b42664e64b7aba7fc6aef791633b","id":"1602"}, {"dataset":"MSV000096380","datasetNum":"96380","title":"Proximity interactome of alphavirus replicase component nsP3 includes proviral host factors eIF4G ","user":"adityath","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731413734000","created":"Nov. 12, 2024, 4:15 AM","description":"All positive-strand RNA viruses replicate their genomes in association with modified intracellular membranes, inducing either membrane invaginations termed spherules, or double-membrane vesicles. Alphaviruses encode four non-structural proteins nsP1-nsP4, all of which are essential for RNA replication and spherule formation. To understand the host factors associated with the replication complex, we fused the efficient biotin ligase miniTurbo with Semliki Forest virus (SFV) nsP3, which is located on the cytoplasmic surface of the spherules. We characterized the proximal proteome of nsP3 in three cell lines, including cells unable to form stress granules, and identified >300 host proteins constituting the microenvironment of nsP3. These included all the nsPs, as well as several previously characterized nsP3 binding proteins. However, the majority of the identified interactors had no previously identified roles in alphavirus replication, including 39 of the top 50 interacting proteins. The most prominent biological processes involving the proximal proteins were nucleic acid metabolism, translational regulation, cytoskeletal rearrangement and membrane remodeling. siRNA silencing identified six novel proviral factors, USP10, AHNAK, eIF4G1, SH3GL1, XAB2 and ANKRD17, which are associated with distinct cellular functions. All of these except SH3GL1 were also important for the replication of chikungunya virus. We discovered that the small molecule 4E1RCat, which inhibits the interaction between the canonical translation initiation factors eIF4G and eIF4E, exhibits antiviral activity against SFV. Since the same molecule was previously found to inhibit coronaviruses, this suggest the possibility that translation initiation factors could be considered as targets for broadly acting antivirals","fileCount":"7","fileSizeKB":"21708648","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mesocricetus auratus (NCBITaxon:10036)","instrument":"timsTOF Pro","modification":"no","keywords":"Alphavirus;Biotin labeling;miniTurbo;DatasetType:Proteomics","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"},{"name":"Tero Ahola","email":"tero.ahola@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f2b1a2ddea934c229ba37d8a961d5226","id":"1603"}, {"dataset":"MSV000096379","datasetNum":"96379","title":"diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling","user":"golkom","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731354353000","created":"Nov. 11, 2024, 11:45 AM","description":"Protein-protein interactions (PPIs) underlie most biological functions. Devastating human conditions like cancers, neurological disorders, and infections, hijack PPI networks to initiate disease, and to drive disease progression. Understanding precisely how diseases remodel PPI networks can, therefore, help clarifying disease mechanisms and identifying therapeutic targets. Protein kinases control most cellular processes through protein phosphorylation. The 518 human kinases, known as the kinome, are frequently dysregulated in disease and highly druggable with ATP-competitive inhibitors. Kinase activity, localization, and substrate recognition are regulated by dynamic PPI networks composed of scaffolding and adapters proteins, other signaling enzymes like small GTPases and E3 ligases, and phospho-substrates. Accordingly, mapping kinase PPI networks can help determining kinome activation states, and, in turn, cellular activation states; this information can be used for studying kinase-mediated cell signaling, and for prioritizing kinases for drug discovery. Previously, we have developed a high-throughput method for kinome PPI mapping based on mass spectrometry (MS)-based chemoproteomics that we named kinobead competition and correlation analysis (kiCCA). Here, we introduce 2nd generation (gen) kiCCA which utilizes data independent acquisition (DIA) with parallel accumulation serial fragmentation (PASEF) MS and a re-designed CCA algorithm with improved selection criteria and the ability to predict multiple kinase interaction partners of the same proteins. Using neuroblastoma cell line models of the noradrenergic-mesenchymal transition (NMT), we demonstrate that 2nd gen kiCCA (1) identified 6.1-times more kinase PPIs in native cell extracts compared to our 1st gen approach, (2) determined kinase-mediated signaling pathways that underly the neuroblastoma NMT, and (3) accurately predicted pharmacological targets for manipulating NMT states. Our 2nd gen kiCCA method is broadly useful for cell signaling research and kinase drug discovery.","fileCount":"5510","fileSizeKB":"342835429","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"protein kinase;protein-protein interaction;chemoproteomics;kinase inhibitor;anaplastic lymphoma kinase;neuroblastoma;plasticity;noradrenergic-mesenchymal transition;DatasetType:Proteomics","pi":[{"name":"Martin Golkowski","email":"martin.golkowski@utah.edu","institution":"University of Utah","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD057757","task":"6cffcd76496c45e5b711873486807ca8","id":"1604"}, {"dataset":"MSV000096377","datasetNum":"96377","title":"The interactome of tau phosphorylated at T217 in Alzheimers disease human brain tissue","user":"Trixi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731344483000","created":"Nov. 11, 2024, 9:01 AM","description":"Tau phosphorylation and aggregation are pathological features of Alzheimers disease. Tau phosphorylated at threonine 217 (pT217) and threonine 231 (pT231) are early fluid biomarkers of Alzheimers disease, suggesting early involvement in disease. However, little is known about the specific actions of these types of phosphorylated tau in Alzheimers disease. Here we performed affinity purification mass spectrometry of pT217 and pT231 tau to determine how phosphorylation of specific tau residues alters its interactome in Alzheimers disease post-mortem brain tissue (n=10). These patients were a balanced cohort of APOE e3\/e3 and e4\/e4 genotypes (n=5 each) to explore how the most significant AD genetic risk factor altered phosphorylated tau interactions. Results were also compared to our previous interactome dataset examining tau phosphorylated at S396\/S404 (enriched using the PHF1 antibody) generated using the same cases. pT217 affinity purification mass spectrometry identified 23 interacting proteins (SAINT score > 0.65). pT217 enriched tau had a constrained phosphorylation signature compared to PHF1 enriched tau, but interactors shared significant overlap. The phosphorylation patterns of pT217 enriched tau included lower intensities of phosphorylation at epitopes serine 396 and serine 404 than PHF1 enriched tau, suggesting pT217 tau was at an earlier state of dysregulation. pT217 interacting proteins were most significantly enriched for biological processes involved in protein catabolism, highlighting the CTLH E3 ubiquitin ligase complex as a novel interactor of multiple phosphorylated tau species (5 interacting subunits: WDR26, ARMC8, GID8, RANBP9, MAEA). In APOE e3\/e3 cases pT217 significantly interacted with 46 proteins compared to 28 in APOE e4\/e4 cases. These interacting proteins were significantly overlapped, with 13 proteins in common (Fishers exact p = 9x10-23). CTLH E3 ubiquitin ligase subunits significantly interacted with phosphorylated tau in both APOE genotypes. pT231 immunoprecipitation failed to sufficiently enrich tau but results are provided in supplementary data. The phosphorylated tau interaction with p62 and the CTLH component WDR26 were validated using co-immunoprecipitation and immunofluorescent microscopy of fixed post-mortem human brain tissue. In conclusion, our results report the interactome of pT217 in human Alzheimers disease brain tissue for the first time and highlight the CTLH complex as a significant novel interactor of multiple types of phosphorylated tau, including those increased early in Alzheimers disease. The mass spectrometric files of this AP-MS experiment are included here. ","fileCount":"45","fileSizeKB":"32048156","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phospho Tau;pT217;ALzheimers Disease brain;DatasetType:Proteomics","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"NYU School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057755","task":"eae57d15794d42ef9c6af945d3b199f9","id":"1605"}, {"dataset":"MSV000096376","datasetNum":"96376","title":"Spatial Proteomics by Trapped Ion Mobility supported MALDI MS\/MS Imaging: A First Glance into Multiplexed and Spatial Peptide Identification","user":"oliver_schilling","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731343027000","created":"Nov. 11, 2024, 8:37 AM","description":"RATIONALE\nIn spatial proteomics, matrix-assisted laser desorption\/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS\/MS imaging.\nMETHODS\nAn initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS\/MS imaging. Finally, precursors are identified by peptide to spectrum matching.\nRESULTS\nThis study presents the first multiplexed MALDI TIMS MS\/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.\nCONCLUSIONS\nIn the present study, we demonstrate the feasibility of TIMS-based MALDI MS\/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.\n\nThe datasets will be uploaded separately. This data set contains the PDX MSMS data. There are two tissues vissible on the.tif image. The relevant one is on the left side of the slide (away from the barcode).\n","fileCount":"56","fileSizeKB":"1092401","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"MALDI imaging, MALDI TIMS MSMS imaging, peptide imaging, spatial proteomics, TIMS;DatasetType:Proteomics","pi":[{"name":"Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"University of Freiburg","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bf9bc3e89dec458c80b31c87d204fb77","id":"1606"}, {"dataset":"MSV000096375","datasetNum":"96375","title":"Spatial Proteomics by Trapped Ion Mobility supported MALDI MS\/MS Imaging: A First Glance into Multiplexed and Spatial Peptide Identification","user":"oliver_schilling","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731342811000","created":"Nov. 11, 2024, 8:33 AM","description":"RATIONALE\nIn spatial proteomics, matrix-assisted laser desorption\/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS\/MS imaging.\nMETHODS\nAn initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS\/MS imaging. Finally, precursors are identified by peptide to spectrum matching.\nRESULTS\nThis study presents the first multiplexed MALDI TIMS MS\/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.\nCONCLUSIONS\nIn the present study, we demonstrate the feasibility of TIMS-based MALDI MS\/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.\n\nThe datasets will be uploaded separately. This data set contains the Kidney MSMS data. There is an additional Liver tissue vissible on the .tif image. This was used for another experiment\n","fileCount":"63","fileSizeKB":"519662","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"MALDI imaging, MALDI TIMS MSMS imaging, peptide imaging, spatial proteomics, TIMS;DatasetType:Proteomics","pi":[{"name":"Prof. Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"Institute for Surgical Pathology, University Medical Center Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4725dc20f4104169a9b4daae8a8ce5f6","id":"1607"}, {"dataset":"MSV000096374","datasetNum":"96374","title":"Spatial Proteomics by Trapped Ion Mobility supported MALDI MS\/MS Imaging: A First Glance into Multiplexed and Spatial Peptide Identification","user":"oliver_schilling","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731342535000","created":"Nov. 11, 2024, 8:28 AM","description":"RATIONALE\nIn spatial proteomics, matrix-assisted laser desorption\/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS\/MS imaging.\nMETHODS\nAn initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS\/MS imaging. Finally, precursors are identified by peptide to spectrum matching.\nRESULTS\nThis study presents the first multiplexed MALDI TIMS MS\/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.\nCONCLUSIONS\nIn the present study, we demonstrate the feasibility of TIMS-based MALDI MS\/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.\n\nThe datasets will be uploaded separately. This data set contains the PDX MS1 data. There are two tissues vissible on the.tif image. The relevant one is on the left side of the slide (away from the barcode).\n","fileCount":"46","fileSizeKB":"23803325","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"MALDI TIMS MSMS imaging, MALDI imaging, peptide imaging, spatial proteomics, TIMS;DatasetType:Proteomics","pi":[{"name":"Prof. Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"Institute for Surgical Pathology, University Medical Center Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"37da4ec1f09e44988d648c8fd1f81f64","id":"1608"}, {"dataset":"MSV000096373","datasetNum":"96373","title":"Spatial Proteomics by Trapped Ion Mobility supported MALDI MS\/MS Imaging: A First Glance into Multiplexed and Spatial Peptide Identification","user":"oliver_schilling","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731342130000","created":"Nov. 11, 2024, 8:22 AM","description":"RATIONALE\nIn spatial proteomics, matrix-assisted laser desorption\/ionization (MALDI) imaging enables rapid and cost-effective peptide measurement. Yet, in situ peptide identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) into MALDI imaging of peptides to enable multiplexed MS\/MS imaging.\nMETHODS\nAn initial MALDI TIMS MS1 survey measurement is performed, followed by a manual generation of a precursor list containing mass over charge values and ion mobility windows. Inside the dual TIMS system, submitted precursors are trapped, separately eluted by their ion mobility and analyzed in a quadrupole time-of-flight device, thereby enabling multiplexed MALDI MS\/MS imaging. Finally, precursors are identified by peptide to spectrum matching.\nRESULTS\nThis study presents the first multiplexed MALDI TIMS MS\/MS imaging (iprm-PASEF) of tryptic peptides. Its applicability is showcased on two histomorphologically distinct tissue specimens in a 4-plex and 5-plex setup. Precursors were successfully identified by the search engine MASCOT in one single MALDI imaging experiment for each respective tissue. Peptide identifications were corroborated by liquid-chromatography tandem mass spectrometry experiments and fragment colocalization analyses.\nCONCLUSIONS\nIn the present study, we demonstrate the feasibility of TIMS-based MALDI MS\/MS imaging for the multiplexed and rapid identification of tryptic peptides in a spatial manner. Hence, it represents a first step towards the integration of MALDI imaging into the emerging field of spatial proteomics.\n\nAll Datasets are uploaded separateley. This file contains the dataset for mouse kidney MS1 data. \nOn the same slice a mouse liver was measured for a different experiment. ","fileCount":"1355","fileSizeKB":"582210224","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"MALDI imaging, TIMS, peptides, iprm-PASEF, MALDI TIMS MS\/MS Imaging, spatial Proteomics;DatasetType:Proteomics","pi":[{"name":"Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"University of Freiburg","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d72aa31060f147f8b7c32e0e593b34a0","id":"1609"}, {"dataset":"MSV000096370","datasetNum":"96370","title":"GNPS - Validated list AntiTB plants extract collection","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731265493000","created":"Nov. 10, 2024, 11:04 AM","description":"UHPLC-PDA-CAD-HRMS\/MS data in dual mode for a collection of natural extracts derived form plants and fractions","fileCount":"1073","fileSizeKB":"27130131","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Natural Products;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"8f280bf58ebc49f49c184e0b1c3585a2","id":"1610"}, {"dataset":"MSV000096369","datasetNum":"96369","title":"GNPS - Expert selection plants extract collection ","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731265212000","created":"Nov. 10, 2024, 11:00 AM","description":"UHPLC-PDA-HRMS\/MS data of a selection of natural extracts derived from plants (Expert selection)","fileCount":"1370","fileSizeKB":"25210463","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Natural Products;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"191f0a1617b746928d9262a0e1cdd545","id":"1611"}, {"dataset":"MSV000096366","datasetNum":"96366","title":"GNPS - Smart selection plants extract collection ","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731241582000","created":"Nov. 10, 2024, 4:26 AM","description":"UHPLC-PDA-CAD-HRMSMS data of a collection of natural extracts (Smart selection)","fileCount":"2524","fileSizeKB":"21326626","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Natural products;plant extracts;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ea0996154780419a9bd2c3bad770deec","id":"1612"}, {"dataset":"MSV000096365","datasetNum":"96365","title":"GNPS - Validation list AntiTB plants extract collection ","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731241514000","created":"Nov. 10, 2024, 4:25 AM","description":"UHPLC-PDA-CAD-HRMSMS data of a collection of natural extracts (Validation list TS hits)","fileCount":"953","fileSizeKB":"49155521","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Natural Products;Natural Extracts;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"06c79fa5ce1c4136974203a8883fc8a7","id":"1613"}, {"dataset":"MSV000096364","datasetNum":"96364","title":"GNPS - Untargeted metabolomics data for pooled human plasma sample","user":"463751202","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731155805000","created":"Nov. 9, 2024, 4:36 AM","description":"A pooled plasma of patients with chronic kidney disease and healthy controls analyzed by 13 individual CEs and stepped NCE 20\/40\/60% across 4 modes.","fileCount":"113","fileSizeKB":"53190774","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pooled human plasma;DatasetType:Metabolomics","pi":[{"name":"Xian Fu","email":"1639749394@qq.com","institution":"Chongqing Medical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"09ec66efe5044bfd8341883bc16135c0","id":"1614"}, {"dataset":"MSV000096363","datasetNum":"96363","title":"Evaluation Of Wharton's Jelly Mesenchymal Stem Cells Secretome Profiling Derived In Time And Passage Dependent Manner","user":"Anastasha97","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731141888000","created":"Nov. 9, 2024, 12:44 AM","description":"The data provided is from LCMS run of Wharton's Jelly Mesenchymal Stem Cells (WJMSC) derived secretomes. The samples consist of secretomes harvested at different time points (24, 48, and 72 hours) and passage numbers (P3, P5, and P10). The samples used were taken from 3 donors, with 3 technical runs for each sample. Thus, a total of 81 samples of data were collected. The research aims to understand how the composition of the secretome changes over time and with different cell passages. Advanced proteomic techniques are used to analyze the bioactive molecules secreted by WJMSCs, highlighting the impact of time and cell passage number on the therapeutic potential of these cells. This research seeks to enhance the clinical efficiency of WJMSCs for regenerative medicine applications by revealing the dynamic nature of their secretome.","fileCount":"244","fileSizeKB":"107304345","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Secretomes;Wharton's Jelly;Mesenchymal Stem Cells;Time Dependent Harvest;Passage Dependent Harvest;DatasetType:Proteomics","pi":[{"name":"Wan Safwani Wan Kamarul Zaman","email":"wansafwani@um.edu.my","institution":"Universiti Malaya","country":"Malaysia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057695","task":"36edb14343554f5c94b72227cfb19d8f","id":"1615"}, {"dataset":"MSV000096362","datasetNum":"96362","title":"Systems analysis of Chromochloris zofingiensis during copper, iron, and zinc deficiencies","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731123310000","created":"Nov. 8, 2024, 7:35 PM","description":"A systems level analysis of Chromochloris zofingiensis during copper, iron, and zinc deficiencies when grown photoautotrophically and mixotrophically in a revised TP medium with special K mineral nutrients.","fileCount":"577","fileSizeKB":"148085434","spectra":"0","psms":"4108128","peptides":"1575028","variants":"1873117","proteins":"31023","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chromochloris zofingiensis (NCBITaxon:31302)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"algae;copper;zinc;iron;photosynthesis;mixotrophy;metal deficiency;metal;nutrition;DatasetType:Proteomics","pi":[{"name":"Sabeeha Merchant","email":"sabeeha@berkeley.edu","institution":"California Institute for Quantitative Biosciences, University of California, Berkeley","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD057690","task":"1badcaf854bd4d71b30ad0339c317e6f","id":"1616"}, {"dataset":"MSV000096361","datasetNum":"96361","title":"CycT1\/Pol II IP-MS DDA dataset","user":"yukiaoi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731113769000","created":"Nov. 8, 2024, 4:56 PM","description":"DDA MS dataset for Cyclin T1 or RNA Polymerase II co-immunoprecipitants prepared from human DLD-1 cells treated with or without heat shock (42C, 2 h). 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Mechanistic insight into drivers of the NRF2 dependency remains poorly understood. Here, we defined a novel NRF2 target gene set linked to NRF2-dependency in cancer cell lines,and observed that a significant portion of these genes is devoid of promoter-proximal NRF2. Using integrated genomic analyses, we characterized extensive NRF2-dependent enhancer RNA (eRNA) synthesis and NRF2-mediated H3K27ac deposition at proximal and distal enhancer regions regulating these genes. While CBP\/p300 is a well-validated direct interaction partner of NRF2 with prominent functions at enhancers, we report that this interaction is not required for NRF2-dependent NSCLC cell growth, indicating that NRF2 can sustain sufficient\ntranscriptional activity in the absence of CBP\/p300 coactivation. Broad metabolic profiling established a primary role for CBP\/p300 in NRF2-dependent accumulation of glutathione and glutathione-related metabolites. While redox homeostasis via enhanced glutathione production is commonly associated with the normal physiological role of NRF2, collectively our results suggest that NRF2-dependent cancer cell growth does not require this enhanced glutathione production.","fileCount":"12","fileSizeKB":"6621940","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"NRF2;EP300;CBP;A549 cell;DatasetType:Proteomics","pi":[{"name":"Scott Foster","email":"foster.scott@gene.com","institution":"Genentech","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"bf71314d72674fbaa1d358e2578cd382","id":"1620"}, {"dataset":"MSV000096355","datasetNum":"96355","title":"Plasma samples were labeled with dimethylation on lysine residue","user":"ahson","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731095844000","created":"Nov. 8, 2024, 11:57 AM","description":"Plasma samples were labeled with dimethylation, using covalent protein painting method.\n","fileCount":"8907","fileSizeKB":"1195381460","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"UNIMOD:199 - \\\"DiMethyl-CHD2.\\\"","keywords":"protein structure;DatasetType:Proteomics","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4d36129273c0401eb470f840d123c808","id":"1621"}, {"dataset":"MSV000096353","datasetNum":"96353","title":"Quorum sensing modulates microbial community structure through regulation of secondary metabolites","user":"pabraham_ornl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731085421000","created":"Nov. 8, 2024, 9:03 AM","description":"Bacteria are recognized for their diverse metabolic capabilities, yet the impact of microbe-microbe interactions on multispecies community structure and dynamics is poorly understood. Cell-to-cell signaling in the form of quorum sensing (QS) often regulates secondary metabolite production and microbial interactions. Here we examine how acylhomoserine lactone (AHL) mediated QS impacts microbial community structure in a 10-member synthetic community of isolates from Populus deltoides. To explore the role of QS in microbial community structure and dynamics, we disrupted AHL signaling using purified AiiA-lactonase, an enzyme that cleaves the lactone ring. Microbial community structure resulting from signal inactivation, as measured by 16S amplicon sequencing and secondary metabolite production, was assessed after successive passaging of the community. Further, we investigated the impact of quorum quenching on microbe-microbe interactions using pairwise inhibition assays. Our results indicate that AHL inactivation alters the relative abundance of dominant community members at later passages but does not impact the overall membership in the community. Quorum quenching significantly alters the metabolic profile in AiiA-lactonase treated communities. This metabolic alteration impacts microbe-microbe interactions through decreased inhibition of other community members. Together, these results indicate that QS impacts microbial community structure through the regulation of secondary metabolites in dominant members and that membership of microbial communities can be relatively stable despite changes in metabolic profiles","fileCount":"136","fileSizeKB":"12927697","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas (NCBITaxon:286);Caulobacter (NCBITaxon:75);Sphingobium (NCBITaxon:165695);Bacillus (NCBITaxon:1386);Paraburkholderia sp. (NCBITaxon:1926495);Rhizobium;Variovorax (NCBITaxon:34072);Duganella (NCBITaxon:75654);Pantoea (NCBITaxon:53335);Streptomyces (NCBITaxon:1883)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbiome;quorum sensing;acylhomoserine lactone;DatasetType:Metabolomics","pi":[{"name":"Paul Abraham","email":"abrahampe@ornl.gov","institution":"ORNL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"884dc491ce664fec99035f73e8f06e69","id":"1622"}, {"dataset":"MSV000096349","datasetNum":"96349","title":"Top-Down Proteomics of Cape Coral Snake Venom","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731079262000","created":"Nov. 8, 2024, 7:21 AM","description":"Venoms were passed through a reduction process before being analyzed using bottom-up proteomics","fileCount":"10","fileSizeKB":"950976","spectra":"5595","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspidelaps lubricus (NCBITaxon:889328)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"venom;snake;DatasetType:Proteomics","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ba93db525f26421da78718357c1b1c68","id":"1623"}, {"dataset":"MSV000096347","datasetNum":"96347","title":"GNPS - Dynamic rhizodeposition in the woody perennial Populus trichocarpa","user":"mappidi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731076202000","created":"Nov. 8, 2024, 6:30 AM","description":"Under nutrient-limited conditions, plants undergo physiological and metabolic changes that release specific molecules into the rhizosphere (i.e., rhizodeposition). These plant-derived compounds modify the rhizosphere environment, mobilizing otherwise inaccessible nutrients and recruiting stress-adaptive microbial communities that support stress resilience. Currently, the chemical diversity of rhizodeposition has yet to be fully realized but is expected to be a complex mixture that includes soluble organic compounds excreted from root cells, along with products of root cell turnover. Here, we developed a methodological and conceptual framework for an in-depth measurement of rhizodeposition through critical advancements in untargeted metabolomics. This approach provided foundational insights into the dynamic changes in rhizodeposition for the woody perennial Populus trichocarpa and rhizodeposit profiles varying by genotype, time, location, and environment. More broadly, this study provides a framework that will help formulate the next steps to effectively study rhizodeposition.","fileCount":"2929","fileSizeKB":"546841979","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Populus trichocarpa (NCBITaxon:3694)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"root;exudate;rhizodeposition;metabolite;DatasetType:Metabolomics","pi":[{"name":"Paul Abraham","email":"abrahampe@ornl.gov","institution":"ORNL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0caca9dd991f42be8e531da3c5a2ad0a","id":"1624"}, {"dataset":"MSV000096340","datasetNum":"96340","title":"MGAT3 and MGAT5 overexpression alters the protein cargo of extracellular vesicles released by metastatic melanoma cells","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731059341000","created":"Nov. 8, 2024, 1:49 AM","description":"Extracellular vesicles (EVs) are potential non-invasive diagnostic, prognostic, and therapeutic tools. Additionally, they are important contributors to tumorigenesis. Glycosylation has been found to modulate the composition of the EV proteome, and increased amounts of beta 1,6-branched N-glycans, synthesized by N-acetylglucosaminyltransferase V (GnT-V), are most commonly observed in melanoma and associated with decreased cell adhesion and increased metastasis. The opposite effect is caused by the addition of bisecting GlcNAc by N-acetylglucosaminyltransferase III (GnT-III). To date, the impact of these enzymes on EV cargo in melanoma remains unexplored. Methods: Flow cytometry was used to study the surface glycosylation of genetic variants of WM266-4 melanoma cells with induced overexpression of GnT-III or GnT-V encoding genes (MGAT3 or MGAT5) and EVs released by these cells. LC-MS\/MS proteomics was applied to analyze the effect of altered glycosylation on the proteome of released EVs, followed by thorough bioinformatic analysis. Results: Flow cytometry analysis showed dynamic changes in surface glycosylation of EVs derived from melanoma cells overexpressing MGAT3 or MGAT5. Induced MGAT3 or MGAT5 overexpression also resulted in significant changes in EVs proteome. Proteomic analysis identified the total number of 1770 microvesicular and 704 exosomal proteins that play diverse roles in melanoma progression, including those with established diagnostic\/prognostic potential and those closely linked to melanoma onset. Conclusions: Proteomic profiling of EVs derived from MGAT3 and MGAT5 overexpressing cells revealed functional shifts in EV protein content driven by glycosylation modifications. The study presented a potential multidimensional use of melanoma-derived EVs for diagnostic and prognostic purposes. 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This study aims to investigate how these VOCs affect host cells at proteome level to better understand the mechanisms of disease. To achieve this, we first analyzed the (phospho)proteome changes of host cells infected with Alpha, Beta, Delta, and Omicron BA.1 and BA.5 variants over time frames extending from 1 to 36?h post infection. Our results revealed distinct temporal patterns of protein expression across the VOCs, with notable differences in the (phospho)proteome dynamics that suggest variant-specific adaptations. Specifically, we observed enhanced expression and activation of key components within crucial cellular pathways such as the RHO GTPase cycle, RNA splicing, and endoplasmic reticulum-associated degradation (ERAD)-related processes. We further utilized proximity biotinylation mass spectrometry (BioID-MS) to investigate how specific mutation of these VOCs influence viral?host protein interactions. Our comprehensive interactomics dataset uncovers distinct interaction profiles for each variant, illustrating how specific mutations can change viral protein functionality. Overall, our extensive analysis provides a detailed proteomic profile of host cells for each variant, offering valuable insights into how specific mutations may influence viral protein functionality and impact therapeutic target identification. These insights are crucial for the potential use and design of new antiviral substances, aiming to enhance the efficacy of treatments against evolving SARS-CoV-2 variants.","fileCount":"4728","fileSizeKB":"45899094","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Trichuris sp. ex Chlorocebus sabaeus JP-2011 (NCBITaxon:1035822)","instrument":"timsTOF Pro 2","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"virus, proteomics, variant, SARS-CoV-2;DatasetType:Proteomics","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2320a6b7cb6041e6b38910919a3c702d","id":"1626"}, {"dataset":"MSV000096338","datasetNum":"96338","title":"Phosphoproteomic analysis of legumain deficient mice","user":"tsever","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731055034000","created":"Nov. 8, 2024, 12:37 AM","description":"Asparagine endopeptidase (AEP), a cysteine proteinase found in plants and animals, plays a crucial role in regulating kidney homeostasis, immune response, and bone remodelling. It is dysregulated in cancer and neurodegenerative diseases. A study analysing protein phosphorylation in legumain knock-out mice revealed YBX1 phosphorylation on serine 102 as a key site, activating the NF-kB pathway and enhancing inflammation response in the kidney. The study also identified potential novel legumain substrates, providing insights into its role in cellular processes.","fileCount":"2843","fileSizeKB":"246672811","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"LTQ Velos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Legumain, mouse, phosphorylation, proteomics;DatasetType:Proteomics","pi":[{"name":"Marko Fonovic","email":"marko.fonovic@ijs.si","institution":"Jozef Stefan Institute","country":"Slovenia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057650","task":"9d752089b8a643fbbedd75dd9e896dfc","id":"1627"}, {"dataset":"MSV000096332","datasetNum":"96332","title":"Protein correlation of Mus musculus tissues","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731014253000","created":"Nov. 7, 2024, 1:17 PM","description":"SILAC based protein correlation profiling using size exclusion of protein complexes derived from Mus musculus tissues (Heart, Liver, Lung, Kidney, Skeletal Muscle, Thymus)","fileCount":"469","fileSizeKB":"1911076899","spectra":"5886638","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive;Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mouse;Silam;Lcmsms;DatasetType:Proteomics","pi":[{"name":"Leonard J. Foster","email":"foster@msl.ubc.ca","institution":"Michael Smith Laboratories, Biochemistry and Molecular Biology, University of British Columbia, Canada","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD022309","task":"f56e9a61eca2421fb3f322c2583f014a","id":"1628"}, {"dataset":"MSV000096331","datasetNum":"96331","title":"Protein correlation of Mus musculus tissues","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1731013764000","created":"Nov. 7, 2024, 1:09 PM","description":"SILAC based protein correlation profiling using size exclusion of protein complexes derived from seven Mus musculus tissues (Heart, Brain, Liver, Lung, Kidney, Skeletal Muscle, Thymus)","fileCount":"769","fileSizeKB":"1532758058","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Interactomes;Silac;Pcp;Interactions;DatasetType:Proteomics","pi":[{"name":"Leonard Foster","email":"foster@chibi.ubc.ca","institution":"Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia,Canada, V6T 1Z4 ( lab head )","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD007288","task":"d43fafc086dc46a196935662a7af22d3","id":"1629"}, {"dataset":"MSV000096330","datasetNum":"96330","title":"TurboID proximity labeling for EFNB1 in steady state (no stimulation) and under EPHB3 stimulation (+EPHB3)","user":"BissonLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730998204000","created":"Nov. 7, 2024, 8:50 AM","description":"TurboID proximity labeling of EFNB1 in steady state (EFNB1+HEK) and under EPHB3 stimulation (EFNB1+EPHB3). Sample identification as follows: \nEFNB1+HEK: NB1335 (R1), NB1453 (R2) and NB1490 (R3).\nEFNB1+EPHB3: NB1336 (R1), NB1454 (R2) and NB1491 (R3).\nYFP+HEK: NB1339 (R1), NB1457 (R2) and NB1494 (R3). \nYFP+EPHB3: NB1340 (R1), NB1458 (R2) and NB1495 (R3).\n","fileCount":"75","fileSizeKB":"25486544","spectra":"0","psms":"472765","peptides":"231061","variants":"277433","proteins":"68899","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"EFNB1, EGFR, TurboID;DatasetType:Proteomics","pi":[{"name":"Nicolas Bisson","email":"Nick.Bisson@crchudequebec.ulaval.ca","institution":"Universite Laval","country":"Canada"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD057627","task":"a4d07b7fc0304e7a98c3cdf6b0d4de21","id":"1630"}, {"dataset":"MSV000096329","datasetNum":"96329","title":"Nanobody-thioesterase chimeras to specifically target protein palmitoylation","user":"SheonMary","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730997943000","created":"Nov. 7, 2024, 8:45 AM","description":"Global (TMT) proteome and palmitoylated (LFQ) proteome after expression of APT2-LAMA-G97. The detailed methodology and results are available in the manuscript Nanobody-thioesterase chimeras to specifically target protein palmitoylation","fileCount":"30","fileSizeKB":"14272965","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"TMT10plex;LFQ;Palmitoylated proteome;ATP2 overexpression;HEK293;DatasetType:Proteomics","pi":[{"name":"Sheon Samji","email":"Sheon.Samji@glasgow.ac.uk","institution":"University of Glasgow","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057626","task":"2792de29284748a3b3b3397623f6a85d","id":"1631"}, {"dataset":"MSV000096328","datasetNum":"96328","title":"GNPS - Taxodiverse plant extract collection","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730993540000","created":"Nov. 7, 2024, 7:32 AM","description":"UHPLC-PDA-CAD-HRMS\/MS data of a collection of 182 natural extracts (Methanol and Ethyl acetate) in pos and neg ionization modes","fileCount":"1266","fileSizeKB":"12167686","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"natural products;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"d290bd1783f14ec0943d211e6d8549f1","id":"1632"}, {"dataset":"MSV000096327","datasetNum":"96327","title":"Ovarian cancer metastasis to the human omentum disrupts organ homeostasis and induces fundamental tissue reprogramming","user":"Sandra","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730990182000","created":"Nov. 7, 2024, 6:36 AM","description":"The omentum, a visceral adipose tissue with critical metabolic, immunological, and stem cell functions is the preferred site for ovarian cancer metastasis. However, its role in maintaining homeostasis and its responses to metastatic colonization remain incompletely understood. Using single-cell transcriptomics, we profiled different anatomical regions of the omentum in patients with benign conditions and ovarian cancer metastasis. We cataloged the benign omentum and found stable cell type composition and preservation of a stem and progenitor niche. Upon metastatic colonization, the immune landscape diversified accompanied by a gradual loss of mesothelial and progenitor cells. The lesser omentum, which is not routinely removed during surgical debulking, was identified as a premetastatic niche characterized by neutrophil infiltration, NETosis, and the presence of micrometastases. At established metastatic sites, resident cells exhibited cancer-associated phenotypes with regulatory, anti-adipogenic, and immunosuppressive functions. Cancer cells orchestrated the cell reprogramming via a repertoire of signaling factors affecting both proximal and distal omental tissue. This cell atlas illuminates the cellular and molecular determinants of organ homeostasis and reveals a high degree of plasticity and cellular reprogramming promoted by cancer colonization. \r\n","fileCount":"661","fileSizeKB":"2957141648","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Omentum, visceral adipose tissue, ovarian cancer, metastasis, tumor microenvironment, tissue reprogramming, premetastatic niche, adipose stem and progenitor cells, mesothelial cells, cell-cell interactions, single-cell RNA sequencing;DatasetType:Proteomics","pi":[{"name":"Sandra Goetze","email":"sgoetze@ethz.ch","institution":"ETHZ","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4e2f1efaea2e42ad91b21850f5a8b490","id":"1633"}, {"dataset":"MSV000096326","datasetNum":"96326","title":"GNPS - Combretaceae Familly plants extract collection ","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730988201000","created":"Nov. 7, 2024, 6:03 AM","description":"UHPLC-PDA-CAD-HRMS\/MS data (pos and neg) of a collection of 38 plant species of the botanical family Combretaceae. Several plant parts are included for each species and each was extracted with ethyl acetate and then methanol. both extracts were analysed.","fileCount":"482","fileSizeKB":"17747135","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Combretaceae;Natural products;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"965823a9d268416f8563065ce9e0a5a3","id":"1634"}, {"dataset":"MSV000096324","datasetNum":"96324","title":"Enhancing the bothropic antivenom through a reverse antivenomics approach","user":"aktashima","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730976100000","created":"Nov. 7, 2024, 2:41 AM","description":"Antivenoms are the only effective treatment for snakebite envenomation and have saved countless lives over more than a century. Despite its value, antivenoms often present risks of adverse reactions. Current formulations contain a substantial fraction of non-specific antibodies and serum proteins that do not neutralize venom toxins. While new alternatives are being researched and promising candidates emerge as the next generation of antivenoms, it remains clear that animal-derived antivenoms will still play a critical role for years to come. And current antivenom formulations could still be optimized for safety and efficacy. In this study, we used a reverse antivenomics approach to improve the bothropic antivenom (BAv), capturing toxin-specific antibodies through affinity chromatography using Bothrops jararaca venom toxins immobilized on CNBr-activated resin. This process produced an improved antivenom formulation (iBAv) enriched in neutralizing antibodies and depleted of serum protein contaminants. Proteomic analysis showed that iBAv was 87% depleted in albumin and 37-83% lower in other serum proteins compared to the original BAv. Functional assessments demonstrated that iBAv had a 2.9-fold higher affinity for B. jararaca venom toxins via surface plasmon resonance and a 2.8-fold lower ED50 in vivo in a mice model, indicating enhanced potency and efficacy. Our findings suggest that enriching specific neutralizing antibodies while depleting serum proteins may reduce the overall protein dose required and potentially decrease the risk of adverse reactions. Although technical and economic considerations remain for large-scale implementation, this affinity-enriched antivenom formulation represents a significant advancement in enhancing antivenom efficacy against Bothrops jararaca envenomations.","fileCount":"8","fileSizeKB":"5466052","spectra":"0","psms":"3176","peptides":"417","variants":"454","proteins":"52","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Equus caballus (NCBITaxon:9796)","instrument":"impact II","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"antivenom;reverse antivenomics;affinity chromatography;DatasetType:Proteomics","pi":[{"name":"Alexandre Keiji Tashima","email":"aktashima@unifesp.br","institution":"Escola Paulista de Medicina\/UNIFESP","country":"Brasil"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057613","task":"784bb70064bc4bb4884f8a402f77df6f","id":"1635"}, {"dataset":"MSV000096322","datasetNum":"96322","title":"Baculoviral IAP repeat-containing protein 6 Ubiquitinates KRAS4A","user":"Trixi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730937990000","created":"Nov. 6, 2024, 4:06 PM","description":"Transcripts of the KRAS locus are alternatively spliced to generate two proteins, KRAS4A and KRAS4B, that differ in their membrane targeting sequences. These splice variants have been conserved for more than 450 million years, suggesting non-overlapping functions driven by differential membrane association. Here we use proximity labeling to map the differential interactomes of the KRAS splice variants. We found 24 and 10 proteins that interact specifically with KRAS4A or KRAS4B, respectively. The KRAS interacting protein most specific to KRAS4A was BIRC6, a large member of the inhibitor of apoptosis protein family unique in possessing E2\/E3 ubiquitin ligase activity. We found that this interaction takes place on the Golgi apparatus and results in the mono- and di-ubiquitination of KRAS4A at lysines 128 and 147. Silencing BIRC6 diminished GTP-loading of and growth stimulation by KRAS4A but not KRAS4B. Thus, BIRC6 is a ubiquitin ligase that inhibits apoptosis and also modifies KRAS4A.\nThe mass spectrometry files for figures 1D, 1E, S1B, S1C, Supplemental figure 4A are included here. \n","fileCount":"209","fileSizeKB":"12372952","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;Orbitrap Eclipse;timsTOF HT","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"KRAS4A;proximity labeling;BIRC6;DatasetType:Proteomics","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"NYU Langone Grossman School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057589","task":"f4e40f2c96474c99a2417ab88347ade0","id":"1636"}, {"dataset":"MSV000096320","datasetNum":"96320","title":"Mass Spectrometry-Based Proteomics of Extracellular Vesicle Proteins (EVPs)","user":"NathanDuda","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730920822000","created":"Nov. 6, 2024, 11:20 AM","description":"For proteomic analysis, isolated EVPs were subjected to mass spectrometry (MS). Briefly, proteins were extracted from EVP pellets, and concentrations were measured using the Pierce MicroBCA kit. Each sample underwent processing with 20 micrograms of protein, first reduced with DTT, then alkylated with iodoacetamide, and finally digested with trypsin in 25 mM NH4HCO3. The resulting tryptic peptides were cleaned using a C18 column and reconstituted in 25 microliters of 0.1% formic acid; 12 microliters of this solution was analyzed by LC-MS\/MS over a 110-minute run.","fileCount":"26","fileSizeKB":"10693943","spectra":"412398","psms":"83140","peptides":"6656","variants":"10714","proteins":"1510","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LC\\\/MS\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"trophoblast stem cell secretome;extracellular vesicles and particles;exosomes;senescence;aging;DatasetType:Proteomics","pi":[{"name":"Kotb Abdelmohsen","email":"abdelmohsenk@mail.nih.gov","institution":"Staff Scientist","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057583","task":"ed6ac0d47492466799f85cf8673b6e03","id":"1637"}, {"dataset":"MSV000096319","datasetNum":"96319","title":"Self-organizing human heart organoids with an autologous tissue-resident macrophage immune niche","user":"shakhlo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730918741000","created":"Nov. 6, 2024, 10:45 AM","description":"Mascot parameters for all databases were as follows: \nAllow up to 2 missed tryptic sites \nFixed modification of Carbamidomethyl Cysteine, \nVariable modification of Oxidation of Methionine, \nPeptide tolerance of \/- 10ppm \nMS\/MS tolerance of 0.02 Da \nFDR calculated using randomized database search ","fileCount":"15","fileSizeKB":"1097178","spectra":"0","psms":"4407","peptides":"1135","variants":"1367","proteins":"391","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human Heart Organoid;Monocyte;DatasetType:Proteomics","pi":[{"name":"Aitor Aguirre","email":"aaguirre@msu.edu","institution":"Michigan State University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057582","task":"0e3e3801a51240c08767bf075823133c","id":"1638"}, {"dataset":"MSV000096318","datasetNum":"96318","title":"The E3 ligase HECTD4 regulates COX-2 dependent tumor progression and metastasis","user":"sambhavi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730917335000","created":"Nov. 6, 2024, 10:22 AM","description":"Dataset 1\r\nProteomics:\r\nThis quantitative proteomics experiment aimed to characterize changes in global protein expression in order to identify HECTD4 substrates. For this, HECTD4-KD (n=3) and scrambled control MDA-MB-231 (n=3) cells were cultured in vitro under anchorage-independent conditions in ultra-low adherent plates for 3 days. The cells were treated with proteasome (MG132) and lysosome inhibitors (Bafilomycin-1, BafA1) for 6 hours and collected for proteomic analysis. Multiplexed mass spectrometry-based proteomics was performed using TMTpro barcoding reagents (PMID-33900084) and the SPS-MS3 method on an Orbitrap Lumos mass spectrometer. Prior to mass spectrometry analysis, the TMT set was fractionated offline by basic pH reversed-phase chromatography (bRPLC) into 24 fractions.\r\n\r\nSamples were labeled as follows\r\n129c -Control_R1\r\n130n - Control_R2\r\n130c - Control_R3\r\n131n - HECTD4 KD_R1\r\n131c - HECTD4 KD_R2\r\n132n - HECTD4 KD_R3\r\n\r\nDataset 2\r\nDiGly Proteomics:\r\nThis quantitative proteomics experiment aimed to characterize changes in protein ubiquitination in order to identify HECTD4 substrates. For this, HECTD4-KD (n=3) and scrambled control MDA-MB-231 (n=3) cells were cultured in vitro under anchorage-independent conditions in ultra-low adherent plates for 3 days. The cells were treated with proteasome (MG132) and lysosome inhibitors (Bafilomycine-1, BAF1) for 6 hours and collected for proteomic analysis. The Di-Gly peptides were enriched by co-immunoprecipitation of K-GG-modified peptides according to the manufacturers instructions (Cell Signaling PTMScan, Cat 59322). Multiplexed mass-spectrometry-based proteomics was performed using TMTpro barcoding reagents (PMID-33900084) using a high-resolution MS2 data-dependent acquisition method on an Orbitrap Lumos mass spectrometer. Before mass spectrometry analysis, the peptides were fractionated into seven fractions using Pierce High pH Reversed-Phase Peptide Fractionation Kit (Thermo Scientific Cat 84868) according to the manufacturers instructions. The six fractions were each used once, and one was used twice for the mass spectrometry analysis.\r\nSamples were labeled as follows\r\n129c -Control_R1\r\n130n - Control_R2\r\n130c - Control_R3\r\n131n - HECTD4 KD_R1\r\n131c - HECTD4 KD_R2\r\n132n - HECTD4 KD_R3\r\n","fileCount":"66","fileSizeKB":"43376893","spectra":"4302115","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"304.207146 Lysine, N-Terminus static;57.021464, Cysteine,(IAA) Static;15.9949146221 (oxidation) Methionine,Variable;114.042927 Lysine, Variable","keywords":"HECTD4;COX2;E3 ligase;SPS MS3;Di-Gly Mapping;TMT18;DatasetType:Proteomics","pi":[{"name":"Daniel Haber","email":"dhaber@mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center and Harvard Medical School","country":"US"},{"name":"Shyamala Maheswaran","email":"maheswaran@helix.mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center and Harvard Medical School Boston","country":"USA"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f81aa41beecf49449fde32827fd6ea70","id":"1639"}, {"dataset":"MSV000096317","datasetNum":"96317","title":"GNPS - Quantifying the ecophysiology of growing microbes responding to warming along a productivity gradient of the Marr Ice Piedmont Glacier, West Antarctic Peninsula","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730914196000","created":"Nov. 6, 2024, 9:29 AM","description":"Our overarching goal is to understand how microbes along a glacier forefield chronosequence and productivity gradient interact with their environment, how this influences carbon and nitrogen cycling, and how the microbes respond to temperature increases. Specifically, using the novel approach of quantitative SIP paired with metagenomic sequencing, we will calculate growth rates for targeted functional genes and metagenome assembled genomes, quantifying their ecophysiology, in situ. And when paired with gene expression using metatranscriptomic libraries and metabolite production, we will gain a clearer understanding of how microbes grow, how they cycle carbon and nitrogen and how their metabolic activity changes in response to warming.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008115) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"739","fileSizeKB":"57339776","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"glacier microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"glacier;warming;carbon cycling;nitrogen cycling;DatasetType:Metabolomics","pi":[{"name":"Alicia Purcell","email":"amp753@nau.edu","institution":"Northern Arizona University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6b48c9c4dfdb47c5801ba3f075993a99","id":"1640"}, {"dataset":"MSV000096316","datasetNum":"96316","title":"GNPS - Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730914180000","created":"Nov. 6, 2024, 9:29 AM","description":"Rice paddies contribute substantially to atmospheric methane (CH4) and these emissions are expected to increase as the need to feed the human populationgrows. Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduced cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over the growth period compared with controls. Genome-resolved metatranscriptomic data from rhizosphere soils reveal lower ratios of gene activities for CH4 production versus consumption, decrease in activity of H2-producing genes, and increase in bacterial H2 oxidation pathways in the PSY genotypes. Metabolic modeling using metagenomic and metabolomic data predicts elevated levels of H2 oxidation and suppressed H2 production in the PSY rhizosphere. The H2- oxidizing bacteria have more genes for utilization of gluconeogenic acids than H2- producing counterparts, and their activities were likely stimulated by the observed enrichment of gluconeogenic acids (mostly amino acids) in PSY root exudates. Together these results suggest that decreased CH4 emission is due to the reduction of H2 available for hydrogenotrophic methanogenesis. The combination of rice phenotypic characterization, microbiome multi-omic analysis, and metabolic modeling described here provides a powerful strategy to discover the mechanisms by which specific plant genotypes can alter biogeochemical cycles to reduce CH4 emissions.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008481) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"371","fileSizeKB":"28894079","spectra":"678772","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Oryza sativa ssp. Japonica cultivar Kitaake","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"rice;roots;root exudates;DatasetType:Metabolomics","pi":[{"name":"Pam Ronald","email":"pcronald@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3349af8926624635af24c6b01babebd1","id":"1641"}, {"dataset":"MSV000096315","datasetNum":"96315","title":"GNPS - Temperature Effects on Metabolite-Mediated Autotroph-Heterotroph Carbon Transfer","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730914164000","created":"Nov. 6, 2024, 9:29 AM","description":"Much of the bacterial secondary production in the aquatic ecosystems is supported by rapid uptake of labile metabolites released from phytoplankton, either directly through excretion and diffusion or indirectly through lysis and predation. This project seeks to investigate the effects of temperature stress on the metabolite pools produced and released by three model phytoplankton species (a diatom, a coccolithophore, and a cyanobacterium) that will assess changes in the composition and fate of metabolites transferredto bacteria. While focused on estuarine microbes, findings of this project will be broadly relevant to temperature effects on microbial autotrophic-heterotrophic metabolite transfer in freshwater, marine, and soil ecosystems.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001361) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"526","fileSizeKB":"34535729","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Thalassiosira pseudonana\\tCCMP1335; Synechococcus sp.\\tWH8102; Emiliania huxleyi RCC1258","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"temperature stress;metabolite transfer;DatasetType:Metabolomics","pi":[{"name":"Mary Ann Moran","email":"mmoran@uga.edu","institution":"University of Georgia","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"203e5eed6a9946a5b01cd418618f3465","id":"1642"}, {"dataset":"MSV000096314","datasetNum":"96314","title":"GNPS - Nitrate in coastal waters: shifting the balance from carbon sink to carbon source","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730914111000","created":"Nov. 6, 2024, 9:28 AM","description":"Different salt marsh habitats, which are dominated by different plant species, will havedistinct metabolomic profiles that are driven by phyto-compounds released as plantexudates. However, within a given habitat, NO3 - will alter the metabolomic profile such thatthere will be a decrease in the most labile metabolites compared to reference marshes.Rates of decomposition depend on both the availability of a powerful electron acceptor anda supply of labile carbon that can be oxidized. In salt marshes that carbon is largelygenerated by primary production from halophytic plants, which have distinct zonationpatterns based on elevation above mean high water. The root exudates from these plants fuelmicrobial metabolism when there is a sufficient supply of electron acceptors present, but ourpreliminary metabolomic data suggest that different marsh habitats generate different plantexudates, which could largely explain why we see distinct microbial communitieswithin different marsh habitats. However, with our preliminary metabolomics datawe do not have enough samples to determine whether, within a given habitat, there is a shiftin the metabolic profile of the plant-microbe association that results from nutrientenrichment.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001192) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"343","fileSizeKB":"25316664","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"salt marsh;nitrogen enrichment;DatasetType:Metabolomics","pi":[{"name":"Jennifer Bowen","email":"je.bowen@northeastern.edu","institution":"Northeastern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"545f68a5898744379819f2ab2a945a4e","id":"1643"}, {"dataset":"MSV000096313","datasetNum":"96313","title":"GNPS - Botryllus_schlosseri_multiomics ","user":"balunaslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730910717000","created":"Nov. 6, 2024, 8:31 AM","description":"Environmental samples of dissected Botryllus schlosseri colonies collected on Avery Point, Connecticut, during spring 2023\r\nSeawater samples collected at the marina on Avery Point, Connecticut, during spring 2023.","fileCount":"1278","fileSizeKB":"9338522","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Botryllus schlosseri (NCBITaxon:30301)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"multiomics, metabolomics, microbiome, metallome;DatasetType:Metabolomics","pi":[{"name":"Marcy J. Balunas","email":"mbalunas@umich.edu","institution":"University of Michigan","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6b6b031e177043cfbbbc5546bf0ccc8d","id":"1644"}, {"dataset":"MSV000096310","datasetNum":"96310","title":"Multifaceted Mechanisms Underlying the Efficacy of a Postbiotic and its Components in Promoting Colonic Transit and Alleviating Chronic Constipation in Humans and Mice","user":"18447054019","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730899821000","created":"Nov. 6, 2024, 5:30 AM","description":"Non-targeted metabolome analysis of stool in patients with constipation.","fileCount":"1653","fileSizeKB":"54793090","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;constipation;clinical trial;DatasetType:Metabolomics","pi":[{"name":"teng ma ","email":"18447054019@163.com","institution":"Inner Mongolia Agricultural University","country":"china"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e86110fccb834bfb92de1ae23d7395c8","id":"1645"}, {"dataset":"MSV000096305","datasetNum":"96305","title":"GNPS - Fe-Nanoparticle for enrichment of Siderophore; washes, eluate, sup","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730869126000","created":"Nov. 5, 2024, 8:58 PM","description":"Iron nanoparticles are effective in enriching siderophore from complex microbiome","fileCount":"47","fileSizeKB":"812121","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"pseudomonas","instrument":"QExactive LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"siderophore;nanoparticle;DatasetType:Other (method development)","pi":[{"name":"Allegra Aron","email":"allegra.aron@du.edu","institution":"University of Denver","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8d95657f0bbd4e138aea23e73a649f49","id":"1646"}, {"dataset":"MSV000096304","datasetNum":"96304","title":"Affinity purification mass spectrometry on the Orbitrap-Astral mass spectrometer enables high-throughput protein-protein interaction mapping ","user":"liaserrano","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730856691000","created":"Nov. 5, 2024, 5:31 PM","description":" \tClassical proteomics experiments offer high-throughput protein quantification but lack direct evidence of the spatial organization of the proteome, including protein\u2013protein interaction networks. While Affinity Purification Mass Spectrometry (AP-MS) is the method of choice for generating these networks, technological impediments have stymied the throughput of AP-MS sample collection, and therefore constrained the rate and scale of experiments that can be performed. Here, we build on advances in mass spectrometry hardware that have rendered high-flow liquid chromatography separations a viable solution for faster-throughput quantitative proteomics. We describe our methodology using the Orbitrap Astral mass spectrometer with 7-minute, high-flow separations to analyze 216 AP-MS samples in ~29 hours. We show that the ion focusing advancements, rapid mass analysis, and sensitive ion detection facilitate narrow-bin data-independent acquisition on a chromatographically practical timescale. Further, we highlight several aspects of state-of-the-art confidence scoring software that warrant re-investigation given the analytical characteristics of the Orbitrap-Astral mass spectrometer through comparisons with an enrichment-based thresholding technique. With our data, we generated an interaction map between 998 human proteins and 59 viral proteins. These results hold promise in expediting the throughput of AP-MS experiments, enabling more high-powered protein\u2013protein interaction studies. ","fileCount":"222","fileSizeKB":"303545726","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Vaccinia virus (NCBITaxon:10245)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"protein-protein interactions;affinity purification-mass spectrometry;DatasetType:Proteomics","pi":[{"name":"Danielle Swaney","email":"danielle.swaney@gladstone.ucsf.edu","institution":"UCSF","country":"United States"},{"name":"Joshua J. Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"ed5dff95333241b29e9ed2b0e40be990","id":"1647"}, {"dataset":"MSV000096303","datasetNum":"96303","title":"Human coronavirus-229E infection alters the structure of host RNA processing complexes","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730848397000","created":"Nov. 5, 2024, 3:13 PM","description":"The purpose of this experiment was to evaluate the human host cellular response to wild-type human coronavirus strain 229E (HCoV-229E)(ncbitaxon:11137) infection. Sample data was obtained for mock and infected (MOI 3) immortalized human lung epithelial cells (A549), immortalized human lung fibroblasts cells (MRC5), and primary human airway epithelial cells from lung tissue, and processed for proteome expression analysis using Limited Proteolysis (LiP) methods for Tandem Mass Tag 16-Plex (TMT16) and global proteomic measurements. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and data was processed and compiled using MaxQuant software (v1.6.17.0).","fileCount":"197","fileSizeKB":"153844930","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"host-pathogen interactions;human coronavirus 229E (HCoV-229E);limited proteolysis-based mass spectrometry (LiP-MS);protein structural changes;therapeutic targets;viral infections;DatasetType:Proteomics","pi":[{"name":"John T. Melchior","email":"john.melchior@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD057552","task":"45c5a095ff2b44afb3b5ad764b9514d7","id":"1648"}, {"dataset":"MSV000096301","datasetNum":"96301","title":"Lacouture_mammary_glands_organoids","user":"LambertLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730842848000","created":"Nov. 5, 2024, 1:40 PM","description":"This submission contains the mass spectrometry files for the manuscript by Aurelie Lacouture et al. that describes the quantitative proteomics analysis of mammary glands organoids proteome. Experiments were performed from mammary glands organoids derived from mouse and the MS files were acquired on Orbitrap Fusion mass spectrometer. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca).","fileCount":"17","fileSizeKB":"14527040","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"mammaray gland organoids;DatasetType:Proteomics","pi":[{"name":"Jean-Philippe Lambert","email":"jean-philippe.lambert@crchudequebec.ulaval.ca","institution":"Universite Laval","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5bb3ccb7162d4cf8bf9785b0f5a57790","id":"1649"}, {"dataset":"MSV000096300","datasetNum":"96300","title":"Phosphorylation sites identified in human PPARg2 AF-1 domain in vitro phosphorylated by ERK2","user":"G_Tsaprailis","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730838222000","created":"Nov. 5, 2024, 12:23 PM","description":"The focus of the study was to identify phosphorylation sites in human PPARg2 AF-1 domain","fileCount":"13","fileSizeKB":"3586328","spectra":"90928","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion ETD","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"DatasetType:Proteomics;PPARg2;nuclear receptor;tsanscription factor","pi":[{"name":"Douglas Kojetin","email":"douglas.kojetin@Vanderbilt.Edu","institution":"Vanderbilt University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057549","task":"95cb42f834b648fca6051065968ceb35","id":"1650"}, {"dataset":"MSV000096297","datasetNum":"96297","title":"GNPS - Lipidomics Dataset for Isolated LetAB Protein","user":"michaelmarty","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730824502000","created":"Nov. 5, 2024, 8:35 AM","description":"Lipidomics analysis of E. coli LetAB protein purified in detergent with co-isolated lipids. Control samples include a positive control of the starting E. coli membrane prior to purification and a negative control of the detergent buffer. Experiments were performed with DDA on each replicate sample to identify the pool of possible lipids. Quantitation was performed using MS1 accurate mass and retention time mapping, with three technical replicates for each of the three biological replicates. ","fileCount":"777","fileSizeKB":"42894908","spectra":"13877","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Synapt XS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"Michael Marty","email":"mtmarty@arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"82aec434eb9241fbac2c849d87cbaeb8","id":"1651"}, {"dataset":"MSV000096296","datasetNum":"96296","title":"A methyltransferase-independent role for METTL1 in tRNA aminoacylation and oncogenic transformation","user":"Martolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730824112000","created":"Nov. 5, 2024, 8:28 AM","description":"Data supporting the manuscript: A methyltransferase-independent role for METTL1 in tRNA aminoacylation and oncogenic transformation","fileCount":"661","fileSizeKB":"128776228","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"mass spectrometry;DIA-PASEF;timsTOF;DatasetType:Proteomics","pi":[{"name":"Jarrod A Marto","email":"jarrod_marto@dfci.harvard.edu","institution":"Dana-Farber Cancer Institute","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9d17bcf8eb494fc099b8ef59dc2684f2","id":"1652"}, {"dataset":"MSV000096295","datasetNum":"96295","title":"Small molecule-induced alterations of protein polyubiquitination revealed by mass-spectrometric ubiquitome analysis","user":"janning","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730821988000","created":"Nov. 5, 2024, 7:53 AM","description":"Mammalian cells were treated with different small molecules which interfere with the ubiquitin system. After cell lysis, ubiquitinated proteins were enriched with biotin-tagged TUBE, digested with Trypsin\/LysC and labelled with TMT. 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Acquisition was conducted in both ionization modes, resulting in a total of 4 individual datasets. mzmine batches were supplemented as well as the utilized custom lipid classes. Unzip MS2 files before processing. ","fileCount":"3158","fileSizeKB":"5032425","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-TIMS-MS;MALDI-TIMS-MS;SIMSEF;Lipid A;DatasetType:Metabolomics","pi":[{"name":"Ansgar Korf","email":"ansgar.korf@mzio.io","institution":"mzio GmbH","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c6730fd0fa244b73a2477b968ce75b29","id":"1654"}, {"dataset":"MSV000096292","datasetNum":"96292","title":"Mitochondrial ribosomal RNA is the target of functionally dominant hotspot mutations in cancer","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730805880000","created":"Nov. 5, 2024, 3:24 AM","description":"The vast majority of recurrent somatic mutations arising in tumors affect protein-coding genes in the nuclear genome. Here, through population-scale analysis of 14,079 whole tumor genomes, we report the discovery of highly recurrent mutations affecting both the small (12S, MT-RNR1) and large (16S, MT-RNR2) RNA subunits of the mitochondrial ribosome. Compared to non-hotspot positions, mitochondrial rRNA hotspots preferentially affected positions participating in Watson-Crick base pairing and tended to arise at positions under strong purifying selection in the germline. Using precision mtDNA base editing, we engineered models of an exemplar MT-RNR1 hotspot mutation, m.1227G>A. Multimodal profiling revealed a heteroplasmy-dependent decrease in mitochondrial function and loss of respiratory chain subunits from a heteroplasmic dosage of ~10%, which were corroborated with single cell profiling of mtDNA heteroplasmy and gene expression. Mutation of evolutionarily conserved and germline constrained positions in ribosomal RNA that disrupt mitochondrial translation therefore represent a novel class of functionally dominant, pathogenic mtDNA mutations that are under positive selection in cancer genomes.","fileCount":"74","fileSizeKB":"7531669","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MITOCHONDRIAL RIBOSOMAL RNA;HOTSPOT MUTATION;CANCER;HETEROPLASMY;MT-RNR1;m.1227G>A;DatasetType:Metabolomics","pi":[{"name":"David Sumpton","email":"d.sumpton@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Jacqueline Tait-Mulder","email":"j.tait-mulder@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Payam Gammage","email":"payam.gammage@glasgow.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6092e888d60046748562b38be3ca2e20","id":"1655"}, {"dataset":"MSV000096291","datasetNum":"96291","title":"GNPS-Ion_mobility_bile_acid_fragmentation_paper_dataset","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730768074000","created":"Nov. 4, 2024, 4:54 PM","description":"MS\/MS fragmentation data of bile acids acquired on timsTOF pro2 - with\r\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"6978","fileSizeKB":"34878523","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No species","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acid;Fragmentation;ion mobility;DatasetType:Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a9da614e256546b3a63c469dd7965dac","id":"1656"}, {"dataset":"MSV000096290","datasetNum":"96290","title":"GNPS - Rattlesnakes Venom Bacterial Cultures GNPS","user":"kambriah246","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730760901000","created":"Nov. 4, 2024, 2:55 PM","description":"Non-targeted analysis of bacterial isolates from snake venom ","fileCount":"39","fileSizeKB":"2054690","spectra":"36612","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crotalus atrox (NCBITaxon:8730)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Venom;Rattlesnake;Symbiont;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California, Riverside","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d4cda0890aa24e3793794a3500bcf1cf","id":"1657"}, {"dataset":"MSV000096287","datasetNum":"96287","title":"GNPS - Sourdough Culture Non-targeted Analysis GNPS","user":"kambriah246","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730748389000","created":"Nov. 4, 2024, 11:26 AM","description":"Positive mode, non-targeted analysis of sourdough crude extracts and cultured isolates. ","fileCount":"143","fileSizeKB":"12839974","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lactobacillus (NCBITaxon:1578)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sourdough;LB;Practical;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California, Riverside","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"64c7a106548441188c5a09da0f3f6c92","id":"1658"}, {"dataset":"MSV000096286","datasetNum":"96286","title":"GNPS - Metabolic regulation of feeding affinity behavior through GLP-1-like signaling","user":"LangDing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730747787000","created":"Nov. 4, 2024, 11:16 AM","description":"Metabolic regulation of feeding affinity behavior through GLP-1-like signaling","fileCount":"21","fileSizeKB":"16824129","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics;c elegans;LC-MS;GLP-1;DatasetType:Other (Lipidomics)","pi":[{"name":"Keith Blackwell","email":"keith.blackwell@joslin.harvard.edu","institution":"Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"867697b5eb1f4f58b64086def83a2ee8","id":"1659"}, {"dataset":"MSV000096284","datasetNum":"96284","title":"GNPS - Guy_H-Mannheim laboratory 2024","user":"Samy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730721645000","created":"Nov. 4, 2024, 4:00 AM","description":"LC-MS laboratory study of 3 forest fruits from Cameroon","fileCount":"147","fileSizeKB":"1013150","spectra":"19920","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichoscypha acuminata (NCBITaxon:289776);Coula edulis (NCBITaxon:397382);Myrianthus arboreus (NCBITaxon:1781621)","instrument":"LTQ Orbitrap XL","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Food plant;H-Mannheim Laboratory;DatasetType:Metabolomics","pi":[{"name":"Ebede guy roland","email":"samyebede@gmail.com","institution":"University of Yaounde 1","country":"Cameroon"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7234b39425a3447fa594bc67e140f0ac","id":"1660"}, {"dataset":"MSV000096283","datasetNum":"96283","title":"LC-MS\/MS data of Tinospora cordifolia","user":"tsk_prasad","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730716678000","created":"Nov. 4, 2024, 2:37 AM","description":"Tinospora cordifolia has been used for thousands of years to treat various health conditions, including neurodegenerative diseases. The study aimed to elucidate the mechanism of action and protein targets of T. cordifolia in the context of Alzheimers disease through untargeted metabolomics and network pharmacology. LC-MS\/MS analysis resulted in 1186 metabolites, including known bioactive compounds such as liquiritin, Plastoquinone 3, and Shoyuflavone A, to name a few. The network pharmacology analysis highlighted the metabolite-protein interaction with the enrichment of 591 human proteins, including neurotransmitter receptors and other regulatory proteins. Pathway analysis highlighted the enrichment of cAMP, mTOR, MAPK, and PI3K-Akt signaling pathways along with cholinergic, dopaminergic, serotonergic, glutamatergic synapse, and apoptosis. The docking results suggest that T. cordifolia metabolites could interact with key Alzheimer's disease targets BACE1 and MAO-B, suggesting its role in neuroprotection. These findings provide insights into the biochemical pathways underlying T. cordifolia's therapeutic effects and provides a foundation for future exploration of T. cordifolia in the context of translational research. ","fileCount":"18","fileSizeKB":"279607","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Tinospora cordifolia (NCBITaxon:285590)","instrument":"QTRAP 6500","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Medhya rasayana;Neuroprotection;Alzheimer's disease;network pharmacology;metabolomics;Therapeutic targets;DatasetType:Metabolomics","pi":[{"name":"Dr. Prashant Modi","email":"prashantmodi21@gmail.com","institution":"Yenepoya (Deemed to be University)","country":"India"},{"name":"Dr. T. S. Keshava Prasad","email":"tskprasad@gmail.com","institution":"Yenepoya (Deemed to be University)","country":"India "}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"153ee42745524ea5809596f410c102f0","id":"1661"}, {"dataset":"MSV000096282","datasetNum":"96282","title":"Serum N-glycomics with nanoLC-QToF LC-MS\/MS reveals N-glycan biomarkers for glioblastoma, meningioma, and high-grade meningioma","user":"mrussalv","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730699630000","created":"Nov. 3, 2024, 9:53 PM","description":"Alteration of glycosylation in cancer cells leaded to the expression of tumor-associated glycans that could be used as a biomarker for diagnosis and prognostic prediction of the diseases. In this study, we used nanoLC-QToF LC-MS\/MS for the identification of serum N-glycan biomarkers for detection of brain tumors. We identified the increase of sialylated N-glycans and decrease of fucosylated N-glycans in serum of patients with glioblastoma (GBM) and meningioma (MG) compared with healthy persons. ","fileCount":"5310","fileSizeKB":"52844090","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6520A Quadrupole Time-of-Flight LC\\\/MS","modification":"N-glycans","keywords":"N-glycan;Biomarker;Brain tumor;Cancer;Glycosylation;DatasetType:Metabolomics","pi":[{"name":"Carlito B. Lebrilla","email":"cblebrilla@ucdavis.edu","institution":"University of California, Davis","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"3188c3b633004dfbb5d1780c9b17d08a","id":"1662"}, {"dataset":"MSV000096281","datasetNum":"96281","title":"Social Network Architecture of Human Immune Cells Unveiled by Quantitative Proteomics","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730684165000","created":"Nov. 3, 2024, 5:36 PM","description":"The immune system is unique in its dynamic interplay between numerous cell types. However, a system-wide view of how immune cells communicate to protect against disease has not been established. Here, we applied high-resolution mass spectrometry-based proteomics to generate a publicly accessible protein atlas of 28 primary human immune cell populations in steady and activated states at a depth of > 10,000 proteins. Cell-type-specific protein copy numbers reveal that immune cells are most specialized at the level of ligands and receptors, thereby connecting distinct functions of the immune system. By integrating total and secreted proteomes, we deduce paracrine immune dynamics upon microbial encounter and discover fundamental intercellular communication structures as well as novel connections between cellular senders and receivers of biological information. Our comprehensive cell-type-resolved proteomic resource of human immune cells provides a framework for the orchestration of cellular interplay and a reference for altered communication associated with pathology.","fileCount":"710","fileSizeKB":"1263155902","spectra":"13775647","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"Mass spectrometry;Systems immunology;Human immune cells;Proteomics;Intercellular communication;DatasetType:Proteomics","pi":[{"name":"Matthias Mann","email":"mmann@biochem.mpg.de","institution":"Max Planck Institute of Biochemistry Department of Proteomics and Signaltransduction Am Klopferspitz 18 D-82152 Martinsried\/Munich","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD004352","task":"fee2fbebf19e41ea84616097b024859b","id":"1663"}, {"dataset":"MSV000096280","datasetNum":"96280","title":"DIA analysis if of X. laevis egg extracts","user":"LevyLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730663023000","created":"Nov. 3, 2024, 11:43 AM","description":"Mass spectrometry DIA analysis of MG132 treated Xenopus laevis egg extracts and compared with control (untreated) extracts to identify changes in protein levels upon MG132 treatment.","fileCount":"11","fileSizeKB":"10148301","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xenopus laevis (NCBITaxon:8355)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Xenopus;DatasetType:Other (Raw data)","pi":[{"name":"Daniel L Levy","email":"dlevy1@uwyo.edu","institution":"University of Wyoming","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9ca522f4f7634880a40112295229ead0","id":"1664"}, {"dataset":"MSV000096278","datasetNum":"96278","title":"Identification of a damaging variant rs35033974 associated with idiopathic male infertility through degradation of TEX101 protein and its transient interactome","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730538711000","created":"Nov. 2, 2024, 2:11 AM","description":"Human TEX101 is a testis-specific cell membrane protein expressed exclusively in male germ cells and a validated biomarker of male infertility. TEX101 was suggested to function as a cell surface chaperone of numerous proteins involved in sperm migration and sperm-egg interaction. However, the precise functional roles of human TEX101 in spermatogenesis and fertilization are unknown. Here, we show that a common homozygous variant rs35033974 of TEX101 (G99V) with ~1% frequency in the general population may be associated with idiopathic male infertility. Spermatozoa from patients with homozygous rs35033974 exhibited near-complete degradation of variant G99V TEX101 protein and concomitant degradation of its interactome, as revealed by proteomic measurements. Substantially reduced levels of numerous testis-specific membrane proteins involved in sperm migration and sperm-oocyte fusion (including LY6K, IZUMO3 and ADAM29) were confirmed in spermatozoa of men with homozygous G99V variant. These men were previously diagnosed with idiopathic male infertility or oligospermia and failed the treatment by intrauterine insemination. Collectively, these data may facilitate diagnostics of idiopathic male infertility, provides a rational for selection of male infertility treatments and validate TEX101 and its interactome as targets to develop non-hormonal male contraceptives.","fileCount":"447","fileSizeKB":"357203160","spectra":"6647451","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\";MOD:00400 - \\\"A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and loss of a nitrogen and a hydrogen.\\\"","keywords":"A disintegrin and metalloproteinase domain-containing protein 29;interactome;testis-specific proteins;spermatozoa;single nucleotide polymorphism (snp);deleterious variant;unexplained infertility;Tex101;testis-expressed sequence 101 protein;ly6k;lymphocyte antigen 6 complex;Locus k;adam29;DatasetType:Proteomics","pi":[{"name":"Dr. Eleftherios P. Diamandis","email":"eleftherios.diamandis@sinaihealthsystem.ca","institution":"Head of Clinical Biochemistry Mount Sinai Hospital and University Health Network, Professor & Head, Division of Clinical Biochemistry Department of Laboratory Medicine & Pathobiology, University of Toronto","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD008333","task":"3504ba48820b4703a7b0c1f65f3e1255","id":"1665"}, {"dataset":"MSV000096277","datasetNum":"96277","title":"Alternative Polyadenylation is Essential for Tissue Homeostasis by Safeguarding Nuclear Pore Integrity","user":"ericzaniewski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730499292000","created":"Nov. 1, 2024, 3:14 PM","description":"Dataset1:\r\nIn vitro cultured stem cells of the esophageal epithelium (basal cells).\r\nThis experiment aimed to characterize changes in global protein expression during differentiation of esophageal basal cells that express different levels of Nudt21. For this, conditional Nudt21 KO or hypomorphic Nudt21 esophageal basal cells were treated for four days with ETOH (control), 4OHT (Nudt21 KO) or 4OHT+Dox (hypomorph) under self-renewing conditions. On the fourth day calcium was added to induce differentiation. Cells were collected 6 days post calcium exposure and subjected to proteomic analysis (n=3 biol. replicates per condition). Proteome mapping was performed using multiplexed quantitative proteomics with TMTpro reagents (PMID: 33900084) on a Orbitrap Lumos mass spectrometer using an SPS-MS3 method. Prior to mass spectrometry analysis the TMTset was fractionated off-line by basic pH reversed-phase chromatography (bRPLC) into 16 fractions.\r\n\r\nSamples were labeled as follows:\r\n131N - Control_1_Diff\r\n131C - Control_2_Diff\r\n132N - Control_3_Diff\r\n132C - KO_1_Diff\r\n133N - KO_2_Diff\r\n133C - KO_3_Diff\r\n134N - Hypomorph_1_Diff\r\n134C - Hypomorph_2_Diff\r\n135N - Hypomorph_3_Diff\r\n\r\nDataset 2:\r\nIn vitro cultured stem cells of the esophageal epithelium (basal cells).\r\nThis experiment aimed to characterize changes in global protein expression during self-renewal of esophageal basal cells that express different levels of Nudt21.For this, conditional Nudt21 KO or hypomorphic Nudt21 esophageal basal cells were treated for a total of six days with ETOH (control), 4OHT (Nudt21 KO) or 4OHT+Dox (hypomorph) under self-renewing conditions. Cells were collected at day0 (control) day2 (KO), day 4 (KO and hypomorph) and day6 (KO and hypomorph). and subjected to proteomic analysis (n=3 biol. replicates per condition and timepoints). The analysis was performed as described for dataset 1 - 14 bRPLC were analyzed.\r\n\r\nSamples were labeled as follows:\r\n126 - Control_d0_1\r\n127N - Control_d0_2\r\n127C - Control_d0_3\r\n128N - KO_d2_1\r\n128C - KO_d2_2\r\n129N - KO_d2_3\r\n129C - KO_d4_1\r\n130N - KO_d4_2\r\n130C - KO_d4_3\r\n131N - KO_d6_1\r\n131C - KO_d6_2\r\n132N - KO_d6_3\r\n132C - Hypo_d4_1\r\n133N - Hypo_d4_2\r\n133C - Hypo_d4_3\r\n134N - Hypo_d6_1\r\n134C - Hypo_d6_2\r\n135N - Hypo_d6_3\r\n\r\n\r\n\r\n","fileCount":"31","fileSizeKB":"13246139","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"304.207146 (TMTpro16\\\/18), lysine, N-terminus, static;15.9949146221 (oxidation), methionine, variable;57.02146374 (IAA), cysteine, static","keywords":"TMTpro;Orbitrap;Lumos;SPS-MS3;Nudt21;Stem Cells;DatasetType:Proteomics","pi":[{"name":"Konrad Hochedlinger","email":"hochedlinger@molbio.mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ba2081df1ea54bcbaa03627b00cac3e7","id":"1666"}, {"dataset":"MSV000096276","datasetNum":"96276","title":"Data files for manuscript \"Lactate homeostasis is maintained through regulation of glycolysis and lipolysis\"","user":"wdlee","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730492296000","created":"Nov. 1, 2024, 1:18 PM","description":"Data files for manuscript \"Lactate homeostasis is maintained through regulation of glycolysis and lipolysis\"","fileCount":"490","fileSizeKB":"26113784","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lactate;metabolomics;DatasetType:Metabolomics","pi":[{"name":"Joshua Rabinowitz","email":"joshr@exchange.Princeton.EDU","institution":"Princeton University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d5ace7bf899f4b28961f4f613beb49f6","id":"1667"}, {"dataset":"MSV000096275","datasetNum":"96275","title":"An improved synthesis of Compound 11, a unique bicyclic melanocortin-3 antagonist","user":"sjoy1984","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730491780000","created":"Nov. 1, 2024, 1:09 PM","description":"Mass spectra of a melanocortin-3 antagonist, the bicyclic compound 11 (Cpd11), it's dithiol monocyclic precursor compound 4, and a truncated version consisting only of the central thiadiazecane ring (7).","fileCount":"16","fileSizeKB":"79163","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"C57BL\\\/6J mice","instrument":"6230A Time-of-Flight LC\\\/MS","modification":"MOD:00034 - \\\"A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.\\\"","keywords":"melanocortin;appetite;cyclic peptide;Cpd11;agonist;DatasetType:Other (Peptide)","pi":[{"name":"Anna Mapp","email":"amapp@umich.edu","institution":"University of Michigan","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4533fcb2b82e43b9ba32c6d152b538cc","id":"1668"}, {"dataset":"MSV000096274","datasetNum":"96274","title":"Unrecognized bacterial catalyst for N2O reduction","user":"MeganEDavin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730482239000","created":"Nov. 1, 2024, 10:30 AM","description":"(Meta)proteomics analyses were performed with cells collected from the Sab enrichment culture grown with N2O. Growth of Desulfitobacterium sp. strain Sab5 only occurred when N2O was supplied as electron acceptor, and biomass from cultures grown without N2O was not included in the analysis. Comparative proteomics analyses were performed with axenic Sporomusa acidovorans DSM3132 T cells grown with and without N2O.","fileCount":"16","fileSizeKB":"8105995","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sporomusa acidovorans (NCBITaxon:112900);metagenome (NCBITaxon:256318)","instrument":"Q Exactive Plus","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";MOD:00058 - \\\"A protein modification that effectively converts an L-methionine to N-acetyl-L-methionine.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\"","keywords":"Metaproteomics;N2O;Sporomusa acidovorans;Desulfitobacterium sp. strain Sab5;DatasetType:Proteomics","pi":[{"name":"Frank E. Loffler","email":"frank.loeffler@utk.edu","institution":"University of Tennessee-Knoxville","country":"United States of America"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD057435","task":"98782d7fda444aa0b39fddaa186ee958","id":"1669"}, {"dataset":"MSV000096272","datasetNum":"96272","title":"GNPS - Data for metabolome of K. viridogrisea and in-house micobial library","user":"xiaohuochayaya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730426490000","created":"Oct. 31, 2024, 7:01 PM","description":"Std files were used to generate Figure2. Kutzosmac files are used to generate Figure3.","fileCount":"47","fileSizeKB":"16107159","spectra":"65442","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Kutzneria viridogrisea (NCBITaxon:47990)","instrument":"X500R QTOF","modification":"Glycosylation","keywords":"Molecular networking and annotation;natural products;aromatic glucosides;self-detoxification;menaquinone pathway;DatasetType:Metabolomics","pi":[{"name":"Bin Wei","email":"binwei@zjut.edu.cn","institution":"Zhejiang University of Technology","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2d7601057c30471e9375a20e89eda336","id":"1670"}, {"dataset":"MSV000096271","datasetNum":"96271","title":"The HLA-Ligand-Atlas. A resource of natural HLA ligands presented on benign tissues","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730417697000","created":"Oct. 31, 2024, 4:34 PM","description":"The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system. T cells recognize these HLA-presented peptides as self or foreign and can elicit an immune response. In this work, we describe the HLA-Ligand-Atlas, a comprehensive map of HLA-I and HLA-II-presented peptides from 30 benign tissues, 51 HLA-I alleles, and 86 HLA-II alleles. Nearly 50% of HLA ligands have not been previously described. Due to the scarcity of benign human samples, the tissue was extracted from different organs at autopsy from human subjects without any diagnosed malignancy. Furthermore, we were able to identify non-canonical HLA-I peptides on benign tissues, showing that their processing is not unique to cancer. This dataset holds great promise in answering both basic and translational questions in fields such as autoimmunity, organ\/tissue transplantation, and cancer immunotherapy.","fileCount":"6367","fileSizeKB":"1816522835","spectra":"30039801","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human;Hla;Benign tissues;Immunopeptidomics;DatasetType:Proteomics","pi":[{"name":"Hans-Georg Rammensee","email":"hgrhgr2017@gmx.de","institution":"Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University T\uFFFDbingen","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD019643","task":"11590a58978b4268b33a0969eca1d749","id":"1671"}, {"dataset":"MSV000096270","datasetNum":"96270","title":"Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730414880000","created":"Oct. 31, 2024, 3:48 PM","description":"Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technological face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry (MS)-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph? Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, MS-based proteomics approach. We identify 184 protein-altering variants (PAVs) in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.","fileCount":"1987","fileSizeKB":"4044030896","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"MS:1003123","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Protein altering variants;Proteomics;Protein quantitative trait loci;Mass spectrometry;Genome-wide association studies;Proteograph? workflow;DatasetType:Proteomics","pi":[{"name":"Karsten Suhre","email":"kas2049@qatar-med.cornell.edu","institution":"Bioinformatics Core, Weill Cornell Medicine-Qatar","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD042852","task":"29ff0441bf544ede84ca2547adfdb839","id":"1672"}, {"dataset":"MSV000096268","datasetNum":"96268","title":"Human coronavirus-229E infection alters the structure of host RNA processing complexes","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730405039000","created":"Oct. 31, 2024, 1:03 PM","description":"The purpose of this experiment was to evaluate the human host cellular response to wild-type human coronavirus strain 229E (HCoV-229E)(ncbitaxon:11137) infection. Sample data was obtained for mock and infected (MOI 3) immortalized human lung epithelial cells (A549), immortalized human lung fibroblasts cells (MRC5), and primary human airway epithelial cells from lung tissue, and processed for proteome expression analysis using Limited Proteolysis (LiP) methods for Tandem Mass Tag 16-Plex (TMT16) and global proteomic measurements. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and data was processed and compiled using MaxQuant software (v1.6.17.0).","fileCount":"203","fileSizeKB":"160300683","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"host-pathogen interactions;human coronavirus 229E (HCoV-229E);limited proteolysis-based mass spectrometry (LiP-MS);protein structural changes;therapeutic targets;viral infections;DatasetType:Proteomics","pi":[{"name":"John T. Melchior","email":"john.melchior@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD057408","task":"d277175d307540e7b1660da603c50ae2","id":"1673"}, {"dataset":"MSV000096267","datasetNum":"96267","title":"GNPS - Fe-Nanoparticle for enrichment of Siderophore","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730401414000","created":"Oct. 31, 2024, 12:03 PM","description":"Fe Nanoparticle is an effective technique for enriching siderophores from complex microbiome","fileCount":"23","fileSizeKB":"375496","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas","instrument":"QExactive LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"siderophore;nanoparticle;DatasetType:Other (method development)","pi":[{"name":"Allegra Aron","email":"allegra.aron@du.edu","institution":"University of Denver","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d7b9e26375884be2a1cdafb9e020760d","id":"1674"}, {"dataset":"MSV000096266","datasetNum":"96266","title":"GNPS - Fe-Nanoparticle for enrichment of Siderophore","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730398020000","created":"Oct. 31, 2024, 11:07 AM","description":"Fe Nanoparticle serves as an effective technique for the enrichment of siderophores from pseudomonas","fileCount":"23","fileSizeKB":"375496","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas (NCBITaxon:286)","instrument":"QExactive LCMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"FeNanoparticle;Siderophore;DatasetType:Metabolomics;DatasetType:Other (method development)","pi":[{"name":"Allegra Aron","email":"allegra.aron@du.edu","institution":"University of Denver","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c9e7b46d2c364573b913924052136dc9","id":"1675"}, {"dataset":"MSV000096264","datasetNum":"96264","title":"Self-priming of Plk1 binding to BubR1 ensures accurate mitotic progression","user":"Arminja","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730386123000","created":"Oct. 31, 2024, 7:48 AM","description":"\tPlk1 is a key mitotic kinase that localizes to distinct subcellular structures to promote accurate mitotic progression. Plk1 recruitment depends on direct interaction between polo-box domain (PBD) on Plk1 and PBD binding motif (PBD BM) on the interactors. However, recent study showed that PBD BM alone is not enough for stable binding between CENP-U and Plk1 highlighting the complexity of the interaction which warrants further investigation. An important interactor for Plk1 during mitosis is the checkpoint protein BubR1. Plk1 bound to BubR1 via PBD interaction with pT620 phosphorylates BubR1 S676\/T680 to promote BubR1-PP2A\/B56 interaction. The BubR1-PP2A\/B56 complex counteracts the destablizing effect on kinetochore-microtubule attachments by mitotic kinases to promote mitotic progression.\nHere we show that Plk1 phosphorylates T600\/T608 on BubR1 and the double phosphorylation is critical for BubR1-Plk1 interaction. A similar mechanism for Plk1-Bub1 interaction also exists indicating a general principle for Plk1 kinetochore recruitment through self-priming. Mechanistically preventing BubR1 T600\/T608 phosphorylation impairs chromosome congression and checkpoint silencing by reducing Plk1 and PP2A\/B56 binding to BubR1. Increasing the binding affinity towards Plk1 and PP2A\/B56 in BubR1 through protein engineering bypasses the requirement of T600\/T608 phosphorylation for mitotic progression. These results reveal a new layer of regulation for accurate mitotic progression.","fileCount":"42","fileSizeKB":"2911306","spectra":"0","psms":"52349","peptides":"24058","variants":"25333","proteins":"8120","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Mitosis, BubR1, Plk1;DatasetType:Proteomics","pi":[{"name":"Arminja Kettenbach","email":"Arminja.N.Kettenbach@Dartmouth.edu","institution":"Dartmouth College","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057400","task":"fb7951e2cb2c4715b66627738fcdeb39","id":"1676"}, {"dataset":"MSV000096263","datasetNum":"96263","title":"GNPS - HEATSTAR: Metabolomics of human sweat under different stress conditions","user":"aothman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730379165000","created":"Oct. 31, 2024, 5:52 AM","description":"Metabolomics of sweat samples under different stress conditions","fileCount":"533","fileSizeKB":"28140122","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Heat Stress, Sweat Metabolomics;DatasetType:Metabolomics","pi":[{"name":"No\uFFFD Brasier","email":"noekarl.brasier@hest.ethz.ch","institution":"Institute for Translational Medicine, ETH Zurich","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f5d500daef124d21947f0e196735349e","id":"1677"}, {"dataset":"MSV000096261","datasetNum":"96261","title":"GNPS-fenziwangluo-xiaoxue-neg-20241031","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730362400000","created":"Oct. 31, 2024, 1:13 AM","description":"high resolution mass spectrometry Chemical composition characterization","fileCount":"4","fileSizeKB":"237205","spectra":"10492","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"plant","instrument":"high-resolution mass spectrometer","modification":"No PTMs included in the dataset","keywords":"plant;DatasetType:Metabolomics","pi":[{"name":"Li Yu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7f61d44cfafb4d5bac9c469780da41c6","id":"1678"}, {"dataset":"MSV000096259","datasetNum":"96259","title":"The microbiome promotes mitochondrial respiration in a mouse model of PD","user":"Baiyi_Quan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730324066000","created":"Oct. 30, 2024, 2:34 PM","description":"Mitochondrial proteome for alpha-synuclein overexpressing (ASO) mice and wild-type mice. ","fileCount":"65","fileSizeKB":"49888646","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Mitochondrial;Proteomics;Label-free Quantitation;Parkinson's Disease;DatasetType:Proteomics","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD057375","task":"8de01bdc884f4db28ccf8b320491eb52","id":"1679"}, {"dataset":"MSV000096258","datasetNum":"96258","title":"A conserved cysteine-to-serine modification in insulin generates neoepitope-specific CD4 T-cell responses in diabetic autoimmunity","user":"cflichti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730322404000","created":"Oct. 30, 2024, 2:06 PM","description":"We identified a T1D-relevant insulin neoantigen in which C19 of the insulin B chain is converted to serine. This neoantigen is conserved between human and mouse and is recognized by a specific, more highly activated T cell population. We demonstrated that this conversion happens at the protein level as a result of oxidative stress. ","fileCount":"196","fileSizeKB":"108064179","spectra":"0","psms":"533037","peptides":"44567","variants":"68944","proteins":"4389","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:345 - \\\"Cysteine oxidation to cysteic acid.\\\";UNIMOD:548 - \\\"Cys->Ser substitution.\\\"","keywords":"type 1 diabetes, NOD mouse, human, MHC-II peptidome, oxidative stress, crinosomes;DatasetType:Proteomics","pi":[{"name":"Cheryl Lichti","email":"clichti@wustl.edu","institution":"Washington University in St. Louis","country":"United States"},{"name":"Xiaoxiao Wan","email":"wanx@wustl.edu","institution":"Washington University in St. Louis","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD057371","task":"921b975b415b4d6aa9f6d200cc787bc3","id":"1680"}, {"dataset":"MSV000096256","datasetNum":"96256","title":"Proteomic characterization of a foraminiferal test organic matrix","user":"haiyanzheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730321559000","created":"Oct. 30, 2024, 1:52 PM","description":"Foraminifera are unicellular protists capable of precipitating calcite tests, which fossilize and preserve geochemical signatures of past environmental conditions dating back to the Cambrian period. The biomineralization mechanisms responsible for the mineral structures, which are key to interpreting palaeoceanographic signals, are poorly understood. Here, we have performed an extensive analysis of the test-bound proteins. Using liquid chromatography-tandem mass spectrometry, we identify 373 test-bound proteins in the large benthic foraminifer Amphistegina lobifera, the majority of which were highly acidic and rich in negatively charged residues. We have detection of proteins involved in vesicle formation and active Ca2+ trafficking, but in contrast, did not find similar proteins involved in Mg2+ transport. Considering findings from this study and previous ones, we propose a dual ion transport model involving seawater vacuolization, followed by the active release of Ca2+ from the initial vacuoles and subsequent uptake into newly formed Ca-rich vesicles that consequently enrich the calcification fluid. We further speculate that Mg2+ passively leaks through the membrane from the remaining Mg-rich vesicles, into the calcifying fluid at much lower concentrations than in seawater. This hypothesis could not only explain the low Mg\/Ca ratio in foraminiferal tests compared to inorganic calcite but could possibly also account for its elevated sensitivity to temperature compared with inorganically precipitated CaCO3.","fileCount":"7","fileSizeKB":"2743622","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Amphistegina lobifera","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"biomineralization;foraminifera;test;proteome;DatasetType:Proteomics","pi":[{"name":"Paul Falkowski","email":"falko@marine.rutgers.edu","institution":"Rutgers University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5c23a026b032499a9947c8a6fa3f86fa","id":"1681"}, {"dataset":"MSV000096255","datasetNum":"96255","title":"Development of subunit-selective proteasome substrates for Schistosoma species by MSP-MS","user":"elanybs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1730321535000","created":"Oct. 30, 2024, 1:52 PM","description":"Development of optimized subunit-specific substrates for S. mansoni proteasome (Sm20S) based on data generated by Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS). 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Here, quantitative proteomics and cryo-electron microscopy\ndemonstrated that poxvirus infection does not alter ribosomal subunit protein (RP)\ncomposition but skews 40S rotation states and displaces the 40S head domain.\nGenetic knockout screens employing metabolic assays and a dual-reporter virus\nfurther identified two RPs that selectively regulate non-canonical translation of late\npoxvirus mRNAs which contain unusual 5 polyA-leaders: RACK1 and RPLP2.\nRACK1 is a component of the altered 40S head domain while RPLP2 is a subunit of\nthe P-stalk, wherein RPLP0 anchors two heterodimers of RPLP1 and RPLP2 to the\nlarge 60S subunit. RPLP0 was required for global translation, yet RPLP1 was\ndispensable while RPLP2 was specifically required for non-canonical poxvirus\nprotein synthesis. Combined, we demonstrate that poxviruses structurally customize\nribosomes and become reliant upon traditionally non-essential RPs from both\nribosomal subunits for efficient initiation on their late mRNAs.","fileCount":"55","fileSizeKB":"36860652","spectra":"0","psms":"91012","peptides":"49422","variants":"59018","proteins":"14860","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Vaccinia virus Western Reserve (NCBITaxon:696871)","instrument":"Orbitrap Fusion","modification":"NA","keywords":"ribosome customization, P-stalk, RACK1;poxvirus;DatasetType:Proteomics","pi":[{"name":"Derek Walsh","email":"derek.walsh@northwestern.edu","institution":"Northwestern University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"f3653bfa10e442598b9a49fd641cea5d","id":"1698"}, {"dataset":"MSV000096222","datasetNum":"96222","title":"Toxoplasma gondii infection of neurons alters the production and content of extracellular vesicles contributing to the loss of GLT-1 in the infected brain ","user":"etaba004_ucr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729882285000","created":"Oct. 25, 2024, 11:51 AM","description":"Toxoplasma gondii (T. gondii) cyst formation in the central nervous system only occurs in neurons allowing the parasite to remain latent for the lifetime of the host. Astrocytes are fundamental to neuronal health by providing nutrients and structural support and help regulate neurotransmitters by continuous communication with neurons. It is not yet known how infection and the presence of intracellular cysts, disrupts the crucial relationship between these cells. Extracellular vesicles (EVs) function in intracellular communication and can contain proteins, lipids, DNA, miRNA, and other RNA subtypes. EVs are produced by all cells including neurons and play an important role in neuronal-astrocyte interactions including the regulation of glutamate receptors on astrocytes. Previous work has demonstrated Toxoplasma infection reduces astrocytic expression of the primary glutamate transporter, GLT-1. Here we tested if cyst infection of neurons alters the production and content of EVs. EVs were isolated from uninfected and infected primary murine cortical neurons and their size, concentration, and characterization were confirmed with nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), CD63 ELISA, liquid chromatography (LC)-mass spectrometry (MS)\/MS, and microRNA Sequencing. Analysis reveals that infection of neurons reduced neuronal production of EVs and altered their protein and miRNA content. EVs from infected neurons contained secreted Toxoplasma proteins GRA1, GRA2, GRA7, MAG1 and MAG2 associated with cyst formation. Following incubation of neuronal EVs with primary astrocytes, a proportion of EVs colocalize to the nucleus. EVs from infected neurons altered gene expression of astrocytes leading to a downregulation of GLT-1 protein expression and an increase in pro-inflammatory transcriptional signatures. These results demonstrate the ability of a parasitic infection in the brain to alter EV production and the fundamental communication between neurons and astrocytes. ","fileCount":"21","fileSizeKB":"4910545","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Tribrid (Thermo Scientific instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Extracellular vesicles, T. gondii, parasite, cyst, neuron, astrocyte, brain, GLT-1;DatasetType:Proteomics","pi":[{"name":"Emma Wilson","email":"emma.wilson@ucr.edu","institution":"University of California, Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057209","task":"481613a8b8a647e0af614a698b56e1d9","id":"1699"}, {"dataset":"MSV000096221","datasetNum":"96221","title":"GNPS Streptomyces Potent vs Inactive YSPaper01_NEG","user":"jaisi2020","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729882015000","created":"Oct. 25, 2024, 11:46 AM","description":"Methanolic extracts of ISP2 grown Thai actinobacteria sourced from eastern Thai mangrove environment. The extract was tested for Plasmodium falciphrum K1 pLDH assay and analyzed by LCMS QE negative mode","fileCount":"79","fileSizeKB":"4756116","spectra":"198521","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces (NCBITaxon:1883)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plasmodium;actinobacterium;DatasetType:Metabolomics","pi":[{"name":"Amit Jaisi","email":"amit.ja@wu.ac.th","institution":"Walailak University","country":"Thailand"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f7c1ac05f0f34cb0a869517f2d9e1d7b","id":"1700"}, {"dataset":"MSV000096220","datasetNum":"96220","title":"GNPS Streptomyces Potent vs Inactive YSPaper01_POS","user":"jaisi2020","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729880838000","created":"Oct. 25, 2024, 11:27 AM","description":"Methanolic extracts of ISP2 grown Thai actinobacteria sourced from eastern Thai mangrove environment. The extract was tested for Plasmodium falciphrum K1 pLDH assay and analyzed by LCMS QE positive mode","fileCount":"77","fileSizeKB":"4280241","spectra":"198901","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces (NCBITaxon:1883)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plasmodium;actinobacteria;DatasetType:Metabolomics","pi":[{"name":"Amit Jaisi","email":"amit.ja@wu.ac.th","institution":"Walailak University","country":"Thailand"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3e8e3f90adb44020b07d9854abbc47de","id":"1701"}, {"dataset":"MSV000096217","datasetNum":"96217","title":"Bos taurus alpha-casein phosphorylation identification","user":"Aaron_Schimmer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729866727000","created":"Oct. 25, 2024, 7:32 AM","description":"Identification of phosphorylation sites for commercial bos taurus alpha-casein and dephosphorylated alpha-casein.","fileCount":"12","fileSizeKB":"852695","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"alpha casein, phosphorylation;DatasetType:Proteomics","pi":[{"name":"Aaron Schimmer","email":"Aaron.Schimmer@uhn.ca","institution":"UHN, Princess Margaret Cancer Research Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057197","task":"ea75cc47d79d4c0b8408c0b738a781e0","id":"1702"}, {"dataset":"MSV000096215","datasetNum":"96215","title":"SenCat: Redefining human cell senescence through multiomic profiling of multiple senescent cell types","user":"nbasisty","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729863996000","created":"Oct. 25, 2024, 6:46 AM","description":"There is an urgent need to comprehensively catalog senescence markers across the wide range of cell types in an organism. Here, we profiled the transcriptomes and proteomes of over 30 models of senescence in 14 different primary human cell types. We found that senescent cells from all tissue types do not share a unique marker, but they do share broadly activated or repressed pathways, namely pathways of damage response to elicit tissue repair, and unique metabolic pathways. Importantly, the combined use of some of the most widely shared senescence markers validated the presence of senescent-like cells in mice through single-cell RNA-sequencing and immunostaining approaches. The enclosed catalog represents a much-needed resource to identify senescent cells across tissues in the body.","fileCount":"207","fileSizeKB":"220401636","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"senescence;data independent acquisition;DatasetType:Proteomics","pi":[{"name":"Nathan Basisty","email":"nathan.basisty@nih.gov","institution":"National Institute on Aging, NIH","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"31aea67413824106af9c21b7560c6b1c","id":"1703"}, {"dataset":"MSV000096214","datasetNum":"96214","title":"GNPS - Untargeted metabolomics in seeds of Arabidopsis wild-type, TT7 KO and other flavonoid mutants","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729860617000","created":"Oct. 25, 2024, 5:50 AM","description":"Seeds of Arabidopsis thaliana wild type and knockout-mutants for flavonoid genes (tt7 [3 lines], fls1, tt3, tt4, tt7tt4 [2 lines] ) were subjected to untargeted metabolomic analyses (LC-MS\/MS) in positive and negative ionisation mode.","fileCount":"215","fileSizeKB":"34155697","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Seeds;Specialized Metabolites;Untargeted Metabolomics;Flavonoids;DatasetType:Metabolomics","pi":[{"name":"Massimiliano Corso","email":"massimiliano.corso@inrae.fr","institution":"INRAE","country":"France"},{"name":"Sophie Jasinski","email":"sophie.jasinski@inrae.fr","institution":"INRAE","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c6c3b3acd05d46549ca2351ea6bb3e5a","id":"1704"}, {"dataset":"MSV000096212","datasetNum":"96212","title":"Neuropeptidomics of Holothuria scabra","user":"jaresoles","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729848245000","created":"Oct. 25, 2024, 2:24 AM","description":"Neuropeptidomics of the sea cucumber, Holothuria scabra. Peptides from the radial nerve cords of the H. scabra were extracted using a combination of ultrafiltration and acidified methanol-based precipitation.","fileCount":"459","fileSizeKB":"6393725","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Holothuria scabra (NCBITaxon:269548)","instrument":"Xevo G2-XS QTof","modification":"UNIMOD:2 - \\\"Amidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Neuropeptidomics;Neuropeptides;Sea cucumbers;Holothuria scabra;DatasetType:Other (Peptidomics)","pi":[{"name":"Eizadora T. Yu, Ph. D.","email":"etyu@up.edu.ph","institution":"The Marine Science Institute, University of the Philippines, Diliman","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057188","task":"bfd130506fa14c6e955341fbc2b4c9a2","id":"1705"}, {"dataset":"MSV000096209","datasetNum":"96209","title":"The effect of interferons on presentation of defective ribosome products as HLA peptides","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729840239000","created":"Oct. 25, 2024, 12:10 AM","description":"The class I major histocompatibility complex (MHC) bound peptides, produced from immature proteins that are degraded rapidly are called defective ribosome products (DRiPs). Such DRiPs are possibly involved with early alerting of the immune system about impeding infections, thus bringing about faster killing of infected cells before the viruses replicate. Interferons are a major group of cytokines, produced in response to viral infection. The interferons modulate the cellular metabolism and gene expression patterns and increase the expression and cell-surface presentation of the MHC molecules, helping this way coping with the viral infection. In this study, we evaluated whether the interferons also induce rapid degradation of cellular or viral proteins and produce DRiPs MHC-bound peptides to help the alert of the immune system. Cultured human breast cancer cells were treated with interferons and the cells were transferred to growth media containing heavy stable isotope labeled amino acids (dynamic-SILAC)in several time points a few hours after the interferons\u2019 treatment. The rates of synthesis, degradation, and production of the cellular protein and their degradation products, the MHC peptides, were followed by LC-MS\/MS analyses. Detection of large numbers of MHC peptides that incorporate the heavy amino acids into them, faster than their source proteins, indicated to us that not only DRiP-peptides are rather abundant among the MHC peptidome, but that the interferons increase significantly the presentation of DRiP-peptides. Importantly, much of this DRiPome derive from multi-subunit complexes, including the proteasomes and ribosomes, while the degradation of the standard protostome give rise to the immunoproteasome, which is thought to produce peptides that enhance the immune-response; the degradation of the ribosome subunits may aid in reducing the synthesis of viral infection","fileCount":"386","fileSizeKB":"592556301","spectra":"11460107","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Hla peptides;Mhc;Ifns;Drips;DatasetType:Proteomics","pi":[{"name":"Arie Admon","email":"admon@technion.ac.il","institution":"Faculty of Biology, Technion-Israel Institute of Technology","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD022633","task":"f56c19e23b064f12a7933a8fcc60f066","id":"1706"}, {"dataset":"MSV000096207","datasetNum":"96207","title":"Neuropeptidomics of Stichopus cf. horrens","user":"jaresoles","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729835607000","created":"Oct. 24, 2024, 10:53 PM","description":"Neuropeptidomics of the sea cucumber, Stichopus cf. horrens. Peptides from the radial nerve cords of the S. cf. horrens were extracted using a combination of ultrafiltration and acidified methanol-based precipitation. ","fileCount":"357","fileSizeKB":"4661584","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Stichopus cf. horrens","instrument":"Xevo G2-XS QTof","modification":"UNIMOD:2 - \\\"Amidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Neuropeptidomics;Sea cucumber;Stichopus cf. horrens;DatasetType:Other (Peptidomics)","pi":[{"name":"Eizadora T. Yu, Ph. D.","email":"etyu@up.edu.ph","institution":"The Marine Science Institute, University of the Philippines, Diliman","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD057178","task":"c4c3aa82549c49b8850fcf96fac6f01c","id":"1707"}, {"dataset":"MSV000096205","datasetNum":"96205","title":"Activity-Targeted SIP-Metaproteomics of a Full-Scale Biogas Facility ","user":"skylerbio","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729818401000","created":"Oct. 24, 2024, 6:06 PM","description":"In this work, two BONCAT enrichment techniques were evaluated against a conventional untargeted metaproteomics approach for their ability to enrich the SIP signal of SAOB in metaproteomics data from an anaerobic microbiome. The first BONCAT enrichment was based on sorting active cells using fluorescent activated cell sorting (FACS) prior to protein extraction for mass spectrometry. The second BONCAT technique involved protein extraction from bulk biomass followed by purification of newly-translated proteins using click chemistry and a biotin-streptavidin bead pulldown assay prior to preparation for mass spectrometry. We found that both of these techniques improved detection of a highly-active and low-abundance syntrophic bacterium that was responsible for significant acetate turnover within the study full-scale biogas facility. The BONCAT-SIP approaches described here therefore represent a powerful toolbox for unraveling the contributions of active microorganisms to microbial communities--a facet of microbial ecology that holds great potential for improving our comprehension of the untapped metabolic potentials contained within microbiomes.\nMass spectra data were processed using quantms v1.3.1 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects and tools from OpenMS v3.2.0. The workflow was executed with Nextflow v24.04.4. Both 12C-acetate (non-SIP) and 13C-acetate (SIP) samples from all metaproteomic methods were treated identically for peptide identification. Mass spectra were searched against the metagenome-derived protein database using both MSGF+ v2021.03.22 and Comet v2023.01. A target-decoy competition strategy was employed to estimate the rate of false positive peptide-spectrum matches (PSMs). Mass tolerances were set to 5 ppm for precursor (peptide) ions and 0.03 Da for fragment ions. Up to two missed cleavages were allowed and peptide termini were required to match the tryptic cleavage conditions fully. The precursor charge was limited to 2-4 and the peptide length was limited to 6-40. The PSMs were then rescored using Percolator v3.05.0. The two search engine results were combined by retaining only the peptide sequence with the highest E-value for each spectrum and the consensus list of PSMs was filtered with a false discovery rate (FDR) threshold of 10% to reduce decoy and false positive matches.\nQuantification of peptides was performed on the 12C-acetate (non-SIP) samples using the OpenMS tool, proteomicsLFQ. Peptide intensities were scaled such that the median peptide intensity in every sample was equal. The peptides are then evaluated for uniqueness and used for protein inference. The quantification results were filtered with a protein FDR of 1% and a PSM FDR of 1%.\nDetection of isotopically labeled peptides in the labeled condition (13C-acetate) was performed using MetaProSIP v2.3.0 as implemented in OpenMS v2.8.0 in a KNIME Analytics Platform v4.6.3 workflow. The unlabeled condition (12C-acetate) paired samples were used to identify coeluting isotopologues in the labeled condition (13C-acetate).","fileCount":"476","fileSizeKB":"127444858","spectra":"0","psms":"554325","peptides":"118049","variants":"122741","proteins":"90719","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"anaerobic digester metagenome (NCBITaxon:1263854)","instrument":"Q Exactive HF-X;Q Exactive Plus;Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"anaerobic digestion;bioorthogonal noncanonical amino acid tagging;boncat;proteinSIP;stable isotope probing;metaproteomics;DatasetType:Proteomics","pi":[{"name":"Ryan Ziels","email":"ziels@mail.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"true","quant_analysis":"Quantification Results;Study Design","status":"Complete","private":"false","hash":"","px":"PXD057167","task":"40b1cef39d4a4d1fb71f49f941b6ef64","id":"1708"}, {"dataset":"MSV000096204","datasetNum":"96204","title":"GNPS - Discovery of Noninvasive Biomarkers for Radiation Exposure via LC-MS-based Hair Metabolomics","user":"zhang13665","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729811014000","created":"Oct. 24, 2024, 4:03 PM","description":"Ionizing radiation exposure from a potential nuclear energy plant leak or detonation of a nuclear weapon can cause massive casualties to both warfighters and civilians. Biomarkers in biological specimens like blood and tissue, such as RNA, proteins, and metabolites, have shown potential to determine radiation dose levels. However, these biomarkers in blood and urine are short-lived, typically detectable only within hours or a few days. To address the need for stable, long-term radiation exposure biomarkers, we developed two LC-MS-based methods using non-invasive hair samples to identify radiation-induced biomarkers. ","fileCount":"2165","fileSizeKB":"42632084","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hair metabolomics;DatasetType:Metabolomics","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"The Ohio State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8eaf8b711e6843fda0701065c6736596","id":"1709"}, {"dataset":"MSV000096203","datasetNum":"96203","title":"GNPS - Mechanism of action of the toxic proline mimic azetidine 2-carboxylic acid in plants","user":"tnqp624","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729808826000","created":"Oct. 24, 2024, 3:27 PM","description":"Plants have an amazing capacity to outcompete neighboring organisms for space and resources. Toxic metabolites are major players in these interactions, which can have a broad range of effectiveness by targeting conserved molecular mechanisms, such as protein biosynthesis. However, lack of knowledge about defensive metabolite pathways, their modes of action, and resistance mechanisms limits our ability to manipulate these pathways for enhanced crop resilience. Nonproteogenic amino acids (NPAAs) are a structurally diverse class of metabolites with a variety of functions but are typically not incorporated during protein biosynthesis. Here, we investigate the mechanism of action of the NPAA azetidine-2-carboxylic acid (Aze), an analog of the amino acid proline (Pro). Using a combination of plate-based assays, metabolite feeding, metabolomics, and proteomics, we show that Aze inhibits the root growth of Arabidopsis and other plants. Aze-induced growth reduction was restored by supplementing L-, but not D-Pro, and non-targeted proteomics confirms that Aze is misincorporated for Pro during protein biosynthesis, specifically on cytosolically translated proteins. qRT-PCR analysis, free amino acid profiling, and proteomics show that the unfolded protein response is upregulated during Aze treatment implicating that Aze misincorporation results in accumulation of misfolded proteins triggering a global stress response. This study demonstrates the mechanism of action of Aze in plants and provides a foundation for understanding the biological functions of proteotoxic metabolites.","fileCount":"40","fileSizeKB":"14743304","spectra":"0","psms":"684642","peptides":"60013","variants":"84131","proteins":"9836","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Aze, Proline conversion,Arabidopsis, NPAAs;DatasetType:Proteomics","pi":[{"name":"Schenck, Craig","email":"caschenck@missouri.edu","institution":"University of Missouri","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057164","task":"94026361558b4d7aad1dee5daaab4a5c","id":"1710"}, {"dataset":"MSV000096202","datasetNum":"96202","title":"Fast proteomics with dia-PASEF and analytical flow-rate chromatography\n","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729807037000","created":"Oct. 24, 2024, 2:57 PM","description":"The presented approach is a combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and raw data processing using the DIA-NN software suite, to conduct fast, low-cost proteomic experiments that only require moderate sample amounts. The present dataset contains a series of benchmarks. Specifically, a dilution series of a K562 digest standard acquired using 5-minute and 3-minute chromatographic gradients, as well as a mixed-species human\u2013E.coli benchmark for quantitative performance. We further demonstrate the application of the proposed approach to the analysis of plasma proteomes of COVID-19 patients, using a 3-minute gradient acquisition on a dual-column liquid chromatography system at a throughput of 398 samples\/day.\n","fileCount":"20","fileSizeKB":"113123970","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Short gradient;Dia-pasef;Timstof;Fast methods;Plasma proteomics;High-throughput;Covid-19;DatasetType:Proteomics","pi":[{"name":"prof. Markus Ralser","email":"markus.ralser@charite.de","institution":"1)Department of Biochemistry, Charit\uFFFD \uFFFD Universit\uFFFDtsmedizin Berlin, Berlin, Germany. 2)The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK 3)Max Planck Institute for Molecular Genetics, Berlin, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD040205","task":"657d5179d0e94f7389a81cd56a93fce3","id":"1711"}, {"dataset":"MSV000096201","datasetNum":"96201","title":"YME1L1 Degrades Mitochondria Protein Import Complex TIMM17A and TIMM23 Subunits and Protects Cells upon Import Plugging","user":"linlin0727","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729805974000","created":"Oct. 24, 2024, 2:39 PM","description":"Mitochondrial protein import through the outer and inner membranes is key to mitochondrial biogenesis. Recent studies have explored how cells respond when import is impaired by a variety of different insults. Here, we developed a mammalian import blocking system using dihydrofolate reductase (DHFR) fused to the N-terminus of the inner membrane protein MIC60. While stabilization of the DHFR domain by methotrexate inhibited endogenous mitochondrial protein import, it neither activated the transcription factor ATF4, nor was affected by ATAD1 expression or by VCP\/p97 inhibition. On the other hand, surprisingly, plugging the channel of translocase of the outer membrane (TOM) induced YME1L1, an ATP-dependent protease, to eliminate translocase of the inner membrane (TIM23) channel components TIMM17A and TIMM23. The data suggest that unoccupied TIM23 complexes expose a C-terminal degron on TIMM17A to YME1L1 for degradation. Import plugging caused a cell growth defect and loss of YME1L1 exacerbated the growth inhibition, showing the protective effect of YME1L1 activity. YME1L1 appears to play a crucial role in mitochondrial quality control to counteract precursor stalling in the TOM complex and unoccupied TIM23 channels.\n","fileCount":"45","fileSizeKB":"38990984","spectra":"0","psms":"306060","peptides":"38300","variants":"75065","proteins":"3903","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human","instrument":"UltiMate 3000 RSLCnano system (Thermofisher) coupled with Orbitrap Fusion Lumos Mass Spectrometer (Thermofisher)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"YME1L1, mitochondria import, TIMM17A, TIMM23;DatasetType:Proteomics","pi":[{"name":"Koji Yamano","email":"kojibiom@tmd.ac.jp","institution":"Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University","country":"Japan"},{"name":"Meng-Chieh Hsu","email":"mengchiehhsu@gmail.com","institution":"Department of Animal Science and Technology, National Taiwan University","country":"Taiwan"},{"name":"Richard youle","email":"youler@ninds.nih.gov","institution":"Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health","country":"USA"}],"complete":"true","quant_analysis":"Differential Abundance Results","status":"Complete","private":"false","hash":"","px":"PXD057163","task":"b3caf8d4260d4209ac52392998faffd5","id":"1712"}, {"dataset":"MSV000096200","datasetNum":"96200","title":"GNPS - PFAS negative mode DDA analysis_20241023","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729800684000","created":"Oct. 24, 2024, 1:11 PM","description":"RP-ESI(-)-MS\/MS data of PFAS containing samples recorded in DDA mode","fileCount":"494","fileSizeKB":"35703237","spectra":"379089","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PFAS;Decomposition;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"12fb88b1362f47fd91abf7f5593ebcb7","id":"1713"}, {"dataset":"MSV000096198","datasetNum":"96198","title":"SysQuan: repurposing SILAC mice for affordable absolute quantitation of the human proteome","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729790614000","created":"Oct. 24, 2024, 10:23 AM","description":"We have repurposed SILAC mouse tissues\/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation (AbsQuan) of theoretically >2\/3 of the human proteome using 132,380 shared tryptic peptides. We demonstrate that SysQuan enables quantifying 70% and 31% of the largest liver and plasma reference proteomes, respectively. We exemplify for 14 metabolic proteins that abundant standard isotope labeled mouse tissues enable cost-effective reverse AbsQuan in - theoretically 1000s of - human samples. Moreover, 10,000s of light\/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition AbsQuan.","fileCount":"43","fileSizeKB":"51148127","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MOD:01334 - \\\"A protein modification that effectively converts an L-lysine residue to 6x(13)C labeled L-lysine.\\\"","keywords":"absolute quantitation;cross species;silac;DatasetType:Proteomics","pi":[{"name":"Rene Zahedi","email":"rene.zahedi@umanitoba.ca","institution":"University of Manitoba","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"16325767ec914f0bb1fac37b572cd8aa","id":"1714"}, {"dataset":"MSV000096197","datasetNum":"96197","title":"GNPS Antiplasmodial Thai Actinobacteria_NEG","user":"jaisi2020","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729788757000","created":"Oct. 24, 2024, 9:52 AM","description":"Methanolic extracts of ISP2 grown Thai actinobacteria sourced from eastern Thai mangrove environment. 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"charged aerosol detector;plants;DatasetType:Metabolomics","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3f754012383d488cbc7a5d978f1e6707","id":"1720"}, {"dataset":"MSV000096190","datasetNum":"96190","title":"Orofiamma_AMPK_Arf6_TripleTOF6600_P116","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729772743000","created":"Oct. 24, 2024, 5:25 AM","description":"This dataset consists of 18 raw MS files and associated peak lists and results files, acquired on a ABSCiex TripleTOF6600 operated in Data Dependent Acquisition mode. \nSample generation and affinity purification was performed by Geoffrey Hesketh. Mass spectrometry acquisition was performed by Geoffrey Hesketh. Analysis was performed by Geoffrey Hesketh, Laura Orofiamma, Anne-Claude Gingras, and Costin Antonescu. \nThe files are associated with a manuscript submitted for publication by Laura Orofiamma et al. This dataset identifies proximity-dependent interactions of ARF6 in wildtype, GDP-locked and GTP-locked states using BioID in HeLa cells. The associated manuscript identifies AMPK as a regulator of cargo-specific clathrin-dependent endocytosis dynamics, which acts through ARF6 regulation.\nCostin Antonescu is the corresponding author of the manuscript (cantonescu@torontomu.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 2 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence\nTable 3 lists the SAINTexpress interactions\n","fileCount":"116","fileSizeKB":"44798255","spectra":"0","psms":"313616","peptides":"45918","variants":"54269","proteins":"39520","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MOD:00684 - 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This dataset contains a publicly available subset of this dataset.\n\nThe dataset includes raw MS\/MS spectra in their original vendor formats as well as in mzML and Mascot Generic Format (MGF). Additionally, peptide spectral hits (PSMs) identified through a database search and rescoring workflow, along with the dataset-specific protein databases used for annotation, are provided.","fileCount":"2124","fileSizeKB":"420133355","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090);Apis mellifera (NCBITaxon:7460);Bacillus subtilis (NCBITaxon:1423);Solanum lycopersicum (NCBITaxon:4081);Candidatus Thiodiazotropha endoloripes (NCBITaxon:1818881);Escherichia coli (NCBITaxon:562);Vigna mungo (NCBITaxon:3915);Methanosarcina mazei (NCBITaxon:2209);Saccharomyces cerevisiae (NCBITaxon:4932);Salmonella enterica (NCBITaxon:28901)","instrument":"Q Exactive HF-X;timsTOF Pro;TripleTOF 5600+;Orbitrap Astral;6550 iFunnel Q-TOF LC\\\/MS;Q Exactive;Q Exactive HF;Orbitrap Fusion Lumos;LTQ Orbitrap Velos;LTQ Orbitrap;Orbitrap Fusion;Orbitrap Exploris 480;Orbitrap Fusion ETD","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";MOD:00219 - \\\"A protein modification that effectively converts an L-arginine residue to L-citrulline.\\\";UNIMOD:535 - \\\"Ubiquitination.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:3 - \\\"Biotinylation.\\\";MOD:01893 - \\\"A protein modification that effectively converts an L-lysine residue to N6-malonyl-L-lysine.\\\";UNIMOD:354 - \\\"Oxidation to nitro.\\\";UNIMOD:122 - \\\"Formylation.\\\";MOD:01892 - \\\"A protein modification that effectively converts an L-lysine residue to N6-crotonyl-L-lysine.\\\";UNIMOD:64 - \\\"Succinic anhydride labeling reagent light form (N-term & K).\\\";MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:188 - \\\"13C(6) Silac label.\\\";UNIMOD:259 - \\\"13C(6) 15N(2) Silac label.\\\";UNIMOD:267 - \\\"13C(6) 15N(4) Silac label.\\\";UNIMOD:385 - \\\"Loss of ammonia.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\"","keywords":"de novo;benchmark;DatasetType:Proteomics","pi":[{"name":"Wout Bittremieux","email":"wout.bittremieux@uantwerpen.be","institution":"University of Antwerp","country":"Belgium"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0411b1453d124decb7dc27351db4658d","id":"1727"}, {"dataset":"MSV000096180","datasetNum":"96180","title":"Honey bee queen spermathecal fluid at three adult life stages","user":"amcafee","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729721269000","created":"Oct. 23, 2024, 3:07 PM","description":"Spermathecal fluid was extracted from adult queens at two different life stages (virgins and mated 2 week old) and separated from sperm by centrifugation. Queens were all sourced from the same grafting event and mated on the same schedule. Virgin queens were 2 days old at sampling. Some mated 2 week old queens were then held in a queen bank for a further two weeks (final age = 4 weeks), creating three groups of queens. Unbanked mated 2 week old queens were actively ovipositing, whereas banked mated queens were not actively laying.","fileCount":"5","fileSizeKB":"71371488","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"timsTOF Pro 2","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"Developmental stage;Queen;spermatheca;DatasetType:Proteomics","pi":[{"name":"Leonard Foster","email":"foster@msl.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD057117","task":"ef23aa22a43c4d958bf5394c8e245191","id":"1728"}, {"dataset":"MSV000096179","datasetNum":"96179","title":"A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729720250000","created":"Oct. 23, 2024, 2:50 PM","description":"A comprehensive LFQ benchmark dataset to validate data analysis pipelines on modern day acquisition strategies in proteomics using SCIEX TripleTOF5600 and 6600+, Orbitrap QE-HFX, Waters Synapt GS-Si and Synapt XS and Bruker timsTOF Pro.","fileCount":"1158","fileSizeKB":"4254568980","spectra":"56089300","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Candida albicans (NCBITaxon:5476);Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro;Q Exactive HF;TripleTOF 5600;Synapt MS;TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Swath;Dia;Benchmark;DatasetType:Proteomics","pi":[{"name":"Maarten Dhaenens","email":"Maarten.Dhaenens@UGent.be","institution":"Laboratory of Pharmaceutical Biotechnology\/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD028735","task":"88f874de700d4faabaf7d50a9acc9ee5","id":"1729"}, {"dataset":"MSV000096174","datasetNum":"96174","title":"20241023-XXC-STANDARD1-MSMSP-LWT-BUCM","user":"LWTYXL","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729678301000","created":"Oct. 23, 2024, 3:11 AM","description":"20241023-XXC-STANDARD1-MSMSP-LWT-BUCM, agilent, UPLC-Q\/TOF-MS","fileCount":"11","fileSizeKB":"543472","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"reference standards","instrument":"Q\\\/TOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"TCM;DatasetType:Other (NP)","pi":[{"name":"LI WANTING","email":"lwt13558681186@163.com","institution":"BUCM","country":"CHINA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"60bf7e0b86fc4ffbbcf6bbfa4ee534cd","id":"1730"}, {"dataset":"MSV000096172","datasetNum":"96172","title":"Evaluation of linkers and cereblon-directing warheads for the development of orally bioavailable PROTACs","user":"msteger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729672396000","created":"Oct. 23, 2024, 1:33 AM","description":"PROTACs usually occupy physicochemical space outside the one defined by classical drug-like molecules, which often presents considerable challenges in their optimization and development for oral administration. We have previously reported phenyl glutarimide (PG)-based BET PROTAC SJ995973, with improved overall in vitro degradation and antiproliferative activities compared to its direct thalidomide-based analogue dBET1, but similarly poor in vivo pharmacokinetic profile. Here we describe optimization efforts that led to the discovery of an orally bioavailable PG-PROTAC SJ44236, and results of a comprehensive in vitro\/vivo comparative study with direct analogues containing alternative CRBN warheads. 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Samples from nasal Lavage fluid from CRSwNP patients and controls were analysed and revealed a significant difference in protein expression. Dysregulated proteins were linked to airway inflammation, immune response and oxidative stress.","fileCount":"18","fileSizeKB":"12503207","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Chronic Rhinosinusitis, Sinusitis, Nasal Polyposis, Label free quantification , LC MS\/MS, Biomarkers, Oxidative stress Pathways;DatasetType:Proteomics","pi":[{"name":"Musallam Kashoob","email":"Doctorkashoob@hotmail.com","institution":"Otolyngology, Head and Neck surgery Department, College of Medicine, King Saud University","country":"Saudi Arabia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b5bfd3c25913454b8355bed75169793e","id":"1732"}, {"dataset":"MSV000096168","datasetNum":"96168","title":"Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction","user":"triplejey","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729638194000","created":"Oct. 22, 2024, 4:03 PM","description":"Immunoprecipitation of NAT10 using an anti-NAT10 antibody followed by mass spectrometry to determine NAT10-interacting proteins.","fileCount":"10","fileSizeKB":"3238217","spectra":"0","psms":"34711","peptides":"17123","variants":"22994","proteins":"1651","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer ","modification":"NA","keywords":"ribosome, N-acetyltransferase 10, nucleolus, p53, paligenosis;DatasetType:Proteomics","pi":[{"name":"Charles Cho","email":"charles.j.cho@emory.edu","institution":"Emory University","country":"U.S.A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057070","task":"510f4b83e9cf45319927c368c8746fa4","id":"1733"}, {"dataset":"MSV000096166","datasetNum":"96166","title":"Arabidopsis thaliana sprayed with cWP or water","user":"cooperb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729623187000","created":"Oct. 22, 2024, 11:53 AM","description":"Leaves of 3-week-old Arabidopsis thaliana ecotype Columbia-0 were sprayed with 300 uM cWP or water. 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Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings. ","fileCount":"63","fileSizeKB":"14839957","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyclo-Trp-Pro;DatasetType:Metabolomics","pi":[{"name":"Bret Cooper","email":"bret.cooper@ars.usda.gov","institution":"USDA-ARS","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1d32b00beeaa4945add68a27d84b59c3","id":"1734"}, {"dataset":"MSV000096165","datasetNum":"96165","title":"Phaseolus vulgaris infiltrated with cWP and water","user":"cooperb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729622639000","created":"Oct. 22, 2024, 11:43 AM","description":"Primary leaves of 10-day-old Phaseolus vulgaris (common bean) variety Black Valentine plants were infiltrated with 30 uM cWP or water (control) using a flat-nosed 1 mL syringe. The two primary leaves on each plant were each infiltrated 8 times (4 times on each half leaf) with a single compound. Infiltration was performed on the abaxial side without puncturing the leaf, and each infiltration produced a 1 cm2 water-soaked area. After 24 hours, the leaf tissue at the site of infiltration was sampled with a 1 cm diameter cork-borer. Ten to twelve sites were collected from each plant to reach approximately 170 mg total tissue which was extracted in 1 mL 100% methanol. Seven separate plants of each treatment were used to generate seven replicates. Tissues were pulverized with 0.5 mm glass beads with a Qiagen PowerLyzer 24 bead mill (Qiagen, Hilden, Germany) 10 times at 5,000 rpm for 20 sec (cooled on ice for 2 min between cycles). Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without tissue or compounds). The milled extracts were centrifuged for 20 min at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol\/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, sample replicate set 2, Blank 2, QC 2, sample replicate set 3, sample replicate set 4, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings. 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The two primary leaves on each plant were each infiltrated 8 times (4 times on each half leaf) with a single compound. Infiltration was performed on the abaxial side without puncturing the leaf, and each infiltration produced a 1 cm2 water-soaked area. After 24 hours, the leaf tissue at the site of infiltration was sampled with a 1 cm diameter cork-borer. Ten to twelve sites were collected from each plant to reach approximately 170 mg total tissue which was extracted in 1 mL 100% methanol. Four separate plants of each treatment were used to generate four replicates. Tissues were pulverized with 0.5 mm glass beads with a Qiagen PowerLyzer 24 bead mill (Qiagen, Hilden, Germany) 10 times at 5,000 rpm for 20 sec (cooled on ice for 2 min between cycles). Two matrix blank samples were prepared the same way but without tissue or compounds. The milled extracts were centrifuged for 20 min at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol\/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings.","fileCount":"75","fileSizeKB":"17550282","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phaseolus vulgaris (NCBITaxon:3885)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cWP;DatasetType:Metabolomics","pi":[{"name":"Bret Cooper","email":"bret.cooper@ars.usda.gov","institution":"USDA-ARS","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cb1b5e877c5b41db983281706e45f292","id":"1736"}, {"dataset":"MSV000096163","datasetNum":"96163","title":"metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729615001000","created":"Oct. 22, 2024, 9:36 AM","description":"Analysis of large-scale data-independent acquisition mass spectrometry (DIA-MS) metaproteomics data remains a computational challenge. Here, we present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS (DDA-MS), protein identification and quantification using DIA-MS, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap and timsTOF MS instruments. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples indicated that metaExpertPro quantified an average of 45,000 peptides in a 60-minute diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual false discovery rate (FDR) of approximately 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67\u20130.90) in genus diversity and showed a high correlation (rSpearman = 0.73\u20130.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia (DLP) patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.","fileCount":"288","fileSizeKB":"430618250","spectra":"6793912","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro;Orbitrap Exploris 480","modification":"MOD:01153 - \\\"A protein modification that effectively replaces a hydrogen atom with an methylsulfanyl group (thiomethyl group).\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"Computational workflow;Data-independent acquisition mass spectrometry;Metaproteomics;DatasetType:Proteomics","pi":[{"name":"Tiannan Guo","email":"guotiannan@westlake.edu.cn","institution":"1, Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China\n2, School of Medicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China\n3, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051104","task":"9a253234725e489cb7de2856e15b2b26","id":"1737"}, {"dataset":"MSV000096162","datasetNum":"96162","title":"An asymmetric nautilus-like HflK\/C assembly controls FtsH proteolysis of membrane proteins","user":"btelusma","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729611883000","created":"Oct. 22, 2024, 8:44 AM","description":"This dataset compares the steady-state growth profiles of wild-type (WT) and hflKC-null strains cultured in LB media.","fileCount":"25","fileSizeKB":"50826589","spectra":"760789","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Label-free quantification;Differential protein expression;DatasetType:Proteomics","pi":[{"name":"Alireza Ghanbarpour","email":"alirezag@wustl.edu","institution":"Washington University","country":"United States of America"},{"name":"Joseph H. 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This experiment allows for the identification and quantitative comparison of wild-type and Arg719Cys COL2A1 interactomes in HT-1080 cells transiently transfected with COL2A1 under a constitutive promoter. Negative control samples are untransfected HT-1080 cells, used to identify high-confidence collagen-II interactors from non-specific binders.","fileCount":"7","fileSizeKB":"972700","spectra":"0","psms":"2787","peptides":"1089","variants":"1560","proteins":"135","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"COL2A1, interactome, quantitative proteomics, TMT;DatasetType:Proteomics","pi":[{"name":"Matthew Shoulders","email":"mshoulde@mit.edu","institution":"MIT","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD057054","task":"9c9f6b7178314446b9f7aabc5080981c","id":"1739"}, {"dataset":"MSV000096150","datasetNum":"96150","title":"Pseudomonas savastanoi pv. phaseolicola race 5 treated with genistein, daidzein, and DMSO","user":"cooperb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729601774000","created":"Oct. 22, 2024, 5:56 AM","description":"P. savastanoi pv. phaseolicola isolates race 5 (R5) was cultured in 10 mL Luria broth with 400 uM genistein, 400 uM daidzein, or without but with 50 uL DMSO at 28 C at 200 rpm on a shaking platform until the control cultures reached late log-phase growth measured at an optical density of 0.75-0.90 at 600 nm wavelength of visible light. Five replicate cultures of each treatment were centrifuged at 5,000 x g for 10 min, washed once in 1 mL phosphate buffered saline, centrifuged at 5,000 x g for 10 min, resuspended in 1 mL of 1:1:1:1 acetone\/acetonitrile\/methanol\/water and 1,250 pmol prednisone, and pulverized with 0.5 mm glass beads with a Qiagen PowerLyzer 24 bead mill (Qiagen, Hilden, Germany) 10 times at 5,000 rpm for 20 sec (cooled on ice for 2 min between cycles). Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without R5 and without genistein or daidzein). The milled extracts were centrifuged for 20 min at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol\/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m\/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings. 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Later files were collected with a temperature ramp, so all temperatures are collected as different time steps inside a single raw file.","fileCount":"301","fileSizeKB":"2342847","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive UHMR","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Native MS;Aquaporin Z;Protein-Lipid Interactions;DatasetType:Other (Native MS)","pi":[{"name":"Michael Marty","email":"mtmarty@arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"25b1b5bc0fcf415e8b96e21cc4d5357b","id":"1741"}, {"dataset":"MSV000096147","datasetNum":"96147","title":"ACEP library marine invertebrate LC-MS\/MS data","user":"DorringtonGroup","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729545526000","created":"Oct. 21, 2024, 2:18 PM","description":"RP-ESI(+)-MS\/MS (DDA) data of marine invertebrate crude organic extracts from the ACEP library","fileCount":"435","fileSizeKB":"15002774","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Porifera (NCBITaxon:6040)","instrument":"compact","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"marine invertebrate;South Africa;Sponges;DatasetType:Metabolomics","pi":[{"name":"Rosemary Dorrington","email":"r.dorrington@ru.ac.za","institution":"Rhodes University","country":"South Africa"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"52dfe1367b7c45158fa2ee77a3bfe772","id":"1742"}, {"dataset":"MSV000096146","datasetNum":"96146","title":"Gomez-Deza et al 2024 DLK DRP1 phosphoproteomics","user":"clairelepichon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729543764000","created":"Oct. 21, 2024, 1:49 PM","description":"Mass spectrometry of GST-tagged DRP1 expressed in HEK cells either alone or co-expressed with WT DLK or DLK S302A (Kinase dead mutant).\r\n(\"D\" DRP1 only; 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Here, we describe the third iteration of the generation and multimodal LC-MS\/MS analysis of >305,000 synthetic non-tryptic peptides representing HLA Class I & II ligands as well as peptides derived from the N-terminal proteases LysN and ApsN. This resource will be extended to 1.4 million peptides and all data will be made available to the public in ProteomicsDB.","fileCount":"5595","fileSizeKB":"2316395249","spectra":"103458013","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hla;Aspn;Hla class ii;Proteometools;Reference standards;Hla class i;Synthetic peptides;Lysn;DatasetType:Proteomics","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, Technical University of Munich, Germany","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD021013","task":"75bad20d606e4474a82575936a8072a5","id":"1747"}, {"dataset":"MSV000096138","datasetNum":"96138","title":"GNPS -Bacteria fungal interaction co-cultures","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729502450000","created":"Oct. 21, 2024, 2:20 AM","description":"Untargeted metabolomics of microbial strains cultivated on liquid media ","fileCount":"249","fileSizeKB":"21969454","spectra":"372247","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Botrytis cinerea (NCBITaxon:40559);Aspergillus nidulans (NCBITaxon:162425);Zymoseptoria tritici IPO323 (NCBITaxon:336722);Bacillus subtilis (NCBITaxon:1423)","instrument":"Q Exactive HF","modification":"MS:1002864 - 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Seperation using UHPLC Ultimate 3000 system with 5 uL of sample injection onto an Accucore C30 column (2.1 mm * 150 mm, 2.6-um particle size) maintained at 40C. flow rate was set to 300 ul min-1. ACN:H2O (60:40, v\/v) and ACN:IPA (10:90, v\/v) were used as mobile phase A and mobile phase B, respectively. Both eluents were supplemented with 0.1% formic acid and 10 mM ammonium formate.","fileCount":"73","fileSizeKB":"4839916","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics;soil;grassland;DatasetType:Metabolomics;DatasetType:Other (Lipidomics)","pi":[{"name":"wolfgang wanek","email":"wolfgang.wanek@univie.ac.at","institution":"University of vienna","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a46412b59e5a4d4ba28d76aa72a34b93","id":"1750"}, {"dataset":"MSV000096132","datasetNum":"96132","title":"GNPS -Semi-automated monitoring of longitudinal microbial metabolic dynamics","user":"mrjvitor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729299935000","created":"Oct. 18, 2024, 6:05 PM","description":"Raw data from GC-MS analysis of samples collected from P. chrysosporium and T. reesei in mono and co-culture for evaluation of lignin degradation.","fileCount":"60","fileSizeKB":"251994","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phanerochaete chrysosporium (NCBITaxon:5306);Trichoderma reesei (NCBITaxon:51453)","instrument":"GCMS-QP2010SE","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;lignin degradation;coculture;white-rot fungus;DatasetType:Metabolomics","pi":[{"name":"Ricardo Roberto da Silva","email":"ridasilva@usp.br","institution":"University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"24fcf6cf3ab94b21a6e0d92a7b465b15","id":"1751"}, {"dataset":"MSV000096131","datasetNum":"96131","title":"Jade1 and the HBO1 complex are spatial-selective cofactors of Oct4","user":"YifanWu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729285527000","created":"Oct. 18, 2024, 2:05 PM","description":"Oct4 is a master regulator of pluripotency. Potential Oct4 interactors have been cataloged extensively but the manner and significance of these interactions are incompletely defined. Like other POU domain proteins, Oct4 is capable of binding to DNA in multiple configurations, however the relationship between these configurations and cofactor recruitment (and hence transcription output) are unknown. Here, we show that Oct4 interacts with common and unique proteins when bound to DNA in different configurations. One of these proteins is Jade1, a component of the HBO histone acetyltransferase complex. Jade1 preferentially associates with Oct4 when bound to More palindromic Octamer-Related Element (MORE) DNA sequences that bind Oct4 dimers and are associated with strong gene expression. We show that the Oct4 N-terminus is critical for this interaction. ChIP-seq using HBO1, the enzymatic component of the complex, identifies a preference for binding adjacent to Oct4 at MORE sites. Using purified recombinant proteins and nucleosome complexes, we show that the HBO1 complex acetylates histone H3K9 within nucleosomes more efficiently when Oct4 is co-bound to a MORE site. Histone acetylation is further increased when Oct4 is mutated to favor dimeric MORE binding. Cryo-electron microscopy reveals that Oct4 bound to a MORE near the nucleosome entry\/exit site partially unwinds DNA from nucleosome core particles, and identifies additional mass associated with the HBO1 complex. These results identify a novel mechanism of transcriptional regulation by Oct4.","fileCount":"62","fileSizeKB":"31025131","spectra":"0","psms":"21695","peptides":"2498","variants":"3677","proteins":"828","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MOD:00768 - \\\"Oxidation of methionine to methionine sulfone with neutral loss of CH3SO2H.\\\"","keywords":"Oct4;Cofactor;ESCs;Jade1;MORE motif;Octamer motif;DatasetType:Proteomics","pi":[{"name":"Dean Tantin","email":"dean.tantin@path.utah.edu","institution":"University of Utah","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056959","task":"3c34495bbeaf4f45aa8970d65890c171","id":"1752"}, {"dataset":"MSV000096130","datasetNum":"96130","title":"Deep motif deconvolution of HLA-II peptidomes","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729271916000","created":"Oct. 18, 2024, 10:18 AM","description":"CD4 T cells are key for priming and regulating immune recognition of infected and cancer cells, but predictions of class II epitopes have limited accuracy. We profiled over 100\u2019000 HLA-II ligands by Mass Spectrometry and developed a novel motif deconvolution algorithm to analyze these data. Our work demonstrates substantial improvements in the definition of HLA-II binding motifs and enhanced accuracy in HLA-II ligand and class II epitope predictions.","fileCount":"265","fileSizeKB":"162862891","spectra":"3798634","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Immunopeptidomics;Ligand predictions;Mass spectrometry;Hla class ii;Neoantigens;DatasetType:Proteomics","pi":[{"name":"Michal Bassani-Sternberg","email":"michal.bassani@chuv.ch","institution":"Dr Michal BASSANI-STERNBERG \uFFFD Group leader Laboratory Hi-TIDe: Immunopeptidomics Head of clinical Mass spectrometry unit Center of experimental therapeutics Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Biop\uFFFDle 3 Chemin des Boveresses 155, CH-1066 Lausanne","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD012308","task":"a1583f5f653149d9a7ab3be36ec86565","id":"1753"}, {"dataset":"MSV000096128","datasetNum":"96128","title":"Multi-omics integration reveals silencing of Arginosuccinate synthase and upregulation of nucleotide biosynthesis in tamoxifen resistant invasive lobular carcinoma","user":"choueiry_2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729268041000","created":"Oct. 18, 2024, 9:14 AM","description":"Invasive Lobular Carcinoma (ILC), a distinct subtype of breast cancer is hallmarked by E-Cadherin loss, slow proliferation, and hormone receptor positivity. Major challenges in clinical management of ILC is advanced stage at diagnosis, resistance to endocrine therapy, a cornerstone in treating ILC patients, and late recurrence. To elucidate the mechanisms underlying endocrine resistance in ILC, we have generated ILC cell lines (MDA-MB-134-VI and SUM44PE) resistant to tamoxifen, a selective estrogen receptor modulator. Our study reveals methylation mediated silencing of ASS1 and demethylation restored ASS1 expression markedly reducing IC50 for tamoxifen. Treating TAMR cell with Decitabine, a demethylating agent, or Farudodstat, a pyrimidine biosynthesis inhibitor, markedly augmented efficacy of tamoxifen. Collectively, our study unveils ASS1 downregulation as a novel mechanism underlying acquired resistance to tamoxifen in ILC and establishes a metabolic link between ASS1 and nucleic acid biosynthesis. ASS1 can be a potential biomarker and a therapeutic target in tamoxifen resistant ILC patients, warranting further investigation.","fileCount":"122","fileSizeKB":"21076601","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Invasive lobular carcinoma","instrument":"Q Exactive","modification":"shRNA Knockdown","keywords":"ILC;drug resistance;Tamoxifen;metabolomics;multi-omics;DatasetType:Metabolomics","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0fe04d62963a485faa3add466b426126","id":"1754"}, {"dataset":"MSV000096127","datasetNum":"96127","title":"Discovery of peptidic siderophore degradation by screening natural product profiles in marine-derived bacterial mono-and co-cultures ","user":"monicamonge","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729262709000","created":"Oct. 18, 2024, 7:45 AM","description":"Beneficial bacteria in coculture with the marine pathogen V. coralliilyticus Cn52-H1","fileCount":"263","fileSizeKB":"706905","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vibrio coralliilyticus (NCBITaxon:190893);Pseudoalteromonas sp. 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Eluents were lyophilized and reconstituted in twenty microlites of 0.1% formic acid, and 7.5 microliters of each sample was loaded onto Evotip Pure disposable C18 trap columns and analyzed using an Evosep One LC interfaced to an Thermofisher Orbitrap Astral MS. Each sample was analyzed twice using a 30 sample-per-day method, and MS\/MS used data-dependent (DDA) and data-independent acquisition (DIA). Database searching using a Uniprot human database (downloaded on 08\/17\/24) appended with transgenes and common contaminants (20,472 total entries) was performed with Spectronaut 19.2 using the Pulsar search engine with semispecific WALP cleavage specificity (cleavage C-terminal to T,A,S or V with non-specific cleavage on either C- or N-terminus) and variable phosphorylation on S\/T\/Y. The DIA acquisition was used for identification and quantification of peptide precursors and protein groups at a 1% false discovery rate. Local normalization was applied, and protein group quantities were determined using the MaxLFQ algorithm. Phosphorylation site localization used a probability cut-off of 0.75.","fileCount":"13","fileSizeKB":"61658301","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"alpha lytic protease;phosphotyrosine;DatasetType:Proteomics","pi":[{"name":"Dennis C. Ko","email":"dennis.ko@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD056916","task":"08c5c675f5b847c4ac1b3192802269fe","id":"1760"}, {"dataset":"MSV000096119","datasetNum":"96119","title":"GNPS -Data for Increasing Oligonucleotide Sequencing Information and Throughput with Ion Mobility Spectrometry Mass Spectrometry","user":"jpryan3","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729189333000","created":"Oct. 17, 2024, 11:22 AM","description":"Raw .d files containing LC-DTIMS-CID-MS for the sequencing of 5 synthetic single stranded oligonucleotides. Preliminary files were collected using a alternating frames at a single collision energy, while later files used a drift time dependent CID collision energy ramp to optimally fragment multiple charge states for a given oligonucleotide in a single injection","fileCount":"4866","fileSizeKB":"148820551","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Single Stranded Synthetic Oligonucleotides","instrument":"6560 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ion mobility;mass spectrometry;oligonucleotide sequencing;DatasetType:Other (Oligonucleotides)","pi":[{"name":"Erin Baker","email":"ebaker@ncsu.edu","institution":"North Carolina State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8615b66cc0084f5486b631dc282ca57d","id":"1761"}, {"dataset":"MSV000096117","datasetNum":"96117","title":"GNPS -Crambe Crambe DCM:MeOH (50:50) crude extract","user":"Polyzois_A","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729160248000","created":"Oct. 17, 2024, 3:17 AM","description":"Crambe Crambe DCM:MeOH (50:50) crude extract, method focusing on crambescins study.","fileCount":"2","fileSizeKB":"85325","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crambe crambe (NCBITaxon:3722)","instrument":"Q Exactive","modification":"no","keywords":"Crambescin, guanidine, crambe;DatasetType:Metabolomics","pi":[{"name":"Nikolas Fokialakis","email":"fokialakis@pharm.uoa.gr","institution":"Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens","country":"Greece"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0146197bc1b64e9284ada96fde0a0f60","id":"1762"}, {"dataset":"MSV000096116","datasetNum":"96116","title":"Serum, cortex, leptomeninges, and cecum tissues from FMT mice.","user":"Polyzois_A","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729157944000","created":"Oct. 17, 2024, 2:39 AM","description":"Serum, Cortex, Leptomeninges, and Cecum extracted tissues from mice which has received Fecal Matter Transplant (FMT) from an Aged and Young donor. Serum samples from Young and Aged donors, and the methanol blanks between the runs are also included. This dataset is related to ( biorxiv.org\/content\/10.1101\/2024.05.27.595846v1 ).","fileCount":"51","fileSizeKB":"5406472","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus sp. (NCBITaxon:10095)","instrument":"Q Exactive HF","modification":"no","keywords":"cortex, leptomeninges, serum;DatasetType:Metabolomics","pi":[{"name":"Frank Schroeder","email":"schroeder@cornell.edu","institution":"Boyce Thompson Institute, Cornell University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9c049db075834302973dbdda07d02030","id":"1763"}, {"dataset":"MSV000096113","datasetNum":"96113","title":"Spindle integrity is regulated by a phospho-dependent interaction between the Ndc80 and Dam1 kinetochore complexes ","user":"FHproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729112500000","created":"Oct. 16, 2024, 2:01 PM","description":"Kinetochores were purified (via Dsn1-His-Flag) from Saccharomyces cerevisiae lysate from a wildtype background (CN091523_101423_SBY8253, CN040221_042921_SBY8253, CN020524_020824_SBY8253), an mps1-1 genetic background grown at 37 C for 2.5 hours (CN091523_101423_SBY8726, CN020524_020824_SBY8726) and a pGAL-MPS1 background grown in 4% galactose for 2.5 hours (CN020524_020824_SBY8810, CN040221_042921_SBY8810). The Ndc80c (Ndc80-Flag) was purified from S. cerevisiae lysate from a wildtype (CN030221_031021_10651, CN020524_020824_SBY10651) or pGAL-MPS1 genetic background (CN030221_031021_19721, CN020524_020824_SBY19721) grown in 4% galactose for 2.5 hours prior to harvest. The Dam1c (Dad1-Flag) was purified from S. cerevisiae lysate from a wildtype (CN052721_053021_12441, CN020524_020824_SBY12441) or pGAL-MPS1 genetic background (CN052721_053021_20761) grown in 4% galactose for 2.5 hours prior to harvest. Kinetochores were purified (Dsn1-His-Flag) from NDC80WT cells (CN032723_033023_SBY22006, CN051322_052422_SBY21353), ndc80T248A,T252A cells (CN032723_033023_SBY22007, CN051322_052422_SBY21287) and ndc80T248D,T252D cells (CN032723_033023_SBY22008, CN051322_052422_SBY21289). Kinetochores were purified (Dsn1-His-Flag) from NDC80WT (CN032723_033023_SBY22062), ndc80T248A,T252A (CN032723_033023_SBY22063) and ndc80T248D,T252D cells (CN032723_033023_SBY22011), all cdc15-2 (anaphase arrested) at 37 C for 2.5 hours prior to harvest. Harvested yeast were resuspended in Buffer H (25 mM HEPES pH 8.0, 150 mM KCl, 2 mM MgCl2, 0.1 mM EDTA pH 8.0, 0.1% NP-40, 15% glycerol) supplemented with protease and phosphatase inhibitors. After resuspension and re-spinning, yeast pellets were frozen in liquid nitrogen and lysed using a Freezer Mill (SPEX, Metuchen NJ). Lysate was clarified via ultracentrifugation at 24,000 RPM (98,000 x g) for 90 minutes and the protein layer was extracted with a syringe. This extract was incubated with magnetic a-M3DK antibody conjugated Dynabeads (Invirtrogen, Waltham MA) for 3 hours at 4 C with rotation. Dynabeads were washed with 10x bead volume of Buffer H 5 times (the last 3 washes omitting DTT and phosphatase inhibitors). For mass spectrometry, kinetochores were eluted from Dynabeads with 0.2% RapiGest (Waters Corporation, Milford MA) in 50 mM HEPES pH 8.0.","fileCount":"146","fileSizeKB":"117776347","spectra":"0","psms":"296859","peptides":"40663","variants":"55345","proteins":"3980","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Eclipse;Orbitrap Ascend","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mitosis, kinetochore, Ndc80c, Dam1c, Mps1 kinase;DatasetType:Proteomics","pi":[{"name":"Susan Biggins","email":"sbiggins@fredhutch.org","institution":"Fred Hutchinson Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056874","task":"edf1adb3ff8d440f8aa483f86e1034a4","id":"1764"}, {"dataset":"MSV000096112","datasetNum":"96112","title":"Designing a Comparative Proteomics Experiment: Retention-time Alignment and Imputation Algorithms Affect Statistical Comparisons Between Samples ","user":"jess_conforti1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729103758000","created":"Oct. 16, 2024, 11:35 AM","description":"Comparative proteomics experiments reveal biomarkers by using statistical tests to determine proteins expressed with higher abundance in one sample versus another. However, comparative experiments can be complicated by variability from all aspects of proteomics workflows. To account for variability, software for database searching contains retention-time alignment and imputation algorithms to correct for retention-time shifts and assign abundances to missing proteins. While these algorithms improve quantification and reduce processing time, we hypothesize that they alter statistical comparisons between samples when samples are searched together. Herein, we search different cleanup methods or single proteins separately versus together in Progenesis Qi for proteomics database searching software. Our results show that searching samples together increases the number of identifications by each sample, enhances protein similarity between samples, and leads to false transfers. Further, we demonstrate that searching samples together affects protein abundance, differentially expressed proteins, and confidence scores due to retention-time alignment and imputation algorithms. Ultimately, we highlight that careful consideration of the search design is necessary to determine biomarkers in comparative proteomics experiments.","fileCount":"942","fileSizeKB":"190790923","spectra":"0","psms":"12002367","peptides":"34464","variants":"40819","proteins":"30285","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Chicken Egg White;Equine Heart;Equine Skeletal Muscle;Bovine Blood;bovine erythrocytes","instrument":"nanoACQUITY UPLC;Synapt G2-S HDMS","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"Database Searching;Imputation;Missing Proteins;Proteomics;Retention-time Alignment;Stochasticity;DatasetType:Proteomics","pi":[{"name":"Elyssia Gallagher","email":"elyssia_gallagher@baylor.edu","institution":"Baylor University","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056868","task":"de48e48d9f0c43c1b24faf13285c1840","id":"1765"}, {"dataset":"MSV000096110","datasetNum":"96110","title":"GNPS - Interactions between methylerythritol phosphate (MEP) pathway metabolites and Escherichia coli K-12 fatty acid biosynthesis enzymes","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729094690000","created":"Oct. 16, 2024, 9:04 AM","description":"Raw data files from native mass spectrometry analyses examining the interactions between methylerythritol phosphate (MEP) pathway metabolites and Escherichia coli K-12 fatty acid biosynthesis enzymes. Recorded in positive mode direct injection.","fileCount":"22","fileSizeKB":"251843","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"native mass spectrometry;E. coli;methylerythritol phosphate (MEP) pathway;K-12 fatty acid biosynthesis;DatasetType:Proteomics;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"},{"name":"Jingzhe Guo","email":"jzguowhu@hotmail.com","institution":"University of Riverside California","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6b8a5b98adc94314bd677aee368ac029","id":"1766"}, {"dataset":"MSV000096108","datasetNum":"96108","title":"Feng_DownSyndrome_OrbitrapAstral_Ardia","user":"LTRI_proteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729081776000","created":"Oct. 16, 2024, 5:29 AM","description":"This dataset consists of 7 raw MS files, acquired on a Thermo Scientific Orbitrap Astral operated in Data Independent Acquisition mode. \r\nSamples were harvested by Anna Feng. S-trap purification was performed by Cassandra Wong. Mass spectrometry was performed by Cassandra Wong, with advice from Brendon Seale. Analysis was performed by Cassandra Wong, Anna Feng, Brian Kalish, and Ji-Young Youn. \r\nThe files are associated with a manuscript submitted for publication by Anna Feng et al. The main goal of this dataset was to provide a comprehensive understanding of the complex multicellular processes underlying Down Syndrome neurodevelopment. \r\nBrian Kalish (brian.kalish@childrens.harvard.edu) is the corresponding authors of the manuscript; Brendon Seale should be contacted for questions on this dataset (bseale@lunenfeld.ca)\r\n","fileCount":"13","fileSizeKB":"18395362","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Down Syndrome;Global proteome;DatasetType:Proteomics","pi":[{"name":"Brendon Seale","email":"bseale@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"0bfe662dd98547bca0fdf253d87077c9","id":"1767"}, {"dataset":"MSV000096103","datasetNum":"96103","title":"Proteoform-predictor: Increasing the Phylogenetic Reach of Top- Down Proteomics","user":"Tao_maple","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729030601000","created":"Oct. 15, 2024, 3:16 PM","description":"Raw files for the paper named Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics. It contains TDP data of E coli K12 and Serratia marcescens.","fileCount":"13","fileSizeKB":"21311204","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Serratia marcescens (NCBITaxon:615);Escherichia coli K-12 (NCBITaxon:83333)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Proteoform-predictor;Top-down proteomics;DatasetType:Proteomics","pi":[{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ebe25b1c801c4173bda7e3e1a6f84fd2","id":"1768"}, {"dataset":"MSV000096102","datasetNum":"96102","title":"Ion Mobility-Assisted Free Radical Initiated Peptide Sequencing v2","user":"nborotto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729025786000","created":"Oct. 15, 2024, 1:56 PM","description":"Free radical-initiated peptide sequencing (FRIPS) is a tandem mass spectrometry technique (MS\/MS) that enables radical-based dissociation on instruments only capable of collisional activation. In FRIPS, peptides are chemically-derivatized with a compound that undergoes homolytic cleavage and generates radicals upon collisional activation. These radicals then propagate through the peptide backbone enabling the sequencing of peptide ions. This MS\/MS technique has shown promise in sequencing post-translationally modified peptides, but it is typically performed in an MS3 workflow and single-step MS\/MS approaches result in the generation of both collisional- and radical-driven dissociation products and highly complex spectra. Recently, our group developed a method to dissociate peptide ions prior to ion mobility analysis within a trapped-ion mobility spectrometry (TIMS) device. In this work, we examine if this CIDtims technique is capable of initiating the homolytic cleavage of the FRIPS precursor. We then examine if the resultant ion mobility separation results in additional assignments of product ions and improved sequence coverage. We demonstrate that activation within the TIMS device does indeed promote robust radical initiation and fragmentation and that the generated product ions are mobility separated enabling facile assignment and increased sequence coverage. ","fileCount":"159","fileSizeKB":"987372","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mass spectrometry;ion mobility;DatasetType:Other (tandem mass spectrometry)","pi":[{"name":"Nicholas Borotto","email":"nborotto@unr.edu","institution":"University of Nevada","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7a39192e018d4549b7f781bbd48b3bc3","id":"1769"}, {"dataset":"MSV000096101","datasetNum":"96101","title":"Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729015837000","created":"Oct. 15, 2024, 11:10 AM","description":"We describe circadian clock-dependent changes in ribosome composition in Neurospora crassa depending on cell type, stress, or developmental state. Mass spectrometry of ribosomes isolated at different circadian times identified six ribosomal proteins and one ribosome-associated protein with clock-controlled abundance. We confirmed clock control of eL31-HA abundance in purified ribosomes and found that deletion of eL31 altered and inhibited translation rhythms. We examined ribosome protected footprint (RPF)-seq reads mapping past stop codons over circadian time to reveal clock-dependent and eL31-enhanced rhythms in translation termination fidelity. We discovered that eL31 promotes proper ion homeostasis and translation elongation fidelity, and demonstrated that the circadian clock governs daily changes in ribosome composition that control rhythms in translation and impact translation fidelity, likely through changes in intracellular Mg2+ levels.","fileCount":"425","fileSizeKB":"81146715","spectra":"0","psms":"536338","peptides":"45825","variants":"119348","proteins":"733","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Neurospora crassa (NCBITaxon:5141)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:374 - \\\"Half of a disulfide bridge.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"circadian clock;ribosome composition;rhythmic translation;translation fidelity;large ribosomal protein eL31;DatasetType:Proteomics","pi":[{"name":"Deborah Bell-Pedersen","email":"dpedersen@tamu.edu","institution":"Department of Biology, Texas A&M University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056823","task":"8c6029b76d6d447c9d62ba679c289acf","id":"1770"}, {"dataset":"MSV000096100","datasetNum":"96100","title":"Dessauer_Adcy_TripleTOF6600_P124","user":"LTRI_proteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729015551000","created":"Oct. 15, 2024, 11:05 AM","description":"This dataset consists of 32 raw BioID MS files and 8 raw FLAG-AP samples and associated peak lists and results files, acquired on a ABSciex TripleTOF6600 operated in Data Dependent Acquisition mode. \r\nSamples were generated by Taeyeop Park. Streptavidin affinity purification was performed by Zhen-Yuan Lin, anti-FLAG affinity purification performed by Cassandra Wong. Mass spectrometry acquisition was performed by Zhen-Yuan Lin and Cassandra Wong. Analysis was performed by Taeyeop Park, Cassandra Wong, Karen Colwill, and Carmen Dessauer. \r\nThe files are associated with a manuscript submitted for publication by Taeyeop Park et al. The main goal of this dataset was to identify isoform-specific adenylyl cyclase-containing complexes in neonatal cardiomyocytes. \r\nCarmen W. Dessauer (Carmen.W.Dessauer@uth.tmc.edu) is the corresponding authors of the manuscript; Karen Colwill should be contacted for questions on this dataset (colwill@lunenfeld.ca)\r\n\r\nThis submission is associated with 6 Supplementary Files (in addition to this README file)\r\nTable 1 BioID describes the composition of the BioID dataset\r\nTable 1 FLAG-AP describes the composition of the FLAG-AP dataset\r\nTable 2 BioID lists all the peptide identification evidence of the BioID dataset\r\nTable 2 FLAG-AP lists all the peptide identification evidence of the FLAG-AP dataset\r\nTable 3 BioID lists the SAINTexpress interactions for BioID dataset\r\nTable 3 FLAG-AP lists the SAINTexpress interactions for FLAG-AP dataset\r\n","fileCount":"251","fileSizeKB":"90519917","spectra":"0","psms":"618322","peptides":"84612","variants":"99543","proteins":"91393","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus rattus (NCBITaxon:10117)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Affinity purification;BioID;protein-protein interaction;Adenylyl cyclase;cardiomyocytes;Adcy;DatasetType:Proteomics","pi":[{"name":"Karen Colwill","email":"colwill@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056822","task":"b9a71fb661344beca8fdc6eac3888c1d","id":"1771"}, {"dataset":"MSV000096099","datasetNum":"96099","title":"GNPS -Untargeted metabolomics unveils an accumulation of flavonoids associated with the microbiome in low-performing sorghum ","user":"ciarag1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729012787000","created":"Oct. 15, 2024, 10:19 AM","description":"This dataset contains raw spectral data captured from sorghum roots collected from four Sorghum bicolor L. Moench genotypes grown in an arid field setting in Maricopa, Arizona in water-replete and water-limited conditions. We used these data to examine the root metabolome of field-grown sorghum in Arizona, USA, and related metabolomic data to microbial responses to stress.\r\n\r\n","fileCount":"123","fileSizeKB":"22291894","spectra":"58385","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sorghum bicolor (NCBITaxon:4558)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"crop metabolome;sorghum;drought;DatasetType:Metabolomics","pi":[{"name":"A. Elizabeth Arnold","email":"barnoldaz@gmail.com","institution":"University of Arizona","country":"United States of America"},{"name":"Ciara Garcia","email":"ciarag@arizona.edu","institution":"University of Arizona","country":"United States of America"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3c5702c3f1de4ba5959b42726c2ed3a5","id":"1772"}, {"dataset":"MSV000096098","datasetNum":"96098","title":"Ro5-4864, a Ligand of the Mitochondrial Translocator Protein, Protects Against Heart Failure in Mice","user":"gabrig","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1729009487000","created":"Oct. 15, 2024, 9:24 AM","description":"The 18-kDa mitochondrial translocator protein (TSPO), likely through its interaction with the voltage-dependent anion channel (VDAC), has been shown to modulate mitochondrial function and the cardiac response to pressure overload. We have previously shown that conditional knockout of TSPO limited the development of heart failure in the murine model of transverse aortic constriction (TAC). In this study, we tested the hypothesis that similar protection could be achieved by a ligand of TSPO, Ro5-4864 (Ro5), in in-vivo animal model of pressure-overload induced heart failure. To elucidate mechanisms, we performed proteomic and western blot analysis of cardiac tissue after 8 weeks of TAC in mice treated and untreated with Ro5. 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Despite their recognized role in oncogenesis, the proteomic landscape of ETS family members remains underexplored. This study focuses on the systematic analysis of high-throughput proteomics data to decode the protein-protein interaction (PPI) networks and signal transduction pathways regulated by ETS factors in human cellular systems. Our findings uncover key PPIs that highlight both the redundancy and specificity of ETS family proteins, with a particular emphasis on their cooperative interactions with the MYC oncogene. These shared protein networks are strongly implicated in the pathogenesis of kidney renal clear cell carcinoma (KIRC) and other cancer types. By identifying key ETS-regulated proteins, we offer insights into novel molecular mechanisms that hold potential for therapeutic targeting. This proteomics-based approach enhances our understanding of ETS family proteins' regulatory roles, laying the groundwork for future research into oncogenic pathways and their implications in clinical oncology.","fileCount":"6827","fileSizeKB":"211321166","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"no","keywords":"ProCisTranomic;transcription factor;protein interaction;DatasetType:Proteomics","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dec9fdde533f473393925ff5ca14d45e","id":"1776"}, {"dataset":"MSV000096090","datasetNum":"96090","title":"GNPS -Spectral data of 100 emerging chemical risks in the food chain","user":"federicopg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728951611000","created":"Oct. 14, 2024, 5:20 PM","description":"This dataset contains MS2 spectral data for 102 compounds identified as emerging chemical risks in the food chain by the European Food Safety Authority (EFSA) or classified as persistent, mobile, and toxic (PMT) compounds. The spectral data was collected at Wageningen Food Safety Research, part of Wageningen University and Research (The Netherlands), using an Orbitrap IQX instrument in positive ionization mode with a collision energy of 30. The pure standards were acquired as part of the project \"Screening for emerging chemical risks in the food chain (SCREENER), EFSA (europa.eu)\" and the dataset refinement, and dissemination were funded by the Fair Data Fund 2023 grant (The FAIR Data Fund \u2013 4TU.ResearchData). We are sharing the spectral data in .mgf and .msp formats, along with compounds\u2019 metadata such as name, synonyms, retention times, molecular formulae, SMILES, InchIKeys and EFSA-sourced predicted toxicity and toxicological endpoints.","fileCount":"6","fileSizeKB":"585","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"reference standards","instrument":"Orbitrap IQ-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Food Safety;DatasetType:Other (exposomics)","pi":[{"name":"Federico Padilla Gonzalez","email":"federico.padillagonzalez@wur.nl","institution":"Wageningen Food Safety Research","country":"Netherlands"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c9e0b445d4704261abfadabf7d140e48","id":"1777"}, {"dataset":"MSV000096088","datasetNum":"96088","title":"PRDX6 contributes to selenocysteine metabolism and ferroptosis resistance","user":"Zhiyi_Chen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728949002000","created":"Oct. 14, 2024, 4:36 PM","description":"Whole protein mass spectrometry analysis of PRDX6 after reacting with selenium compounds, including sodium selenide (Na2Se), sodium selenite (Na2SeO3) and L-Selenocystine.","fileCount":"22","fileSizeKB":"25220210","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Rattus norvegicus (NCBITaxon:10116)","instrument":"Bruker maXis time-of-flight (TOF) mass spectrometer;SCIEX TripleTOF 6600","modification":"Selenium adducts","keywords":"PRDX6, selenium adducts, whole protein analysis;DatasetType:Other (Whole protein analysis)","pi":[{"name":"Jose Pedro Friedmann Angeli","email":"pedro.angeli@virchow.uni-wuerzburg.de","institution":"University of Wuerzburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c766694559944801b0850ddf00820cea","id":"1778"}, {"dataset":"MSV000096087","datasetNum":"96087","title":"Barley grain proteome assessment using multi-environment trial data and machine learning","user":"gabrig","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728947348000","created":"Oct. 14, 2024, 4:09 PM","description":"Proteomics can be used to assess individual protein abundances, which could reflect genotypic and\/or environmental effects and potentially predict grain\/malt quality. In this study, 79 barley grain samples from a Californian multi-environment trial were assessed using liquid chromatography-mass spectrometry. A total of 3105 proteins were identified across all samples. Location, genotype, and year explained 26.7%, 17.1%, and 14.3% of variance in the relative abundance of individual proteins, respectively. Sixteen proteins with storage, DNA\/RNA binding, or enzymatic functions were found to be significantly higher\/lower in abundance (compared to the overall mean) in the Yolo 3 and Imperial Valley locations, Butta 12 and LCS Odyssey genotypes, and 2017-18 and 2021-22 years. Individual protein abundances were reasonably predictive (RMSECV=1.25-2.04%) for total, alcohol-soluble, and malt protein content and malt fine extract. This study illustrates the role of the environment on the barley proteome and the utility of proteomics and machine learning to predict grain\/malt quality.","fileCount":"3","fileSizeKB":"431146691","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hordeum vulgare (NCBITaxon:4513)","instrument":"timsTOF HT","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"barley, proteomics, malt quality, hordein, timsTOF LC-MS;DatasetType:Proteomics","pi":[{"name":"Christine Diepenbrock","email":"chdiepenbrock@ucdavis.edu","institution":"University of California, Davis","country":"usa"},{"name":"Glen Patrick Fox","email":"gpfox@ucdavis.edu","institution":"University of California, Davis","country":"usa"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056792","task":"ae9e48b4efa042c3a645e26ea8865395","id":"1779"}, {"dataset":"MSV000096086","datasetNum":"96086","title":"GNPS -Discovery of Noninvasive Biomarkers for Radiation Exposure via LC-MS-based Hair Metabolomics","user":"zhang13665","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728938930000","created":"Oct. 14, 2024, 1:48 PM","description":"Ionizing radiation exposure from a potential nuclear energy plant leak or detonation of a nuclear weapon can cause massive casualties to both warfighters and civilians. Biomarkers in biological specimens like blood and tissue, such as RNA, proteins, and metabolites, have shown potential to determine radiation dose levels. However, these biomarkers in blood and urine are short-lived, typically detectable only within hours or a few days. To address the need for stable, long-term radiation exposure biomarkers, we developed two LC-MS-based methods using non-invasive hair samples to identify radiation-induced biomarkers","fileCount":"76","fileSizeKB":"2102647","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Hair metabolomics;DatasetType:Metabolomics","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8915d8ec100840ed9af88dd4ab5bf98f","id":"1780"}, {"dataset":"MSV000096083","datasetNum":"96083","title":"GNPS - Plant transcriptome mining of stephanotic acid-type burpitides","user":"Rolandoo1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728920311000","created":"Oct. 14, 2024, 8:38 AM","description":"Leaf and stem plant material (0.2 g fresh weight) was collected from aerial tissues, frozen and ground with a MP Biomedicals FastPrep-24-5G Tissuelyser in 2ml MP Biomedicals tubes with 2.3mm Zirconia beads for 60 s at 6 m\/s. 1 mL of 80% methanol was added to ground tissue and ground as before for 20 s at 6 m\/s. The methanolic extract was incubated for 10 min in a 60C water bath, centrifuged for 5 min at 16000 x g at room temperature, and filtered through Whatman 0.2 um syringeless LCMS filters (UN503NPEORG) before LCMS analysis. Filtered extracts were transferred to LCMS vials and analyzed by LC-MS\/MS with the following settings: LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100A 150 x 3 mm LC column; LC gradient, solvent A, 0.1% formic acid; solvent B, acetonitrile (0.1% formic acid); 0 min, 10% B; 5 min, 60% B; 5.1 min, 95% B; 6 min, 95% B; 6.1 min, 10% B; 9.9 min, 10% B; 0.5 mL\/min; MS, positive ion mode; full MS, resolution 70000; mass range 400-1200 m\/z; dd-MS2 (data-dependent MS\/MS), resolution 17500; AGC target 1e5, loop count 5, isolation width 1.0 m\/z, collision energy 25 eV and dynamic exclusion 0.5 s.","fileCount":"8","fileSizeKB":"258021","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RiPP, burpitide, stephanotic acid, moroidin;DatasetType:Metabolomics","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan, Ann Arbor","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"20959bf587854448850f0ae82d834343","id":"1781"}, {"dataset":"MSV000096079","datasetNum":"96079","title":"Nanoflow Size Exclusion Chromatography_Native Mass Spectrometry of Intact Proteoforms and Protein Complexes","user":"ZiranZhai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728912905000","created":"Oct. 14, 2024, 6:35 AM","description":"Native size-exclusion chromatography (SEC) and native mass spectrometry (nMS) are techniques used to characterize oligomeric states of protein complexes and their proteoform distributions. Coupling SEC with nMS combines the advantages of liquid-phase separation of oligomeric states (SEC) with molecular measurement of the complex (nMS), reducing bias that may be present in nMS due to ion suppression when oligomers are ionized together and additionally allowing buffer exchange of the sample. SEC-nMS uses volatile buffers and relatively wide-diameter columns (e.g., 1 mm), with flow rates in the tens of microliter per minute. To ionize sample components under this flow regime, relatively harsh electrospray ionization (ESI) desolvation conditions, including nebulization gas heating, electrospray, and in-source dissociation voltages, are needed, which may result in protein dissociation or denaturation. Also, relatively large amounts of samples are required to provide sufficient sensitivity for detection. Herein, we describe the development of a nanoflow SEC-nMS method and its application to the analysis of model proteins and complexes. We studied the influence of several parameters on the separation performance of capillary SEC columns with a 200 um I.D., such as frits and packing solvents. NanoSEC-MS was performed at a flow rate of 0.5 uL min-1, allowing for buffer exchange and oligomer separation. The nanoflow regime utilizes coated fused silica emitters to perform ionization without the assistance of heated gas flow or temperature and reduces the voltages applied (about 1.8 kV). This resulted in a 10-fold increased MS peak intensity with respect to a microflow method using a 1 mm I.D. SEC column. Furthermore, we evaluated the performance of three injection approaches for sensitivity and separation: large-volume injection (1 uL), nano-volume injection (50 nL), and an online mix-bed ion-exchange capillary trap column. The proposed setup and workflow provide opportunities for native top-down analysis of proteins in sample-limited applications.","fileCount":"61","fileSizeKB":"1865367","spectra":"685","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ovalbumin;L-asparaginase;BSA;concanavalin A;myoglobin;alcohol dehydrogenase ;catalase;enolase;proteinase K;Trastuzumab;Ovitrelle;Human Chorionic Gonadotropin ","instrument":"Q Exactive Orbitrap Mass Spectrometer","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"nanoflow rate;size-exclusion chromatography;native mass spectrometry;protein and protein complexes;intact analysis;DatasetType:Proteomics","pi":[{"name":"Ziran Zhai","email":"z.zhai@uva.nl","institution":"University of Amsterdam","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"320423d5abaf4ce192f2434a91a366c3","id":"1782"}, {"dataset":"MSV000096077","datasetNum":"96077","title":"Staphylococcal SplA and SplB serine proteases target ubiquitin(-like) specific proteases","user":"steill","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728910572000","created":"Oct. 14, 2024, 5:56 AM","description":"Staphylococcus aureus is a gram-positive opportunistic pathogen that has colonized nearly 30% of the human population and can cause life-threatening infections. The antibiotic treatment of S. aureus infection is often hindered by several resistances expressed by the pathogen, and therefore alternative therapies are much-needed. S. aureus exports a variety of virulence factors, among them numerous proteases. In 1996, a novel set of extracellular serine proteases was discovered: the serine protease-like proteins (Spls). Spl proteins are expressed by most clinical isolates of S. aureus, but their pathophysiological substrates and role during the infection are largely unknown. Using SplA and SplB recombinantly expressed in E. coli, we identified a group of proteins until now unknown to be targeted by SplA and SplB: ubiquitin(-like) specific proteases. Distinct cleavage sites within these targets of SplA and SplB were identified by mass spectrometry and confirmed by site-directed mutagenesis of the target proteins. Since many cellular immune responses are tightly regulated by ubiquitylation, the specific cleavage of involved proteins could represent a role of Spls during infection.","fileCount":"74","fileSizeKB":"45742540","spectra":"742623","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus arlettae (NCBITaxon:29378)","instrument":"Orbitrap Exploris 480;Q Exactive Plus","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Staphylococcus aureus;DatasetType:Proteomics","pi":[{"name":"Leif Steil","email":"steil@uni-greifswald.de","institution":"University Medicine Greifswald, Department of Functional Genomics","country":"germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1537b48c815a4a8daeaa66f0c2a1aea2","id":"1783"}, {"dataset":"MSV000096075","datasetNum":"96075","title":"THE AGING SYNAPSE: AN INTEGRATED PROTEOMIC AND TRANSCRIPTOMIC ANALYSIS.","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728907147000","created":"Oct. 14, 2024, 4:59 AM","description":"An important hallmark of aging is the loss of proteostasis, which can lead to the formation of protein aggregates and mitochondrial dysfunction in neurons. Although it is well known that protein synthesis is finely regulated in the brain, especially at synapses, where mRNAs are locally translated in activity-dependent manner, little is known as to the changes in the synaptic proteome and transcriptome during aging. Therefore, this work aims to elucidate the relationship between transcriptome and proteome at soma and synaptic level during aging. \nProteomic and transcriptomic data analysis reveal that, in young animals, proteins and transcripts are correlated and synaptic regulation is driven by changes in the soma. During aging, there is a decoupling between transcripts and proteins and between somatic and synaptic compartments. Furthermore, soma-synapse gradient of ribosomal genes changes upon aging, i.e. ribosomal transcripts are less abundant and ribosomal proteins are more abundant in synaptic compartment of old mice with respect to younglings. Additionally, transcriptomics data highlight a difference in the splicing of certain synaptic mRNA with aging. Taken together, our data provide a valuable resource for the study of the aging synapse.\n","fileCount":"55","fileSizeKB":"131542044","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"RNA-Seq, Synaptosomes, Alternative Splicing, Bioinformatics, Aging;DatasetType:Proteomics","pi":[{"name":"Alessandro Cellerino","email":"Alessandro.Cellerino@leibniz-fli.de","institution":"Leibniz Institute on Aging, Beutenbergstr. 11, 07745 Jena","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD056780","task":"b2cf624f9229489eb9f47b22b7e9244f","id":"1784"}, {"dataset":"MSV000096072","datasetNum":"96072","title":"Chemoproteomics analysis revealed photodynamic therapy (PDT) effect of Novel Photo-switchable Photosensitizer","user":"KyungTae","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728881690000","created":"Oct. 13, 2024, 9:54 PM","description":"The study titled \"Dyad system of BOAHY-BODIPY Conjugates as Novel Photo-switchable Photosensitizer for Photodynamic Therapy\" investigated the photodynamic therapy (PDT) potential of a compound that switches structures (Z form to E form) under UV irradiation. The compound generates reactive oxygen species (ROS) when exposed to light, with the Z form producing more ROS than the E form, leading to higher cytotoxicity. Chemoproteomics analysis revealed more protein modifications in the Z form, indicating greater ROS-induced changes compared to the E form. This suggests that the PDT effect and photo-switching ability can significantly impact biological processes, influencing genetic modifications and highlighting its potential in unbiased biomarker discovery for PDT studies.","fileCount":"121","fileSizeKB":"32231728","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Chemoproteomics;photodynamic therapy (PDT);reactive oxygen species (ROS);Photo-switchable Photosensitizer;DatasetType:Proteomics","pi":[{"name":"Jun-Seok Lee","email":"junseoklee@korea.ac.kr","institution":"Korea University College of Medicine","country":"republic of korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2506df1ebd0b4adfb319e8aef6c8c776","id":"1785"}, {"dataset":"MSV000096071","datasetNum":"96071","title":"Fisher et al CoREST Inhibition ","user":"Martolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728866211000","created":"Oct. 13, 2024, 5:36 PM","description":"Immunopeptidome analysis in support of the manuscript \"CoREST Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity\"","fileCount":"232","fileSizeKB":"8824796","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"oxidation [Methionine]","keywords":"immunopeptidomics;mass spectrometry;DatasetType:Proteomics","pi":[{"name":"Jarrod Marto","email":"jarrod_marto@dfci.harvard.edu","institution":"DFCI","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cac8ca528fc04ee39d71610dcff76759","id":"1786"}, {"dataset":"MSV000096065","datasetNum":"96065","title":"Mitochondrial DNA affects tau expression and phosphorylation in Alzheimers Disease and aging in humans and cybrid cell lines","user":"KUMC_Prot","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728658192000","created":"Oct. 11, 2024, 7:49 AM","description":"We investigate the role of mitochondrial DNA in Alzheimers Disease pathology using human cybrid cell lines and investigate the relationships between biomarker expression from cybrids and clinically relevant outcomes from the same individuals. Proteomic analysis of cybrids showed significant alterations in pathways related to mitochondrial dysfunction and energy synthesis in AD and mildly cognitively impared cybrids compared to cognitively healthy controls.","fileCount":"87","fileSizeKB":"290416829","spectra":"0","psms":"1608267","peptides":"31656","variants":"39476","proteins":"5091","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Alzheimers disease;mitochondrial dysfunction;DatasetType:Proteomics","pi":[{"name":"Jill K Morris","email":"jmorris2@kumc.edu","institution":"University of Kansas Medical Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056731","task":"5d9aa567aba34b03b671f08bc0608d69","id":"1787"}, {"dataset":"MSV000096063","datasetNum":"96063","title":"Lysosomal protein atlas of brain cell types identifies SLC45A1-associated disease as a lysosomal disorder","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728656061000","created":"Oct. 11, 2024, 7:14 AM","description":"We identify dozens of novel lysosomal proteins across brain cells, including those linked to disease. Notably, we found that SLC45A1, mutations in which cause a monogenic neurological disease, is a neuron-specific lysosomal protein.\nHere, we characterize the change in proteomic composition of the lysosome upon SLC45A1 KO, under fed and starved (serum deprived) conditions, as well as global whole cell proteomic changes.\n\nNote: Raw file names do not match real conditions. For proper condition assignment, please check the conditions table.","fileCount":"60","fileSizeKB":"370485066","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;nanoACQUITY UPLC System with 1D Technology","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"LysoIP;DatasetType:Proteomics","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD056729","task":"e5e5265c9dcd493f891152383a927215","id":"1788"}, {"dataset":"MSV000096062","datasetNum":"96062","title":"Analysis of changes in the proteome of VIC and VEC cells co-cultured using SILAC medium","user":"egor_repkin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728643267000","created":"Oct. 11, 2024, 3:41 AM","description":"Here we present data from a pilot experiment for co-culturing valve interstitial cells (VIC) and valve endothelial cells (VEC) in SILAC medium and analyzing changes in VIC and VEC proteome to study osteodifferentiation in the aortic valve.\nProtein isolation.\nThe RIPA solution with cells was exposed to ultrasound (2 times for 20 minutes with intermediate incubation on ice for 10 minutes) for protein extraction. Then protein was precipitated by 4 volumes of iced cold acetone (LC-MS Grade; LiChrosolv) and washed with methanol (LC-MS Grade; LiChrosolv). Protein pellet was air-dried and resuspended in 8 M urea (Sigma Aldrich, St. Louis, MO, USA) in 50 mM ammonium bicarbonate (Sigma Aldrich, St. Louis, MO, USA). \nSample preparation for shotgun proteomics.\nProtein concentrations were measured by Qubit 2.0 fluorimeter (Thermo Fisher Sci, Waltham, MA, USA) with QuDye Protein Quantification Kit (Lumiprobe, Moscow, Russia). 15 mkg of each sample were used for further LC-MS\/MS analysis. Samples were incubated for 1 h at 37C with 5 mM DTT (Sigma Aldrich, St. Louis, MO, USA) with subsequent incubation in 15 mM iodoacetamide (Sigma Aldrich, St. Louis, MO, USA) for 30 min in the dark at room temperature, followed by quenching with 5 mM DTT. The samples were diluted with seven volumes of 50 mM ammonium bicarbonate and incubated for 17 h at 37C with Trypsin Gold in ratio 1:50 (Promega, Madison, WI, USA). Tryptic peptides were desalted by solid-phase extraction using stage-tips (Rappsilber et al., 2007) cording to standard protocol (Mamontova et al., 2019). Stage-tips were prepared by filling of polypropylene Vertex pipette tips (200 mkl; SSIbio, USA) with six layers of C18 reversed phase excised from Empore 3M C18 extraction disks (3M-Corporation, Maplewood, MN, USA). The desalted peptides were evaporated in a Labconco Centrivap Centrifugal Concentrator (Labconco, USA) and dissolved in water\/0.1% formic acid (LC-MS Grade; LiChrosolv) to approximate final concentration of 250 ng\/mkl for further LC-MS\/MS analysis.\nLC-MS\/MS analysis.\nApproximate 500 ng of peptides were used for shotgun proteomics analysis by LC-MS\/MS with ion mobility in TimsToF Pro mass spectrometer (Bruker Daltonics, Bremen, Germany) with nanoElute UHPLC system (Bruker Daltonics, Bremen, Germany). UHPLC was performed in one-column separation mode with Aurora Ultimate 25 cm separation column (C18 stationary phase, length 250 mm, diameter 0.075 mm, particle size 1.7 mkm, pore size 120 A; IonOpticks, Fitzroy, Australia) in gradient mode with 300 nL\/min flow rate with column temperature at 60C. Phase A was water\/0.1% formic acid, phase B was acetonitrile\/0.1% formic acid (LC-MS Grade; LiChrosolv). The gradient was from 2% to 18% phase B for 44 min, then to 25% of phase B for 11 min, then to 37% of phase B for 5 min, then to 85% of phase B for 2 min with subsequent wash with 85% phase B for 15 min. The column was equilibrated with 4 column volumes before each sample. Parameters of ion source for electrospray ionization: 4500 V of capillary voltage, 3 l\/min N2 flow, and 180C source temperature. The mass spectrometry acquisition was performed in DDA PASEF mode in positive polarity with the fragmentation of ions with at least two charges in m\/z range from 100 to 1700 and ion mobility range from 0.60 to 1.60 1\/K0.\nDDA-PASEF raw data files were analyzed in Peaks Xpro software (v.10.6) (Bioinformatics Solutions Inc., Canada) using human protein SwissProt database (uploaded on 19 January 2024). The search parameters are as follows: trypsin\/P protease; 2 possible missed cleavage sites; maximum number of variable modifications on a peptide was set to 2; 13C(6) 15N(4) SILAC label, 13C(6) 15N(2) SILAC label, methionine oxidation, N-term acetylation, NQ-deamidation, carbamidomethylation on cysteine were possible modifications; precursor charge range from 2 to 7; parent mass error tolerance 10.0 ppm, fragment mass error tolerance 0.05 Da; FDR 1%.","fileCount":"20","fileSizeKB":"10700178","spectra":"0","psms":"175098","peptides":"29564","variants":"62322","proteins":"3281","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:267 - \\\"13C(6) 15N(4) Silac label.\\\";UNIMOD:259 - \\\"13C(6) 15N(2) Silac label.\\\"","keywords":"Osteodifferentiation, aortic stenosis, VIC, VEC, cell co-cultivation, SILAC, LC-MS\/MS, proteomics;DatasetType:Proteomics","pi":[{"name":"Egor A. Repkin","email":"erepkin53@gmail.com","institution":"Saint-Petersburg State University","country":"Russia"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD056722","task":"8d3111a6f64b4e8eb12a277eb3b5bc0e","id":"1789"}, {"dataset":"MSV000096061","datasetNum":"96061","title":"GNPS - Per- and polyfluoroalkyl substances (PFAS)_Testrun20241010","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728601198000","created":"Oct. 10, 2024, 3:59 PM","description":"Preliminary data from negative ESI test run on PFAS containing samples","fileCount":"11","fileSizeKB":"805008","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PFAS;DatasetType:Metabolomics","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"43f8e791d1dd4dcdbf57252056adb282","id":"1790"}, {"dataset":"MSV000096056","datasetNum":"96056","title":"Sex-specific toxicity with PCB exposures and implications on the gut-liver axis ","user":"mmerchant","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728511299000","created":"Oct. 9, 2024, 3:01 PM","description":"Liver tissue (n=5 per group) from male and female C57BL\/6 mice exposed to Aroclor1260 (20 mg\/kg) and PCB126 (20 ug\/kg) p.o for 2 weeks were extracted from mouse livers in 1% SDS modified RIPA buffer using bead homogenization. Protein lysates (200 ug) were trypsinized using the modified filter-aided sample preparation method. The digested peptides desalted and concentrated using C18 Proto 300 A ultra microspin column. Digested peptide samples (50 ug) were then labeled with tandem mass tag (TMT) TMT10plex isobaric label reagent set (Thermo Fisher Scientific). Labeled samples were concentrated and desalted with Oasis HLB extraction cartridges (Waters Corporation, Milford, MA). Admixed samples were then separated by high pH reversed phase separation with fraction concatenation. Concatenated samples were dried, resuspended in 2% acetonitrile\/0.1% formic aid and 1 uL of each fraction was analyzed on EASY nLC 1000 UHPLC system (Thermo Fisher Scientific) and an Orbitrap Elite ETD mass spectrometer (Thermo Fisher Scientific). The raw spectral data obtained from the mass spectrometer were analyzed using Proteome Discoverer (2.5.0.400 Settings) considering TMT modifications. Peptide and protein assignments were used at a 1% FDR filter.","fileCount":"60","fileSizeKB":"30685207","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"liver;PCB;sexual dimorphism;multiomics","pi":[{"name":"Michael L. Merchant, PhD","email":"mlmerc02@louisville.edu","institution":"University of Louisville","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1605887c863c4f5d826b3f51366fc054","id":"1791"}, {"dataset":"MSV000096052","datasetNum":"96052","title":"Human Hair Atlas: the metabolome and lipidome landscape across hair lengths","user":"AnnemiekevandeLavoir","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728462214000","created":"Oct. 9, 2024, 1:23 AM","description":"HILIC-POS: MS1, MS2, 5x QC pool\nHILIC-NEG: MS1, MS2, 5x QC pool\nRPLC-POS: MS1, MS2, iterative MS2, 6x QC pool\nRPLC-NEG: MS1, MS2, iterative MS2, 6x QC pool","fileCount":"6736","fileSizeKB":"45942157","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6560 Q-TOF LC\\\/MS;6530A Q-TOF LC\\\/MS","modification":"PRIDE:0000398","keywords":"LC-MS\/MS, Ion mobility, lipid identification, lipidomics and metabolomics profiling, segmental hair analysis, hair cosmetics, exposome","pi":[{"name":"Maria van de Lavoir","email":"maria.vandelavoir@uantwerpen.be","institution":"University of Antwerp","country":"Belgium"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ffa60e21df8d4a35b2d078f981f64f72","id":"1792"}, {"dataset":"MSV000096051","datasetNum":"96051","title":"GNPS -LC-MS\/MS analysis of Sindora siamensis_GNPS2","user":"LOOKie","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728458986000","created":"Oct. 9, 2024, 12:29 AM","description":"This research focuses on the bioactive compounds from Sindora siamensis extracts with two different solvents: ethanol and ethyl acetate. The antioxidant and anticancer properties of S. siamensis have been reported in this study.","fileCount":"49","fileSizeKB":"1418876","spectra":"92900","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sindora siamensis (NCBITaxon:327149)","instrument":"compact","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sindora siamensis;phytochemical;antioxidant;anticancer;Plant extraction","pi":[{"name":"Thapanee Pruksatrakul","email":"thapanee.pru@biotec.or.th","institution":"National Center for Genetic Engineering and Biotechnology (BIOTEC) ","country":"Thailand"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"03a1ac43b15b49628ab57b40f83ace54","id":"1793"}, {"dataset":"MSV000096049","datasetNum":"96049","title":"GNPS - Quantification N-acyl lipids (stool samples and microbial monocultures)","user":"helenamrusso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728429520000","created":"Oct. 8, 2024, 4:18 PM","description":"Stool samples are part of the MSV000092833 dataset (HNRC cohort). Microbial monocultures contained histamine, cadaverine, and putrescine added to the media. MS\/MS data was acquired on a Q Exactive Orbitrap in positive ionization mode. Quantification of N-acyl lipids was performed (histamine-C2:0, histamine-C3:0, histamine-C4:0, histamine-C5:0, cadaverine-C2:0, cadaverine-C3:0, cadaverine-C5:0, cadaverine-C6:0, and dopamine-C2:0), while retention time matching was also done for histamine-C6:0, cadaverine-C7:0, serotonin-C2:0, and tryptophan-C3:0. All the N-acyl lipids used were acquired as pure standards from commercial vendors.","fileCount":"1250","fileSizeKB":"45780832","spectra":"1735191","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Catenibacterium mitsuokai DSM 15897 (NCBITaxon:451640);Collinsella aerofaciens ATCC 25986 (NCBITaxon:411903);Dorea longicatena DSM 13814 (NCBITaxon:411462);Eubacterium siraeum DSM 15702 (NCBITaxon:428128);Holdemanella biformis (NCBITaxon:1735);Megasphaera sp. (NCBITaxon:2023260);Prevotella buccae D17 (NCBITaxon:575611);Roseburia inulinivorans DSM 16841 (NCBITaxon:622312);Streptococcus thermophilus LMD-9 (NCBITaxon:322159);Desulfovibrio piger ATCC 29098 (NCBITaxon:411464)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"N-acyl lipids;stool;microbial monocultures","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0a88fc387c7b4ba5b34d7ee3135efce6","id":"1794"}, {"dataset":"MSV000096046","datasetNum":"96046","title":"Nascent transcript O-MAP reveals the molecular architecture a single-locus subnuclear compartment built by RBM20 and the TTN noncoding RNA","user":"shaoen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728417737000","created":"Oct. 8, 2024, 1:02 PM","description":"We here adapt Oligonucleotide-mediated proximity-interactome mapping (O-MAP), a novel RNA-targeted microenvironment-mapping method, to biochemically characterize the molecular neighborhoods near individual genomic loci. By targeting O-MAP to introns within the TTN pre-mRNA, we have systematically mapped the chromatin loci, RNAs, and proteins within a cardiomyocyte-specific \"RNA factory\" nucleated on these TTN-derived noncoding transcripts. This revealed an unanticipated compartmental architecture that organizes trans-chromosomal domains into a hub of transcriptionally silenced chromatin, and which recruits dozens of unique RNA-binding and chromatin-scaffolding factors, including QKI and SAFB, along with their target transcripts. Loss of the cardiac-specific splicing factor RBM20, a master regulator of TTN splicing, remodels nearly every facet of factor architecture, suggesting new mechanisms in RBM20-driven dilated cardiomyopathy. This establishes O-MAP as a pioneering method for probing single-locus, microcompartment-level interactions that are opaque to conventional tools, and suggests new mechanisms by which coding genes can \"moonlight\" as nuclear-architectural noncoding RNAs.","fileCount":"13","fileSizeKB":"9841113","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"omap;dia","pi":[{"name":"David Shechner","email":"shechner@uw.edu","institution":"University of Washington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056627","task":"042d9f549d904e73af3b86b38a420dfa","id":"1795"}, {"dataset":"MSV000096045","datasetNum":"96045","title":"Identification of Plasmodium vivax Receptors of erythroid cell lines","user":"droeth","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728416576000","created":"Oct. 8, 2024, 12:42 PM","description":"Identification of PvRBP1a binding proteins in the erythroid cell line JK-1 using turboID","fileCount":"25","fileSizeKB":"13706666","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:3 - \\\"Biotinylation.\\\"","keywords":"Plasmodium vivax;turboID;Receptors;Membrane Proteins;Malaria","pi":[{"name":"Manuel Alfonso Patarroyo","email":"mapatarr.fidic@gmail.com","institution":"Fundacion Instituto de Inmunologia de Colombia ","country":"Colombia"},{"name":"Markus Kalkum","email":"mkalkum@coh.org","institution":"City of Hope","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"65744e8a39d946d996997fd5eff55ba3","id":"1796"}, {"dataset":"MSV000096043","datasetNum":"96043","title":"Metabolic Control of Glycosylation Forms for Establishing Glycan-Dependent Protein Interaction Networks","user":"xie753951","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728392130000","created":"Oct. 8, 2024, 5:55 AM","description":"Protein-protein interactions (PPIs) provide essential insights into the complex molecular mechanisms and signaling pathways within cells that regulate development and disease-related phenotypes. However, for membrane proteins, the impact of various forms of glycosylation has often been overlooked in PPI studies. In this study, we introduce a novel approach, glycan-dependent affinity purification followed by mass spectrometry (GAP-MS), to assess variations in PPIs for any glycoprotein of interest under different glycosylation conditions. As a proof of principle, we selected four glycoproteins\u2014BSG, CD44, EGFR, and SLC3A2\u2014as baits to compare their co-purified partners across five metabolically controlled glycan conditions. The findings demonstrate the capability of GAP-MS to identify PPIs influenced by altered glycosylation states, establishing a foundation for systematically exploring the Glycan-Dependent Protein Interactome (GDPI) for other glycoproteins of interest.","fileCount":"125","fileSizeKB":"208885674","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"Glycosylation","keywords":"Glycosylation;Glycorotein Interactome;Glycoprotein;AP-MS","pi":[{"name":"Benjamin A. Garcia","email":"bagarcia@wustl.edu","institution":"Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine","country":"United States"},{"name":"Yixuan Xie","email":"axexie@126.com","institution":"Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b95f50572be64fa68fa53e1c26e72de5","id":"1797"}, {"dataset":"MSV000096042","datasetNum":"96042","title":"AMBRA1 controls the translation of immune-specific genes in T lymphocytes","user":"BHaeup","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728391905000","created":"Oct. 8, 2024, 5:51 AM","description":"T cell receptor (TCR) engagement causes a global cellular response that entrains signaling pathways, cell cycle regulation, and cell death. The molecular regulation of mRNA translation in these processes is poorly understood. During a whole-genome CRISPR screen for regulators of CD95 (Fas\/APO-1)-mediated T cell death, we identified AMBRA1, a protein previously studied for its roles in autophagy, E3 ubiquitin ligase activity, and cyclin regulation. T cells lacking AMBRA1 resist Fas-mediated cell death by down-regulating FAS expression at the translational level. We show that AMBRA1 is a vital regulator of ribosome protein biosynthesis and loading on select mRNAs that plays a key role in balancing TCR signaling with cell cycle regulation pathways. We also found that AMBRA1 itself is translational controlled by TCR stimulation via the CD28-PI3K-mTORC1-EIF4F pathway. Together, these findings shed light on the molecular control of translation after T cell activation and implicate AMBRA1 as a translational regulator that governs TCR signaling, cell cycle progression and T cell death.","fileCount":"35","fileSizeKB":"35859834","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Protein translation, Fas signaling pathway, AMBRA1, T cell death, T cell activation","pi":[{"name":"Michael J. Lenardo","email":"lenardo@nih.gov","institution":"1Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20814","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056612","task":"827660205c36415f9f30597f79e77cc9","id":"1798"}, {"dataset":"MSV000096039","datasetNum":"96039","title":"GNPS - Mouse Feces from Germ Free Animal (3xTG, 5xFAD, and WT) - U19 AGMP Caltech","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728340529000","created":"Oct. 7, 2024, 3:35 PM","description":"Mouse fecal samples from germ free (GF) animals model 3xTG and 5xFAD. Study part of the Alzheimers Gut Microbiome Project (AGMP). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"490","fileSizeKB":"14632571","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Feces;Mouse;3xTG;5xFAD;Germ Free;Alzheimer's disease","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"55ec7f9e84124ca0827f0d7958192c34","id":"1799"}, {"dataset":"MSV000096038","datasetNum":"96038","title":"GNPS - Mouse Cecal Content (3xTG, 5xFAD, and WT) - U19 AGMP Caltech","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728340430000","created":"Oct. 7, 2024, 3:33 PM","description":"Mouse cecal content samples from animal models 3xTG and 5xFAD. Study part of the Alzheimers Gut Microbiome Project (AGMP). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"871","fileSizeKB":"25634952","spectra":"847342","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cecal Content;Mouse;3xTG;5xFAD;Alzheimer's disease","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7d99b115a6d346d5b787c7ce10030a79","id":"1800"}, {"dataset":"MSV000096037","datasetNum":"96037","title":"GNPS - Mouse Liver (3xTG, 5xFAD, and WT) - U19 AGMP Caltech","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728340201000","created":"Oct. 7, 2024, 3:30 PM","description":"Mouse liver samples from animal models 3xTG and 5xFAD. Study part of the Alzheimers Gut Microbiome Project (AGMP). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"457","fileSizeKB":"15992819","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Liver;Mouse;3xTG;5xFAD;Alzheimer's disease","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"60905386a3f944e1b859b8d96592980b","id":"1801"}, {"dataset":"MSV000096036","datasetNum":"96036","title":"GNPS - Mouse Serum (3xTG, 5xFAD, and WT) - U19 AGMP Caltech","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728340099000","created":"Oct. 7, 2024, 3:28 PM","description":"Mouse serum samples from animal models 3xTG and 5xFAD. Study part of the Alzheimers Gut Microbiome Project (AGMP). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"420","fileSizeKB":"11401554","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Serum;Mouse;3xTG;5xFAD;Alzheimer's disease","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8249c40f7e3d4ea8a4e20871725a7ca3","id":"1802"}, {"dataset":"MSV000096035","datasetNum":"96035","title":"GNPS - Mouse Brain (3xTG, 5xFAD, and WT) - U19 AGMP Caltech","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728339777000","created":"Oct. 7, 2024, 3:22 PM","description":"Mouse brain samples from animal models 3xTG and 5xFAD. Study part of the Alzheimers Gut Microbiome Project (AGMP). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"393","fileSizeKB":"13932868","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Brain;Mouse;3xTG;5xFAD;Alzheimer's disease","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b467af929b9347b8b0aa13f41957fa4d","id":"1803"}, {"dataset":"MSV000096034","datasetNum":"96034","title":"Inferring post-transcriptional regulation within and across cell types in human testis","user":"saadsultankhan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728330745000","created":"Oct. 7, 2024, 12:52 PM","description":"Single cell proteomic datasets analyzing primary human testes. Work in the study consisted of 5 nPoP sample preparations (3 via SCoPE2\/DDA, 1 via SCoPE2\/pSCoPE acquired on the QExactive and 1 via plexDIA acquired on the TIMS-ToF SCP). \n\nMore information and links to the searched\/processed data are available via the project website: https:\/\/scp.slavovlab.net\/BayesPG","fileCount":"10069","fileSizeKB":"980088818","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;timsTOF SCP","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Single Cell Proteomics;plexDIA;SCoPE2;Primary Tissue;Testes;Post Transcriptional Regulation","pi":[{"name":"Nikolai Slavov","email":"n.slavov@northeastern.edu","institution":"Northeastern University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"22015f916a9b4c19a8c7df07f81bafb8","id":"1804"}, {"dataset":"MSV000096028","datasetNum":"96028","title":"GNPS - DogFood_MS\/MS analysis on Orbitrap in positive-ion mode","user":"hgouda","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728069212000","created":"Oct. 4, 2024, 12:13 PM","description":"DogFood_MS\/MS analysis on Orbitrap in positive-ion mode","fileCount":"8","fileSizeKB":"454566","spectra":"4992","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No Species","instrument":"Q Exactive GC Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dog_Food","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7a53b99e52d74012ba064940ce095508","id":"1805"}, {"dataset":"MSV000096027","datasetNum":"96027","title":"Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress","user":"Trixi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728068880000","created":"Oct. 4, 2024, 12:08 PM","description":"Ubiquitin-dependent proteolysis regulates diverse cellular functions with high substrate specificity, which hinges on the ability of ubiquitin E3 ligases to decode the targets degradation signals, i.e., degrons. Here we show that BACH1, a transcription repressor of antioxidant response genes, features two distinct unconventional degrons encrypted in the quaternary structure of its homodimeric BTB domain. These two degrons are both functionalized by oxidative stress and are deciphered by two complementary E3s. FBXO22 recognizes a degron constructed by the BACH1 BTB domain dimer interface, which is unmasked from transcriptional co-repressors after oxidative stress releases BACH1 from chromatin. When this degron is impaired by oxidation, a second BACH1 degron manifested by its destabilized BTB dimer is probed by a pair of FBXL17 that remodels the substrate into E3-bound monomers for ubiquitination. Our findings highlight the multidimensionality of protein degradation signals and the functional complementarity of different ubiquitin ligases targeting the same substrate. The entry contains the mass spectrometric raw file for the in vitro S-nitrosylation assay using NO donor NOR3.","fileCount":"3","fileSizeKB":"980251","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:275 - \\\"S-nitrosylation.\\\"","keywords":"Bach1;S-nitrosylation;Degron","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"New York University School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056513","task":"c119ea69572c47e1978d503ba04835af","id":"1806"}, {"dataset":"MSV000096026","datasetNum":"96026","title":"Sirtuin-5 is recruited to hepatic peroxisomes in mice fed dodecanedioic acid but has little impact on the peroxisomal succinylome","user":"JoannaBons","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728060429000","created":"Oct. 4, 2024, 9:47 AM","description":"Lysine succinylation, and its reversal by sirtuin-5 (SIRT5), is known to modulate mitochondrial fatty acid beta-oxidation (FAO). We recently showed that feeding mice dodecanedioic acid, a 12-carbon dicarboxylic acid (DC12) that can be chain-shortened four rounds to succinyl-CoA, drives high-level protein hypersuccinylation in the peroxisome, particularly on peroxisomal FAO enzymes. But the ability of SIRT5 to reverse DC12-induced peroxisomal succinylation, or to regulate peroxisomal FAO in this context, remained unexplored. Here, we showed that feeding DC12 strongly recruits SIRT5 into hepatic peroxisomes. Knocking out SIRT5 impaired peroxisomal FAO as evidenced by reduced 14C-DC12 flux in liver homogenates and elevated levels of partially shortened DC12 catabolites in urine. Further, mass spectrometry revealed a trend toward less peroxisomal protein succinylation in SIRT5 knockout liver. This is consistent with reduced flux of DC12 through the peroxisomal FAO pathway, thereby reducing production of the succinyl-CoA that chemically reacts with lysine residues to produce protein succinylation. Mass spectrometry comparisons of site-level succinylation in wildtype and SIRT5 knockout liver did not reveal any clear pattern of SIRT5 target sites in the peroxisome after DC12 feeding. However, SIRT5 co-immunoprecipitated with 15 peroxisomal proteins including the key peroxisomal FAO enzymes acyl-CoA oxidase-1 and enoyl-CoA\/3-hydroxyacyl-CoA dehydrogenase (EHHADH). In vitro, recombinant SIRT5 partially desuccinylated chemically modified recombinant ACOX1a, ACOX1b, and EHHADH. Desuccinylation by SIRT5 had no effect on enzyme activity for ACOX1a and EHHADH. For ACOX1b, SIRT5-mediated desuccinylation decreased activity by about 15%. Possible interpretations of this data are discussed.","fileCount":"81","fileSizeKB":"149885753","spectra":"4447196","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:64 - \\\"Succinic anhydride labeling reagent light form (N-term & K).\\\"","keywords":"Peroxisome;Sirtuin-5;Lysine succinylation;Data-independent acquisition;Fatty acid oxidation;Quantitative proteomics","pi":[{"name":"Birgit Schilling","email":"bschilling@buckinstitute.org","institution":"Buck Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD056506","task":"21320bba927a4e409db5416af1651591","id":"1807"}, {"dataset":"MSV000096025","datasetNum":"96025","title":"Allelic effects on KLHL17 expression likely mediated by JunB\/D underlie a PDAC GWAS signal at chr1p36.33","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728057113000","created":"Oct. 4, 2024, 8:51 AM","description":"Pancreatic Ductal Adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths in the U.S. Both rare and common germline variants contribute to PDAC risk. Here, we fine-map and functionally characterize a common PDAC risk signal at 1p36.33 identified through a genome wide association study (GWAS). One of the fine-mapped SNPs, rs13303160 (r2=0.93 in 1000G EUR samples, OR=1.23, P value=2.74x10-9) demonstrated allele-preferential gene regulatory activity in vitro and allele-preferential binding of JunB and JunD in vitro and in vivo. Expression Quantitative Trait Locus (eQTL) analysis identified KLHL17 as a likely target gene underlying the signal. Proteomic analysis identified KLHL17 as a member of the Cullin-E3 ubiquitin ligase complex in PDAC-derived cells. In silico differential gene expression analysis of the GTExv8 pancreas data suggested an association between lower KLHL17 (risk associated) and pro-inflammatory pathways. We hypothesize that KLHL17 may mitigate inflammation by recruiting pro-inflammatory proteins for ubiquitination and degradation thereby influencing PDAC risk.","fileCount":"81","fileSizeKB":"78186313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"KLHL17, functional genetics, GWAS, (pancreatic) cancer","pi":[{"name":"Laufey Anumdadottir","email":"amundadottir@nih.gov","institution":"NCI\/DCEG","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e357b08275e34f89b280e716ccd20d8f","id":"1808"}, {"dataset":"MSV000096023","datasetNum":"96023","title":"Red-shifted chlorophyll a absorption in Light-Harvesting Complexes - The case of Trachydiscus minutus ","user":"konik","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1728051425000","created":"Oct. 4, 2024, 7:17 AM","description":"Photosynthetic organisms harvest light for energy. Some eukaryotic algae have specialized in harvesting far-red light by tuning chlorophyll a absorption through a mechanism still to be elucidated. Here, we combined optically detected magnetic resonance and pulsed electron paramagnetic resonance measurements on red-adapted light-harvesting complexes, rVCP, isolated from the freshwater eustigmatophyte alga Trachydiscus minutus to identify the location of the pigments responsible for this remarkable adaptation. The pigments have been found to belong to an excitonic cluster of chlorophylls a at the core of the complex, close to the central carotenoids in L1\/L2 sites. A pair of structural features of the Chl a403\/a603 binding site, namely the histidine-to-asparagine substitution in the magnesium-ligation residue and the small size of the amino acid at the i-4 position, resulting in a [A\/G]xxxN motif, are proposed to be the origin of this trait. Phylogenetic analysis of various eukaryotic red antennae identified several potential LHCs that could share this tuning mechanism.","fileCount":"58","fileSizeKB":"1045554","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trachydiscus minutus","instrument":"timsTOF Pro","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Light-harvesting;Red-shifted LHC;triplet;ODMR;EPR;eustigmatophyte","pi":[{"name":"Alessandro Agostini","email":"alessandro.agostini.1@unipd.it","institution":"Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy; Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic","country":"Italy, Czech Republic"},{"name":"Radek Litvin","email":"rlitvin@prf.jcu.cz","institution":"Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; Institute of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic ","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056502","task":"7eca8890abed44a1a4aaefb4cc8e03e6","id":"1809"}, {"dataset":"MSV000096022","datasetNum":"96022","title":"Human skeletal muscle bioenergetic pathways are altered in Alzheimers disease","user":"KUMC_Prot","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727973104000","created":"Oct. 3, 2024, 9:31 AM","description":"Skeletal muscle involvement in Alzheimers disease (AD) is supported by reduced lean mass, motor function and mitochondrial respiration in early disease. However, no one has comprehensively assessed molecular alterations in muscle that could underly these findings. We used two human muscle types, quadriceps (n=81) and temporalis (n=66), to compare the skeletal muscle proteome between individuals with and without AD (AD: n= 54 temporalis, 44 quadriceps; controls: n=27 temporalis, 22 quadriceps). We compared the effects of diagnosis between muscle types and in APOE4 carriers versus APOE4 non-carriers. Mitochondrial pathways in skeletal muscle are downregulated in AD. These effects are greatest in the temporalis compared to the quadriceps and in APOE4 carriers compared to APOE4 non-carriers. 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Includes reversed-phase liquid chromatography retention times, collision cross section (CCS) values, and m\/z ratios for 174 PFAS and their resulting 280 ion types in positive and negative modes with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources. To use, please select the sheet which most accurately reflects your ionization method and mode, then copy and paste columns B-G, including column headers listed in row 4. 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Glucocorticoids are an essential part of many multi-agent treatment regimens for lymphoid malignancies. However, the emergence of glucocorticoid resistance is a significant barrier to cure, which is in part due to epigenetic alterations, including aberrant chromatin accessibility and hypermethylation at lymphocyte-specific glucocorticoid-response elements (GREs). To gain a deeper understanding of regulatory mechanisms leading to these epigenetic alterations, we conducted a multi-omics study, including chromosome conformation capture sequencing (HiC), to examine changes in the 3D genome structure following the in vivo treatment of acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) with glucocorticoid. We found that glucocorticoid treatment led to distinct patterns of topologically associated domains (TADs) in glucocorticoid sensitive compared to resistant PDXs. Furthermore, we show that these TADs were primed by the development-related pioneer transcription factor PU.1, which extensively interacts with the glucocorticoid receptor (GR) exclusively in glucocorticoid-sensitive ALL PDXs. An integrative analysis of rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) and ChIP-seq revealed that PU.1 binding was associated with lymphocyte-specific activation of GREs and GRE-interacting super-enhancers. The PU.1-associated TADs modulated epigenetic marks, and particularly the eviction of PU.1 promoted GR binding and the expression of signature genes, including BIM, ZBTB16 and RASA1, mediating glucocorticoid-induced apoptosis in ALL. These findings were phenocopied using a PU.1 inhibitor DB2313 to restore glucocorticoid sensitivity in ALL. Taken together, this study identified a new epigenetic pathway integrating PU.1 priming and PU.1-GR interaction which ultimately leads to PU.1 eviction in ALL. This pathway provides the first link between the activity of a lineage-specific transcription factor and epigenetic modulators mediating the response to glucocorticoids and thus offers a new avenue to translate fundamental epigenetic research into the clinic.","fileCount":"23","fileSizeKB":"9380023","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF HT","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"PU.1;Acute Lymphoblastic Leukemia;Glucocorticoids;Resistance","pi":[{"name":"Duohui Jing","email":"jdh12262@rjh.com.cn","institution":"Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai","country":"China"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD056483","task":"40590778931e40069c67314db2b3275b","id":"1812"}, {"dataset":"MSV000096015","datasetNum":"96015","title":"UHPLC-MS2 data of Buddleja officinalis Maxim. flower microfractions","user":"andiw","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727956046000","created":"Oct. 3, 2024, 4:47 AM","description":"Dataset used for molecular network-based biochemometric analysis of Buddleja offincalis Maxim. flowers microfractions for anti-oxidant activities (DPPH assay) and cytotoxicity in HCE-T cells (WST-1 assay).","fileCount":"1599","fileSizeKB":"3145174","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Buddleja officinalis (NCBITaxon:714454)","instrument":"6546 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Buddleja;Biochemometrics;Dry eye disease","pi":[{"name":"Andreas Wasilewicz","email":"andreas.wasilewicz@univie.ac.at","institution":"University of Vienna","country":"Austria"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"70d2453bb7ce4498adacefd908c68fbb","id":"1813"}, {"dataset":"MSV000096014","datasetNum":"96014","title":"Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology","user":"alangen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727930298000","created":"Oct. 2, 2024, 9:38 PM","description":"Raw .d mass spectrometry files for Boucher et al. grouped by sample including replicates.","fileCount":"22","fileSizeKB":"228048128","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cryptococcus neoformans","instrument":"timsTOF Pro 2","modification":"Carbamidomethylation 57.021464 [C];Deamidation 0.984016 [NQ];Oxidation (M) 15.994915 [M];Acetylation (N-term) 42.010565 [X]@N","keywords":"Cryptococcus neoformans;Fungal pathogen","pi":[{"name":"Balyn Zaro","email":"balyn.zaro@ucsf.edu","institution":"University of California, San Francisco","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ad79c16f9b9944b79c6279f2f896db13","id":"1814"}, {"dataset":"MSV000096013","datasetNum":"96013","title":"GNPS - HNRC sample co-migration with drug microbial incubations","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727927649000","created":"Oct. 2, 2024, 8:54 PM","description":"HNRC sample spiked by drug microbial incubations to check retention time match of drug microbial metabolites","fileCount":"54","fileSizeKB":"3707872","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"NA","keywords":"NA","pi":[{"name":"Pieter C. 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Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dc369608f0d145c295b039780b659488","id":"1816"}, {"dataset":"MSV000096011","datasetNum":"96011","title":"Urolithin A protects hepatocytes from palmitic acid-induced ER stress by regulating calcium homeostasis in the MAM","user":"juyeon4444","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727921740000","created":"Oct. 2, 2024, 7:15 PM","description":"An ellagitannin-derived metabolite Urolithin A (UA) has emerged as a potential therapeutic agent for metabolic disorders due to its antioxidant, anti-inflammatory, and mitochondrial function-improving properties, but its efficacy in protecting against ER stress remains underexplored. The endoplasmic reticulum (ER) is a cellular organelle involved in protein folding, lipid synthesis, and calcium regulation. Perturbations in these functions can lead to ER stress, which contributes to the development and progression of metabolic disorders such as metabolic-associated fatty liver disease (MAFLD). In this study, we identified a novel target protein of UA and elucidated its mechanism for alleviating palmitic acid (PA)-induced ER stress. CETSA-LC-MS\/MS analysis revealed that UA binds directly to the sarcoplasmic\/endoplasmic reticulum Ca2+-ATPase (SERCA), an important regulator of calcium homeostasis in mitochondria-associated ER membranes (MAMs). As an agonist of SERCA, UA attenuates abnormal calcium fluctuations and ER stress in PA-treated liver cells, thereby contributing to cell survival. In addition, UA inhibits PA-induced mitochondrial ROS and lipid accumulation, further supporting its protective role. The lack of UA activity in SERCA knockdown cells suggests that UA regulates cellular homeostasis through its interaction with SERCA. Collectively, our results demonstrate that UA protects against PA-induced ER stress and enhances cell survival by regulating calcium homeostasis in MAM through SERCA. This study highlights the potential of UA as a therapeutic agent for metabolic disorders associated with ER stress","fileCount":"14","fileSizeKB":"20095835","spectra":"0","psms":"66879","peptides":"45448","variants":"50376","proteins":"5551","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Urolithin A; ER stress; MAM; CETSA-LC-MS\/MS; SERCA; MAFLD","pi":[{"name":"Ho Jeong Kwon","email":"kwonhj@yonsei.ac.kr","institution":"Yonsei University","country":"South Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"412e5767882e4c80a859ab30d04e3d74","id":"1817"}, {"dataset":"MSV000096007","datasetNum":"96007","title":"Ultra-fast label-free quantification and\ncomprehensive proteome coverage\nwith narrow-window data-independent\nacquisition. Fractionation","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727822537000","created":"Oct. 1, 2024, 3:42 PM","description":"Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependent and independent methods. This is achieved by pairing a Quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer that provides >200 Hz MS\/MS scanning speed, high resolving power and sensitivity, as well as low ppm-mass accuracy. Narrowwindow DIA enables profiling of up to 100 full yeast proteomes per day, or ~10,000 human proteins in half-an-hour. Moreover, multi-shot acquisition of fractionated samples allows comprehensive coverage of human proteomes in ~3h, showing comparable depth to next-generation RNA sequencing and with 10x higher throughput compared to current state-of-the-art MS. High quantitative precision and accuracy is demonstrated with high peptide coverage in a 3-species proteome mixture, quantifying 14,000+ proteins in a single run in half-an-hour.","fileCount":"562","fileSizeKB":"1202204854","spectra":"20026466","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dia; Astral; Proteomics","pi":[{"name":"Jesper V.","email":"jesper.olsen@cpr.ku.dk","institution":"Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046372","task":"492415d097bb47e79b39c920bc6ea550","id":"1818"}, {"dataset":"MSV000096004","datasetNum":"96004","title":"GNPS - DOM_AtlanticOcean_NTA_LC-HRMS_DDA_Eclipse","user":"JessPat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727811675000","created":"Oct. 1, 2024, 12:41 PM","description":"Marine dissolved organic matter from the Atlantic Ocean. Samples were analyzed by LC-MS\/MS in positive and negative electrospray ionization mode using DDA (Orbitrap Eclipse).","fileCount":"379","fileSizeKB":"68389772","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DOM, non-targeted LC-HRMS, ocean","pi":[{"name":"Jordi Dachs","email":"jordi.dachs@idaea.csic.es","institution":"IDAEA-CSIC","country":"Spain"},{"name":"Maria Vila Costa","email":"maria.vila@idaea.csic.es","institution":"IDAEA-CSIC","country":"Spain"},{"name":"Pablo Gago Ferrero","email":"pablo.gago@idaea.csic.es","institution":"IDAEA-CSIC","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"84e809edcb45429898795f4ef9690e5b","id":"1819"}, {"dataset":"MSV000096003","datasetNum":"96003","title":"Ward_2024_VS1_ Mapping C. difficile TcdB interactions with host proteins by BioID","user":"Younlab_Toronto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727804189000","created":"Oct. 1, 2024, 10:36 AM","description":"This dataset consists of 41 raw mass spectrometry files and associated peak lists and results files, acquired on a Thermo Orbitrap Exploris 480 operated in Data-Dependent Acquisition mode. Protein affinity purification was performed by Jennifer Ward, while Jennifer Ward and John Tam generated samples. Mass spectrometric acquisition was performed by Karl Schreiber. Analysis was performed by Jennifer Ward, Karl Schreiber, Ji-Young Youn, and Roman Melnyk. The files are associated with a manuscript by Jennifer Ward et al. that uses proximity-dependent biotinylation approaches to identify host targets of Diphtheria Toxin (DT) and the Clostridioides difficile toxin B (TcdB). Roman Melnyk is the corresponding author for the manuscript and should be contacted for questions regarding this dataset (roman.melnyk@sickkids.ca). ","fileCount":"171","fileSizeKB":"72746539","spectra":"0","psms":"1626967","peptides":"333296","variants":"388788","proteins":"37898","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:00408 - \\\"A protein modification that effectively replaces a residue amino or imino hydrogen with an acetyl group.\\\"","keywords":"Affinity purification;BioID;Proximity-dependent biotinylation;Protein-protein interaction;Diphtheria Toxin;Clostridioides difficile toxin B","pi":[{"name":"Ji-Young Youn","email":"jiyoung.youn@sickkids.ca","institution":"Hospital for Sick Children","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056431","task":"53b3ef3dd94141f387c5ae629c5fbd1f","id":"1820"}, {"dataset":"MSV000096001","datasetNum":"96001","title":"A Multiplexed SEC-MS Approach to Systematically Study the Interplay Between Protein Assembly-States and Phosphorylation Events","user":"mj2794","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727797539000","created":"Oct. 1, 2024, 8:45 AM","description":"A proteins molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly-states and PTMs from the same sample is critically missing. Here, we introduce SEC-MX (Size Exclusion Chromatography fractions MultipleXed), a global quantitative method combining Size Exclusion Chromatography and PTM-enrichment for simultaneous characterization of PTMs and assembly-states. SEC-MX enhances throughput, allows phosphopeptide enrichment, and facilitates quantitative differential comparisons between biological conditions. Applying SEC-MX to HEK293 and HCT116 cells, we generated a proof-of-concept dataset mapping thousands of phosphopeptides and their assembly-states. Our analysis revealed intricate relationships between phosphorylation events and assembly-states and generated testable hypotheses for follow-up studies. Overall, we establish SEC-MX as a valuable tool for exploring protein functions and regulation beyond abundance changes.","fileCount":"142","fileSizeKB":"95972744","spectra":"2549236","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"[S,T, Y] phosphorylation (unimod 21)","keywords":"Protein assembly-states, PTM, Size Exclusion chromatography, protein interactions, phosphorylation","pi":[{"name":"Marko Jovanovic","email":"mj2794@columbia.edu","institution":"Columbia University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD059734","task":"9afc199494e74f4ebafb8f45a522b548","id":"1821"}, {"dataset":"MSV000095999","datasetNum":"95999","title":"GNPS - GC-MS extract Streptomyces sp. 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RC4;Coral bacterium","instrument":"Shimadzu QP2010 Ultra ","modification":"None","keywords":"Bacterial extract","pi":[{"name":"Risa Nofiani","email":"risa.nofiani@chemistry.untan.ac.id","institution":"Universitas Tanjungpura","country":"Indonesia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"462ac0c19afe4160bed116f076b7345d","id":"1822"}, {"dataset":"MSV000095996","datasetNum":"95996","title":"GNPS - 20240930 HNRC sample HIV drug co-migration","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727741434000","created":"Sep. 30, 2024, 5:10 PM","description":"Retention time check by co-migration of HIV drug standards with fecal samples from the HNRC cohort. ","fileCount":"55","fileSizeKB":"4409639","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"NA","keywords":"antiretroviral;retention time check","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"57aa156313f945249438b7256b90dc13","id":"1823"}, {"dataset":"MSV000095995","datasetNum":"95995","title":"Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation","user":"rsearfoss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727734600000","created":"Sep. 30, 2024, 3:16 PM","description":". Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field is more challenging than its bottom-up counterpart because the species are much bigger and have a larger number of possible combinations of sequences and modifications, thus there is a great need for technological development. With improvements in instrumentation and a multiplicity of fragmentation modes available, top-down proteomics is quickly gaining in popularity with renewed attention on increasing confidence in identification and quantification. Here, we systematically evaluated the Sciex ZenoTOF 7600 system for top-down proteomics, applying standards in the field to validate the platform and further experimenting with its capabilities in electron-activated dissociation and post-translational modification site localization. The instrument demonstrated robustness in standard proteins for platform QC, as aided by zeno-trapping. We were also able to apply this to histone post-translational modifications, achieving high sequence coverage that allowed PTMs site-localization across protein sequences with optimized EAD fragmentation. We demonstrated the ability to analyze proteins spanning the mass range and included analysis of glycosylated proteins. This is a reference point for future top-down proteomics experiments to be conducted on the ZenoTOF 7600 system. ","fileCount":"79","fileSizeKB":"4428109","spectra":"4997","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bovinae (NCBITaxon:27592)","instrument":"ZenoTOF 7600","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";MOD:00727 - \\\"A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a mannose group through a glycosidic bond,\\\"","keywords":"Top-Down Proteomics","pi":[{"name":"Benjamin A. Garcia","email":"bgarci@mail.med.upenn.edu","institution":"Department of Biochemistry and Biophysics, University of Pennsylvania","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056407","task":"0e37514c0a1a4b5bb13a7dd74d91cdbf","id":"1824"}, {"dataset":"MSV000095994","datasetNum":"95994","title":"Post-transcriptional regulation of Dufours gland reproductive signals in bumble bees ","user":"tlaremore","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727720229000","created":"Sep. 30, 2024, 11:17 AM","description":"Bumble bees workers produce ester sterility signals in their Dufours gland that differ from gyne-specific esters and are not produced by queens. \nA transcriptome analysis revealed no gene expression differences in the Dufours gland of workers despite differences in both ester production and ovarian activation, suggesting that ester production may be regulated lower down.\nProteomics of the Dufours gland of queens, gynes, and workers recovered over 1500 proteins and broadly matched the previous RNAseq data. However, more than 100 differentially expressed proteins were found between the worker groups, including key genes in fatty acid biosynthesis, indicating that the regulation of reproductive signal biosynthesis in workers is done post-transcription.","fileCount":"52","fileSizeKB":"55296017","spectra":"0","psms":"125212","peptides":"27063","variants":"34757","proteins":"4172","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bombus impatiens (NCBITaxon:132113)","instrument":"Orbitrap Eclipse","modification":"PRIDE:0000398","keywords":"caste-specific pheromone biosynthesis;Dufours gland proteomics","pi":[{"name":"Etya Amsalem","email":"eua6@psu.edu","institution":"The Pennsylvania State University","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD056402","task":"d96126fdae974f53912ad5d02aac0e2c","id":"1825"}, {"dataset":"MSV000095992","datasetNum":"95992","title":"PEPPI-SP3: Robust and Simple Sample Prefractionation Workflow for Top-Down Proteomics","user":"Fornelli_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727707807000","created":"Sep. 30, 2024, 7:50 AM","description":"Precise prefractionation of proteome samples is a potent method for realizing in depth analysis in top-down proteomics. PEPPI MS (Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS), a gel-based sample fractionation method, enables high-resolution proteome fractionation based on molecular weight by highly efficient extraction of proteins from polyacrylamide gels after SDS PAGE separation. In this study, we developed a complete, robust, and simple sample preparation workflow named PEPPI SP3 for top down proteomics by combining PEPPI MS with the magnetic bead-based protein purification approach used in SP3.","fileCount":"30","fileSizeKB":"31768076","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:34 - \\\"Methylation.\\\"","keywords":"Top-down Proteomics;Polyacrylamide gel electrophoresis;Sample fractionation;PEPPI-MS;SP3","pi":[{"name":"Luca Fornelli","email":"luca.fornelli@ou.edu","institution":"University of Oklahoma","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"970fd65fd53e47e0852efb8f89cb98ea","id":"1826"}, {"dataset":"MSV000095991","datasetNum":"95991","title":"dELTA-MS: A Mass Spectrometry-Based Proteomics Approach for Identifying ADP-ribosylation Sites and Forms","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727702154000","created":"Sep. 30, 2024, 6:15 AM","description":"Post-translational modifications (PTMs) involve adding chemical groups to proteins, which modulate their structures and functions. ADP-ribosylation, characterized by the addition of adenosine diphosphate ribose, can occur in both monomeric (MARylation) and polymeric (PARylation) forms. Maintaining the balance between these forms is crucial for regulating cellular processes such as DNA repair, and disruption of this balance can lead to diseases, including cancer, neurodegeneration, and viral infections. Despite its importance, much remains to be learned about the specific contributions of MARylation and PARylation to these processes due to a lack of tools for jointly investigating these individual forms. Here, we present a novel mass spectrometry (MS)-based proteomics approach that preserves information about the native form of ADP-ribosylation associated with the modification site within a single proteomics experiment. Our workflow enables the simplified, binary identification of ADP-ribosylation forms, avoiding some challenges typically presented by PARylated peptides during MS analysis. ","fileCount":"25","fileSizeKB":"18839498","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:213 - \\\"ADP Ribose addition.\\\"","keywords":"ADPr;Marylation;PARylation","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"fc3289a020374a03aad58beaa0eab6fa","id":"1827"}, {"dataset":"MSV000095988","datasetNum":"95988","title":"GNPS Blank Run Ganga Water Metabolome","user":"durgeshbt_2024","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727685856000","created":"Sep. 30, 2024, 1:44 AM","description":"GNPS Blank Run Ganga Water Metabolome of two major bathing ghats in Varanasi","fileCount":"5","fileSizeKB":"895652","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Blank Run Ganga Water Metabolome","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Blank Run","pi":[{"name":"Anil Kumar Tripathi","email":"durgeshbt@gmail.com","institution":"Banaras Hindu University (BHU)","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"973babb842d94b749c508b5929937e44","id":"1828"}, {"dataset":"MSV000095986","datasetNum":"95986","title":"Decoding Microbial Plastic Colonisation: Multi-Omic Insights into the Fast-Evolving Dynamics of Early-Stage Biofilms","user":"chl1Stir","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727623500000","created":"Sep. 29, 2024, 8:25 AM","description":"PARTIAL UPLOAD: Metaproteomic dataset pertaining to marine biofilms analysed after growth on low-density polyethylene (LDPE) for 3 (D3) and 7 (D7) days. Four replicates per condition. ","fileCount":"51","fileSizeKB":"3360870","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Multi-species marine biofilm","instrument":"TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plastisphere;Marine biofilm","pi":[{"name":"Sabine Matallana Surget","email":"sabine.matallanasurget@stir.ac.uk","institution":"University of Stirling","country":"United Kingdom"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD056358","task":"08108db04f5a470aa006fb488207b606","id":"1829"}, {"dataset":"MSV000095985","datasetNum":"95985","title":"LFQ DIA to analyze the proteome of NPC mutant iNeurons with and without ferric ammonium citrate","user":"Yuchen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727615838000","created":"Sep. 29, 2024, 6:17 AM","description":"Label-free quantification (LFQ) using data-independent acquisition (DIA) on the Orbitrap Astral was performed to analyze the proteome of iNeurons with NPC1 and NPC2 knocked out. The experiment includes the following time points of development: day 0, 4, 8, 16, and 22. All samples were cultured in regular media, with or without ferric ammonium citrate (FAC), and processed in triplicates for each time point, genotype, and treatment.","fileCount":"2754","fileSizeKB":"1980992633","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"proteomics;data-independent acquisition;DIA;NPC1;NPC2;iNeuron;human embryonic stem cell;hESC;ferric ammonium citrate;FAC","pi":[{"name":"J. Wade Harper","email":"wade_harper@hms.harvard.edu","institution":"Harvard Medical School - Dpt of Cell Biology","country":"U.S.A"},{"name":"Joshua J. Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD056356","task":"f62ccca1184a405085bceb42f48e3ebf","id":"1830"}, {"dataset":"MSV000095983","datasetNum":"95983","title":"Temporal Dynamics of the Milk Proteome in Women with Gestational Diabetes Mellitus ","user":"muqier","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727593616000","created":"Sep. 29, 2024, 12:06 AM","description":"Objectives To perceive the temporal features of breast milk proteome between women with gestational diabetes mellitus (GDM) and healthy controls across various lactation periods, as well as to explore the potential impacts of these differences on the growth of offspring. \nMethods The study cohort included twenty mothers with GDM and twenty healthy mothers. Human milk samples were obtained at four distinct time points: colostrum (4-6 days postpartum), transitional milk (12-14 days postpartum), early mature milk (42 days postpartum) and mature milk (4 months postpartum). Shotgun proteomics with label free quantification was applied to analyze the milk proteome. Gene Ontology (GO) enrichment analysis, alongside other bioinfomatic tools were conducted to elucidate the function of differentially expressed proteins. Subsequently, a random forest model was utilized to discern proteins that could reliably differentiate milk samples from mothers with gestational diabetes mellitus (GDM) from those of healthy counterparts. Furthermore, correlative analysis was employed to investigate the association between these proteins and the anthropometric indices of infants. \nResults Principal coordinate analysis (PCoA) revealed distinct separations in the milk proteome of GDM and healthy mothers during the initial lactation stages, with these differences diminishing over time. The up-regulated proteins in GDM were predominantly associated with the innate immune system, complement and coagulation cascades, cellular secretion, enzymatic and binding activity, and platelet activation. Six proteins were identified as effective markers for distinguishing milk samples from the two groups, with an average area under the curve (AUC) value of 0.91. Twenty-eight proteins exhibited consistent changes between GDM and healthy groups across at least two lactation stages, many of which were significantly correlated to the anthropometric indices of the offsprings. \nConclusions GDM significantly influences the milk proteome, with the extent of alteration diminishing as lactation progresses into the mature milk phase. ","fileCount":"239","fileSizeKB":"137952192","spectra":"5808444","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LC-MS\\\/MS","modification":"UNIMOD:107 - \\\"Addition of N-formyl met.\\\"","keywords":"gestational diabetes mellitus, milk proteome, breast milk, lactational period, infant growth","pi":[{"name":"MU Qier ","email":"muqier1027@163.com","institution":"Beijing Institute of Nutritional Resources","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056353","task":"428b263bc2d34a47b6d39deb7a325410","id":"1831"}, {"dataset":"MSV000095982","datasetNum":"95982","title":"GNPS - Metabolite analysis of Aeromonas sp. NJAU223 and Delta LuxI\/R strain under 0 and 50 ppm Cd treatments","user":"chenjiale670","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727583022000","created":"Sep. 28, 2024, 9:10 PM","description":"Metabolite analysis of Aeromonas sp. NJAU223 and Delta LuxI\/R strain under 0 and 50 ppm Cd treatments","fileCount":"81","fileSizeKB":"6860827","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aeromonas (NCBITaxon:642)","instrument":"ACQUITY UPLC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cd, quorum sensing","pi":[{"name":"JIALE CHEN","email":"2019103031@njau.edu.cn","institution":"Nanjing agricultural university","country":"China"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0b68f19887954cee88d8dbfc4d5ce6b6","id":"1832"}, {"dataset":"MSV000095981","datasetNum":"95981","title":"Time-resolved analysis reveals rapid dynamics and broad scope of the CBP\/p300 acetylome","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727575979000","created":"Sep. 28, 2024, 7:12 PM","description":"The acetyltransferases CBP and p300 are multifunctional transcriptional co-activators; however, their acetylation targets, site-specific acetylation kinetics, and function in proteome regulation are incompletely understood. We combined quantitative proteomics with novel CBP\/p300-specific catalytic inhibitors, bromodomain inhibitor, and gene knockout to show that CBP\/p300 acetylates thousands of sites, including signature histone sites, as well as a multitude of sites on signaling effectors and enhancer-associated transcriptional regulators. Kinetic analysis identified a subset of CBP\/p300-regulated sites with very rapid (<30min) acetylation turnover, revealing a dynamic balance between acetylation and deacetylation. Quantification of acetylation, mRNA, and protein abundance after CBP\/p300 inhibition reveals a kinetically competent network of gene expression that strictly depends on CBP\/p300-catalyzed rapid acetylation. Collectively, our in-depth acetylome analyses reveal systems attributes of CBP\/p300 targets, and the resource dataset provides a framework for investigating CBP\/p300 functions, as well as for understanding the impact of small molecule inhibitors targeting its catalytic and bromodomain activities.","fileCount":"614","fileSizeKB":"739166453","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\"","keywords":"Cbp; Acetyltransferase; Acetylation; P300","pi":[{"name":"Chunaram Choudhary","email":"chuna.choudhary@cpr.ku.dk","institution":"Proteomics Program Blegdamsvej 3 2200 K\uFFFDbenhavn N Bygning 6 Building: 06-2-36","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD005252","task":"5dc8eec72a71427f9823c1dd9f7a2d44","id":"1833"}, {"dataset":"MSV000095980","datasetNum":"95980","title":"GNPS - PFAS Biotransformation Products: AFFF, AFFF-fed mice liver and urine, PFAS Chemical standards, and Mouse enzyme treated PFAS chemical standards ","user":"jeremykoelmel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727549602000","created":"Sep. 28, 2024, 11:53 AM","description":"This Agilent QTOF data consists of urine and liver of mice fed AFFF, as well as PFAS chemical standards treated with mouse enzymes for biotransformation. Data acquired by Sheng Liu and David A. Dukes. \r\n\r\nIt goes alongside the manuscript:\r\n\r\n\"Expanding PFAS Identification with Transformation Product Libraries: Non-Targeted Analysis Reveals Biotransformation Products in Mice\" published in Environmental Science & Technology\r\n\r\nAn interactive dataset after FluoroMatch annotation for the urine data can be found here:\r\nhttps:\/\/innovativeomics.com\/datasets\/non-targeted-pfas-dataset-from-urine-of-afff-fed-mice\/\r\n\r\nSoftware with the biotransformation libraries can also be found at:\r\nhttps:\/\/innovativeomics.com\r\n\r\nPer- and polyfluoroalkyl substances (PFAS) are widely used persistent synthetic chemicals that have been linked to adverse health effects. While the behavior of PFAS has been evaluated in the environment, our understanding of reaction products in mammalian systems is limited. This study identified biological PFAS transformation products and generated mass spectral libraries to facilitate automated search and identification. The biological transformation products of 27 PFAS, spanning 5 chemical subclasses (alcohols, sulfonamides, carboxylic acids, ethers, and esters), were evaluated following enzymatic reaction with mouse liver S9 fractions. Four major pathways were identified by liquid chromatography-high resolution mass spectrometry: glucuronidation; sulfation; dealkylation and oxidation. Class-based fragmentation rules and associated PFAS transformation product libraries were generated and integrated into an automated non-targeted PFAS data analysis software (FluoroMatch). Fragmentation was additionally predicted for the potential transformation products of more than 2,500 PFAS in the EPA CompTox Chemicals Dashboard PFASSTRUCTv4. Generated mass spectral libraries were validated by applying FluoroMatch to a dataset of urine from aqueous film-forming foam (AFFF)-dosed mice. Toxicity predictions showed identified PFAS transformation products as potential developmental and mutagenic toxicants. This research enables more comprehensive PFAS characterization in biological systems which will improve assessment of exposures and evaluation of the associated health impacts.","fileCount":"13397","fileSizeKB":"15414312","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mouse;PFAS;AFFF;aqeous fire fighting foam;enzyme;liver;urine;biotransformation product;biotransformation;glucuronide;conjugate;non-targeted;LC-HRMS\/MS;FluoroMatch;LC-HRMS","pi":[{"name":"Carrie A McDonough","email":"cmcdonou@andrew.cmu.edu","institution":"Carnegie Mellon University","country":"United States"},{"name":"David Dukes","email":"david.dukes@stonybrook.edu","institution":"Stony Brook University","country":"United States"},{"name":"Jeremy Koelmel","email":"jeremykoelmel@gmail.com","institution":"Yale University","country":"United States"},{"name":"Krystal G. Pollitt","email":"krystal.pollitt@yale.edu","institution":"Yale University","country":"United States"},{"name":"Sheng Liu","email":"sheng.liu@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0027bc032ef84aa6b29547c8fc75d1a8","id":"1834"}, {"dataset":"MSV000095979","datasetNum":"95979","title":"GNPS - GC-HRMS PFAS EI and PCI Data: Standards, AFFF, Dust, Blood, Effluent, Passive Samplers, Personal Exposure, and more!","user":"jeremykoelmel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727546401000","created":"Sep. 28, 2024, 11:00 AM","description":"This is the GC Orbitrap data accompanying the FluoroMatch GC Library manuscript.\r\nReferences and software are available here:\r\nhttps:\/\/innovativeomics.com\/software\/fluoromatch-gc-modular-pfas-annotation\/\r\n\r\nDespite thousands of documented PFAS, approaches to characterize volatile and semi-volatile PFAS are limited. To address this gap, we developed a non-targeted gas chromatography high-resolution mass spectrometry (GC-HRMS) workflow to extend coverage of volatile and semi-volatile PFAS. This workflow includes new FlouroMatch GC mass spectral libraries (>1900 EI and PCI predicted and experimental spectra) and characterization of thousands of PFAS specific EI fragments for fragment screening. Liquid chromatography (LC) and GC-HRMS approaches were highly complementary, with GC-HRMS revealing diverse PFAS profiles in 8 different environmental and biological matrices distinct from PFAS detected in LC approaches. For example, we detected a previously unreported PFAS, 2-(perfluorohexyl)ethanethiol in multiple firefighting foam (AFFF) formulations and a novel feature tentatively annotated as N-methyl-N-(2-hydroxyethyl) perfluorooctanesulfonamide (MeFOSE alcohol) that was consistently detected in various matrices related to point and non-point PFAS exposures including dried blood spots, leachate, industrial effluent, and settled dust collected from homes, which were not detected in corresponding LC approaches. Personal exposure to volatile and semi-volatile PFAS was found to vary significantly across individuals. In a cohort of 48 children in Connecticut wearing wristband passive samplers, GC-HRMS fragment screening revealed that 46% of 40 unique airborne PFAS detected only occurred in a single child, and 58% of 47 unique PFAS detected in settled dust collected from 11 households were only detected in a single home. Findings highlight the importance of personal monitoring using a combination of non-targeted GC and LC-HRMS approaches to comprehensively characterize PFAS exposures. The novel methods that we have established will allow the health burden PFAS to be rigorously evaluated, ultimately informing regulatory policies and public health interventions. ","fileCount":"1395","fileSizeKB":"499529617","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive GC Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"GC;Orbitrap;PFAS;NTA;non-targeted;Aqeous fire fighting foam;AFFF;House Dust;Passive samplers;Fresh Air;Yale;Innovative Omics;Plasma;Whole Blood;EPA;Effluent;Industrial effluent;Software;Libraries;chemical standards","pi":[{"name":"Dr. John A. Bowden","email":"john.bowden@ufl.edu","institution":"University of Florida","country":"United States"},{"name":"Elizabeth Lin","email":"elizabeth.lin@yale.edu","institution":"Yale University","country":"USA"},{"name":"Jeremy Koelmel","email":"jeremykoelmel@gmail.com","institution":"Yale University","country":"United States"},{"name":"Krystal G. Pollitt","email":"krystal.pollitt@yale.edu","institution":"Yale University","country":"United States"},{"name":"Seth Newton","email":"Newton.Seth@epa.gov","institution":"EPA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"64a7a09785bc480b816a86d12da9f4af","id":"1835"}, {"dataset":"MSV000095978","datasetNum":"95978","title":"GNPS - NIST PFAS INTERLAB DATA Yale University Krystal Pollitt Laboratory 6546","user":"jeremykoelmel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727545441000","created":"Sep. 28, 2024, 10:44 AM","description":"NIST A, B, and C with 10x dilution and no dilution. Methods described in NIST interlaboratory results and following manuscripts. \r\nData Acquired by Sheng Liu.","fileCount":"3","fileSizeKB":"28474555","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Agilent 6546 Q-TOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"NIST;PFAS;Interlab;NTA;FluoroMatch;6546;AFFF;Standards","pi":[{"name":"Jeremy Koelmel","email":"jeremykoelmel@gmail.com","institution":"Yale University","country":"United States"},{"name":"Krystal J Godri Pollitt","email":"krystal.pollitt@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ea2aa66921984fe681c75367c2ca5a82","id":"1836"}, {"dataset":"MSV000095977","datasetNum":"95977","title":"Narrow-window DIA: Ultra-fast quantitative analysis of comprehensive proteomes with high sequencing depth. Evaluation of window width and injection time.","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727514386000","created":"Sep. 28, 2024, 2:06 AM","description":"Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here, we present an ultra-fast scanning data-independent acquisition (DIA) strategy consisting on 2-Th precursor isolation windows, dissolving the differences between data-dependent and independent methods. This is achieved by pairing a Quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer that provides >200 Hz MS\/MS scanning speed, high resolving power and sensitivity, as well as low ppm-mass accuracy. Narrow window DIA enables profiling of up to 100 full yeast proteomes per day, or ~10,000 human proteins in half-an-hour. Moreover, multi-shot acquisition of fractionated samples allows comprehensive coverage of human proteomes in ~3h, showing comparable depth to next-generation RNA sequencing and with 10x higher throughput compared to current state-of-the-art MS. High quantitative precision and accuracy is demonstrated with high peptide coverage in a 3-species proteome mixture, quantifying 14,000+ proteins in a single run in half-an-hour.","fileCount":"74","fileSizeKB":"412028064","spectra":"16436357","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dia; Astral; Proteomics","pi":[{"name":"Jesper V.","email":"jesper.olsen@cpr.ku.dk","institution":"Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046285","task":"1c384dd6937d4ca887b20d4396f2447e","id":"1837"}, {"dataset":"MSV000095976","datasetNum":"95976","title":"Ultra-fast label-free quantification and\ncomprehensive proteome coverage\nwith narrow-window data-independent\nacquisition. 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Moreover, multi-shot acquisition of fractionated samples allows comprehensive coverage of human proteomes in ~3h, showing comparable depth to next-generation RNA sequencing and with 10x higher throughput compared to current state-of-the-art MS. High quantitative precision and accuracy is demonstrated with high peptide coverage in a 3-species proteome mixture, quantifying 14,000+ proteins in a single run in half-an-hour.","fileCount":"14","fileSizeKB":"12989079","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dia; Astral; Proteomics","pi":[{"name":"Jesper V.","email":"jesper.olsen@cpr.ku.dk","institution":"Professor, Deputy Head of Centre Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen, DENMARK","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046357","task":"edd7d3031c7f489e966819d8431f3809","id":"1838"}, {"dataset":"MSV000095975","datasetNum":"95975","title":"Ultra-fast label-free quantification and\ncomprehensive proteome coverage\nwith narrow-window data-independent\nacquisition. 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Moreover, multi-shot acquisition of fractionated samples allows comprehensive coverage of human proteomes in ~3h, showing comparable depth to next-generation RNA sequencing and with 10x higher throughput compared to current state-of-the-art MS. 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Rein","email":"krein@fgcu.edu","institution":"The Water School, Florida Gulf Coast University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a790df2418b04a0ea0e6430ac1e61e57","id":"1841"}, {"dataset":"MSV000095970","datasetNum":"95970","title":"GNPS -GCMS Extract Streptomyces sp. SM1P","user":"rnofiani","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727449154000","created":"Sep. 27, 2024, 7:59 AM","description":"Title:Complete Genome Sequence, Biological Activities, and Metabolomic Profiles of Mangrove-derived Streptomyces sp. SM1P Author: Risa Nofiani, Puji Ardiningsih, Rizky, Cantika Dylani Putri, Rifa Rakayati, Rudiyansyah, Elfahmi, Syamsurizal, Agus Sukito, Ario Betha Juanssilfero, Josephine Elizabeth Siregar, Andita Fitri Mutiara Rizki, Wihda Aisarul Azmi, Alexandra J. Weisberg, Taifo Mahmud","fileCount":"9","fileSizeKB":"41232","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces sp. SM1P","instrument":"Agilent 6545 Q-ToF ","modification":"None","keywords":"Bacterial extract","pi":[{"name":"Risa Nofiani","email":"risa.nofiani@chemistry.untan.ac.id","institution":"Universitas Tanjungpura","country":"Indonesia"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"3d39717cf4f649d9a4e737a022a24de2","id":"1842"}, {"dataset":"MSV000095969","datasetNum":"95969","title":"Extensive uORF translation from HIV-1 transcripts elicits specific T cell immune responses in infected individuals and conditions DDX3 dependency for expression of main ORFs","user":"Adeline","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727442821000","created":"Sep. 27, 2024, 6:13 AM","description":"Human immunodeficiency virus type-1 (HIV-1) is a complex retrovirus which relies on alternative splicing, translational and post-translational mechanisms to produce more than 15 functional proteins from its single ~10kb transcriptional unit. Here, we have applied ribosome profiling, nascent protein labelling and quantitative mass-spectrometry at different time points during infection of CD4+ T lymphocytes to characterize the translational landscape of cellular and viral transcripts during the course of infection. Our results indicate a strong impact of viral infection on host cellular transcript levels but a modest impact on global translation rates. Interestingly, analysis of ribosome profiling reads from viral transcripts reveals extensive and productive non-AUG translation of small peptides from multiple upstream open reading-frames (uORFs) located in the 5 prime long terminal repeat. Remarkably, uORF-derived peptides elicit specific T cell responses in people living with HIV suggesting a potential role in the progression of the disease. uORF translation is conserved among other retroviruses and, together with the TAR sequence, condition the dependency on DDX3 for efficient translation of the main viral open-reading frames. ","fileCount":"25","fileSizeKB":"17025567","spectra":"0","psms":"1361191","peptides":"58364","variants":"77093","proteins":"5723","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);HIV-1 vector pNL4-3 (NCBITaxon:151458)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"HIV-1;Infection;Virus;lymphocyte;SupT1;CD4","pi":[{"name":"Emiliano P. Ricci","email":"emiliano.ricci@ens-lyon.org","institution":"Ecole Normale Superieure de Lyon; LBMC (Inserm U1293, UMR5239)","country":"France"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"906c735a58be4bc5845f1a941eb4d07b","id":"1843"}, {"dataset":"MSV000095967","datasetNum":"95967","title":"GNPS - LCMSMS Streptomyces sp. SM1P ISP2 NaCl 2.5%","user":"rnofiani","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727417169000","created":"Sep. 26, 2024, 11:06 PM","description":"Title:Complete Genome Sequence, Biological Activities, and Metabolomic Profiles of Mangrove-derived Streptomyces sp. SM1P \r\n\r\nAuthor: Risa Nofiani, Puji Ardiningsih, Rizky, Cantika Dylani Putri, Rifa Rakayati, Rudiyansyah, Elfahmi, Syamsurizal, Agus Sukito, Ario Betha Juanssilfero, Josephine Elizabeth Siregar, Andita Fitri Mutiara Rizki, Wihda Aisarul Azmi, Alexandra J. Weisberg, Taifo Mahmud7","fileCount":"3","fileSizeKB":"670149","spectra":"1318","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces sp. SM1P;Soil Mangrove Bacterium","instrument":"Agilent 6545 Q-ToF","modification":"None","keywords":"Bacteria","pi":[{"name":"Risa Nofiani","email":"risa.nofiani@chemistry.untan.ac.id","institution":"Universitas Tanjungpura","country":"Indonesia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b3dc5c447d204a5f8ddb09bb9eba7043","id":"1844"}, {"dataset":"MSV000095965","datasetNum":"95965","title":"Peptide Retention Time Prediction for Electrostatic Repulsion-Hydrophilic Interaction Chromatography","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727376495000","created":"Sep. 26, 2024, 11:48 AM","description":"Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) is a legacy separation tools developed by Dr. Andrew Alpert and has been used for developing unique separation methods of hydrophilic compounds, including peptides. We employed a proteomics-derived ~170,000 peptide retention dataset to evaluate major ERLIC retention features using the framework of our Sequence-Specific Retention Calculator model. Separation conditions were adjusted to obtain a wider proteome coverage, particularly for non-modified peptides, resulting in a superior separation orthogonality for a 2D LC combination with reversed-phase C18 LC-MS in the second dimension. The SSRCalc ERLIC model coefficients elucidated known ERLIC retention mechanisms, reflecting a dependence on peptide orientation and the position of charged and hydrophilic residues across the peptide backbone. R2 values of 0.935 and 0.955 accuracy were demonstrated for the standard interpretable SSRCalc model and a GRU-based machine learning algorithm, respectively. The effects of various PTMs on peptide retention were evaluated in this study, covering spontaneous (oxidation, deamidation) and enzymatic (N-terminal acetylation, phosphorylation, glycosylation) modifications.","fileCount":"1555","fileSizeKB":"161263592","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"C+57.021","keywords":"retention prediction models;ERLIC","pi":[{"name":"Oleg Krokhin","email":"oleg.krokhine@umanitoba.ca","institution":"University of Manitoba","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aa9ea4561d1d498981491ce430d1c9e3","id":"1845"}, {"dataset":"MSV000095962","datasetNum":"95962","title":"Protein Interactors of SMARCD1","user":"lisamiljenk","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727359614000","created":"Sep. 26, 2024, 7:06 AM","description":"Analysis of interactors of Smarcd1 following co-immunoprecipitation from 6T1 mouse cells, along with relevant controls. Please see included meta data file for more details on samples and methodology.","fileCount":"10","fileSizeKB":"9279003","spectra":"0","psms":"107177","peptides":"10202","variants":"12479","proteins":"1356","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"SMARCD1;interactome","pi":[{"name":"Lisa Jenkins","email":"jenkinsl@mail.nih.gov","institution":"NCI, NIH","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD056292","task":"ab35c266d55b4f6a9dc088d627df582e","id":"1846"}, {"dataset":"MSV000095961","datasetNum":"95961","title":"GNPS_Humulus_lupulus_cone_development","user":"oligegilo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727351420000","created":"Sep. 26, 2024, 4:50 AM","description":"Submitted publication: Extensive variation between chromosomes of North American and European hop","fileCount":"118","fileSizeKB":"12727252","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Humulus lupulus (NCBITaxon:3486)","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hop;beer;aroma","pi":[{"name":"Birger L. Moller","email":"blm@plen.ku.dk","institution":"University of Copenhagen","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d05e9eb8769247a49a41bc43b62b49b4","id":"1847"}, {"dataset":"MSV000095960","datasetNum":"95960","title":"Site specific N-linked glycosylation of spike protein of HCoV-229E P100E variant and the ectodomain of hAPN","user":"yuxitsai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727341199000","created":"Sep. 26, 2024, 1:59 AM","description":"Site specific N-linked glycosylation of spike protein of HCoV-229E P100E variant and the ectodomain of hAPN","fileCount":"7","fileSizeKB":"8269829","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"N-linked glycans;HCoV-229E S protein;Human Aminopeptidase N (hAPN)","pi":[{"name":"Shang-Te Danny Hsu","email":"sthsu@gate.sinica.edu.tw","institution":"Institute of Biological Chemistry, Academia Sinica","country":"Taiwan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"812a99a2bbda4ed39fddb8bf280917f3","id":"1848"}, {"dataset":"MSV000095959","datasetNum":"95959","title":"HAF prevents hepatocyte apoptosis and progression to MASH and hepatocellular carcinoma through transcriptional regulation of the NF-kB pathway","user":"golkom","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727307907000","created":"Sep. 25, 2024, 4:45 PM","description":"Background: \nHCC incidence is increasing worldwide due to the obesity epidemic, which drives metabolic dysfunction-associated steatohepatitis (MASH) that can lead to HCC. However, the molecular pathways driving MASH-HCC are poorly understood. We have previously reported that male mice with haploinsufficiency of hypoxia-associated factor, HAF (SART1+\/-) spontaneously develop MASH-HCC. However, the cell type(s) responsible for HCC associated with HAF loss are unclear.\n\nResults: \nWe generated SART1-floxed mice, which were crossed with mice expressing Cre-recombinase within hepatocytes (Alb-Cre; hepS-\/-) or myeloid cells (LysM-Cre, macS-\/-). HepS-\/- mice (both male and female) developed HCC associated with profound inflammatory and lipid dysregulation suggesting that HAF protects against HCC primarily within hepatocytes. HAF-deficient hepatocytes showed decreased P-p65 and P-p50 and in many components of the NF-kB pathway, which was recapitulated using HAF siRNA in vitro. HAF depletion also triggered apoptosis, suggesting that HAF protects against HCC by suppressing hepatocyte apoptosis. We show that HAF regulates NF-kB activity by regulating transcription of TRADD and RIPK1. Mice fed a high-fat diet (HFD) showed marked suppression of HAF, P-p65 and TRADD within their livers after 26 weeks, but showed profound upregulation of these proteins after 40 weeks, implicating deregulation of the HAF-NF-kB axis in the progression to MASH. In humans, HAF was significantly decreased in livers with simple steatosis but significantly increased in HCC compared with normal liver.\n\nConclusions: \nHAF is novel transcriptional regulator of the NF-kB pathway and is a key determinant of cell fate during progression to MASH and MASH-HCC.","fileCount":"390","fileSizeKB":"12271594","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HAF;hepatocyte; apoptosis;hepatocellular carcinoma;MASH;NF-kB","pi":[{"name":"Mei Yeh Koh","email":"mei.koh@utah.edu","institution":"University of Utah","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0e9cf2b232ab42a488d7b0c0279bb592","id":"1849"}, {"dataset":"MSV000095957","datasetNum":"95957","title":"Mechanism of allosteric activation in human mitochondrial ClpP protease","user":"mgoncalves","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727303189000","created":"Sep. 25, 2024, 3:26 PM","description":"Continuous labelling HDX on WT ClpP and ClpP_extended, in apo and bortezomib-bound states. \nPulse labelling HDX on WT ClpP and ClpP_extended, 1, 30, 180 minutes post a 100X dilution, samples were subjected to D2O-based buffer for 10 s.\nFolders for each experiment are organized per state, and time points. Peptide mapping and undeuterated controls are included. 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Experiment setup: Immunoaffinity purification of YFP-ERECTA from Arabidopsis thaliana. Two independent experiments conducted in 2013: first experiment has one sample and second experiment has two sample replicates. For each sample, purified YFP-ERECTA was separately digested with trypsin and chymotrypsin. LC-MS\/MS analysis on a Thermo LTQ-Velos Orbitrap. MS in the orbitrap and MS\/MS in the ion trap. Torii's lab provided purified YFP-ERECTA. Villen lab conducted proteomic sample preparation and MS analysis to identify phosphosites. Full search results provided (unfiltered).\r\nraw file\tsample;\r\n07090.raw\tYFP-ERECTA trypsin;\r\n07091.raw\tYFP-ERECTA chymotrypsin;\r\n07462.raw\tYFP-ERECTA trypsin;\r\n07463.raw\tYFP-ERECTA chymotrypsin;\r\n07465.raw\tYFP-ERECTA trypsin;\r\n07466.raw\tYFP-ERECTA chymotrypsin;\t\t\t\t\t\t\t","fileCount":"20","fileSizeKB":"1487836","spectra":"57679","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"LTQ Orbitrap Velos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"ERECTA, plant receptor, A. thaliana, phosphorylation","pi":[{"name":"Judit Villen","email":"jvillen@gmail.com","institution":"University of Washington","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD056259","task":"c1d218e4ab0141c998ddf155f080c3f8","id":"1851"}, {"dataset":"MSV000095952","datasetNum":"95952","title":"Mass Spectrometry-Based analysis of Myelin Proteome in NPC1 mice","user":"Chandimal1991","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727280055000","created":"Sep. 25, 2024, 9:00 AM","description":"Label free quantification was done for enriched myelin from WT and null NPC1 mouse brain. Myelin was enriched from mice cerebellum and rest of the brain separate. ","fileCount":"21","fileSizeKB":"27903292","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Myelin;NPC1","pi":[{"name":"Stephanie Cologna","email":"cologna@uic.edu","institution":"University of Illinois at Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"24423f49076d495bb72c71e84ac36ff8","id":"1852"}, {"dataset":"MSV000095951","datasetNum":"95951","title":"The Role of the Co-Chaperone DNAJB11 in Polycystic Kidney Disease: Molecular Mechanisms and Cellular Origin of Cyst Formation","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727277203000","created":"Sep. 25, 2024, 8:13 AM","description":"Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in PKD1 and \nPKD2, encoding polycystin-1 (PC1) and polycystin-2 (PC2), which are required for the regulation \nof the renal tubular diameter. Loss of polycystin function results in cyst formation. Atypical forms \nof ADPKD are caused by mutations in genes encoding endoplasmic reticulum (ER)-resident \nproteins through mechanisms that are not well understood. Here, we investigate the function of \nDNAJB11, an ER co-chaperone associated with atypical ADPKD. We generated mouse models with \nconstitutive and conditional Dnajb11 inactivation and Dnajb11-deficient renal epithelial cells to \ninvestigate the mechanism underlying autosomal dominant inheritance, the specific cell types \ndriving cyst formation, and molecular mechanisms underlying DNAJB11-dependent polycystic \nkidney disease. We show that biallelic loss of Dnajb11 causes cystic kidney disease and fibrosis, \nmirroring human disease characteristics. In contrast to classical ADPKD, cysts predominantly \noriginate from proximal tubules. Cyst formation begins in utero and the timing of Dnajb11\ninactivation strongly influences disease severity. Furthermore, we identify impaired PC1 cleavage \nas a potential mechanism underlying DNAJB11-dependent cyst formation. Proteomic analysis of \nDnajb11- and Pkd1-deficient cells reveals common and distinct pathways and dysregulated \nproteins, providing a foundation to better understand phenotypic differences between different \nforms of ADPKD.","fileCount":"28","fileSizeKB":"6702911","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Autosomal dominant polycystic kidney disease (ADPKD); Cyst Formation; DNAJB11; PKD1; co-chaperone","pi":[{"name":"Michael Koettgen, MD","email":"michael.koettgen@uniklinik-freiburg.de","institution":"Medical Center; University of Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056244","task":"585cc61888be4845917fd350e6ef1b05","id":"1853"}, {"dataset":"MSV000095950","datasetNum":"95950","title":"The Role of the Co-Chaperone DNAJB11 in Polycystic Kidney Disease: Molecular Mechanisms and Cellular Origin of Cyst Formation","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727273822000","created":"Sep. 25, 2024, 7:17 AM","description":"Autosomal dominant polycystic kidney disease (ADPKD) is caused by muta1ons in PKD1 and \nPKD2, encoding polycystin-1 (PC1) and polycystin-2 (PC2), which are required for the regula1on \nof the renal tubular diameter. Loss of polycystin func1on results in cyst forma1on. Atypical forms \nof ADPKD are caused by mutations in genes encoding endoplasmic reticulum (ER)-resident \nproteins through mechanisms that are not well understood. Here, we investigate the func1on of \nDNAJB11, an ER co-chaperone associated with atypical ADPKD. We generated mouse models with \nconstitutive and conditional Dnajb11 inactivation and Dnajb11-deficient renal epithelial cells to \ninvestigate the mechanism underlying autosomal dominant inheritance, the specific cell types \ndriving cyst formation, and molecular mechanisms underlying DNAJB11-dependent polycystic \nkidney disease. We show that biallelic loss of Dnajb11 causes cystic kidney disease and fibrosis, \nmirroring human disease characteristics. In contrast to classical ADPKD, cysts predominantly \noriginate from proximal tubules. Cyst formation begins in utero and the timing of Dnajb11\ninactivation strongly influences disease severity. Furthermore, we identify impaired PC1 cleavage as a potential mechanism underlying DNAJB11-dependent cyst formation. Proteomic analysis of Dnajb11- and Pkd1-deficient cells reveals common and distinct pathways and dysregulated proteins, providing a foundation to better understand phenotypic differences between different forms of ADPKD.","fileCount":"29","fileSizeKB":"6545603","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Autosomal Dominant Polycystic Kidney Disease (ADPKD); Cyst Formation; DNAJB11; PKD1","pi":[{"name":"Michael Koettgen, MD","email":"michael.koettgen@uniklinik-freiburg.de","institution":"Medical Center; University of Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056240","task":"8b5028aa67484258a886cc7dc4d49b8f","id":"1854"}, {"dataset":"MSV000095949","datasetNum":"95949","title":"CLYBL averts methylmalonyl-CoA mutase inhibition and loss of vitamin B12 by repairing malyl-CoA","user":"coreymgriffith","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727257395000","created":"Sep. 25, 2024, 2:43 AM","description":"Citrate lyase beta-like protein (CLYBL) is a ubiquitously expressed mammalian enzyme known for its role in the degradation of itaconate, a bactericidal immunometabolite produced in activated macrophages. The association of CLYBL loss-of-function with reduced circulating vitamin B12 levels was proposed to result from inhibition of the B12-dependent enzyme methylmalonyl-CoA mutase (MCM) by itaconyl-CoA. The discrepancy between the highly inducible and locally confined production of itaconate and the broad expression profile of CLYBL across tissues, suggested a role for this enzyme beyond itaconate catabolism. We discovered that CLYBL additionally functions as a metabolite repair enzyme for malyl-CoA, a side-product of promiscuous TCA cycle enzymes. We found that CLYBL knockout cells, accumulating malyl-CoA but not itaconyl-CoA, show decreased levels of adenosylcobalamin and that malyl-CoA is a more potent inhibitor of MCM than itaconyl-CoA. Our work thus suggests that malyl-CoA plays a role in the B12 deficiency observed in individuals with CLYBL loss-of-function. Data deposited herein corresponds to the untargeted LC-HRMS\/MS acyl-CoA ester and HILIC analyses conducted for this study. ","fileCount":"118","fileSizeKB":"21497397","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CLYBL;acyl-CoA;metabolite repair;3T3-L1 adipocytes;vitamin B12","pi":[{"name":"Carole Linster","email":"carole.linster@uni.lu","institution":"Luxembourg Centre for Systems Biomedicine","country":"Luxembourg"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a9f1a89aad3b404194eaf72ae836c9e2","id":"1855"}, {"dataset":"MSV000095948","datasetNum":"95948","title":"GNPS - Yeast - Bacteria Interaction from Phyllosphere ","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727250692000","created":"Sep. 25, 2024, 12:51 AM","description":"Non-targeted metabolomics of environmental yeast interacting with bacteria","fileCount":"225","fileSizeKB":"18810879","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Yeast;Bacteria;Interaction","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"39fe48327c794a41b6c960e1c7537fe3","id":"1856"}, {"dataset":"MSV000095946","datasetNum":"95946","title":"Benchmarking Peptide Spectral Library Search Dataset","user":"hax019","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727232748000","created":"Sep. 24, 2024, 7:52 PM","description":"Spectral library search (SLS) is a major approach for peptide identification from tandem mass spectrometry data, offering a complementary approach to conventional database search. Moreover, with the emergence of spectrum prediction models, proteomics database search is progressively becoming more like spectral library search of predicted peptide spectra. The performance of peptide identification algorithms thus frequently depends on how well the underlying Spectrum-Spectrum Matching (SSM) scoring functions distinguish true and false positive matches. However, detailed comparative studies evaluating the performance of SSM scoring functions remain limited by the absence of comprehensive benchmark datasets. We propose new methods to build benchmarks that assess the effectiveness and robustness of SSM scoring functions. The resulting benchmark dataset is composed of (i) a set of 476,063 precursors used to construct 8 query spectrum sets with different levels of noise added to \"ideal\" and real experimental spectra, and (ii) three spectral libraries with different spectra for the same 3,065,819 precursors: experimental spectra, annotated\/de-noised spectra and predicted spectra. The benchmark set was then used to evaluate 9 common spectrum preprocessing scenarios, followed by the evaluation of 3 standard SSM scoring functions, Cosine, Projected-Cosine (commonly used for the analysis of chimeric\/mixture spectra), and Jensen-Shannon divergence, and 2 additional scoring functions used in state-of-the-art SLS tools: SpectraST and EntropyScore. The results revealed that scoring spectrum-spectrum matches is still an important open problem, with the best recall for typical SLS searches still assessed to be poor at just ~70% at the typical 1% error rate. Overall, SpectraST performed best for spectra with little-to-no noise, but JS-divergence performed better in some cases as it was found to be most resistant to noise. Conversely, the performance of Cosine and Entropy score was found to be generally lower than previously reported, with Projected-Cosine performing especially poorly in most cases. However, the performance of the SSM scoring functions was also found to depend quite significantly on the minimum number of matching peaks required for each SSM, with benchmark results showing that the scoring functions' performance and relative ranking can be very significantly affected by how this important parameter is set. The resulting benchmark dataset can be used to test and support the development of SSM scoring functions and the proposed benchmark construction approach, providing a foundation that can be extended for additional types of spectrum-spectrum matching.","fileCount":"481","fileSizeKB":"118258073","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00408 - \\\"A protein modification that effectively replaces a residue amino or imino hydrogen with an acetyl group.\\\";MOD:00398 - \\\"A protein modification that effectively replaces a hydrogen atom with a carbamoyl (carboxamido) group. Replacement of an amino hydrogen produces a ureido group.\\\"","keywords":"Spectral library search;Benchmark dataset;MassIVE-KB;Predicted mass spectra;Noise resistance","pi":[{"name":"Nuno Bandeira","email":"bandeira@ucsd.edu","institution":"UCSD","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056205","task":"a099c8638ffd4dba9eb1fa21f6afcf49","id":"1857"}, {"dataset":"MSV000095941","datasetNum":"95941","title":"Vehicle versus FASN-inhibited human metastatic breast cancer global whole cell lysate and lipid droplets","user":"candolin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727206983000","created":"Sep. 24, 2024, 12:43 PM","description":"Metastatic breast cancer cells (MCF10CA1a) were treated with vehicle (DMSO) or 20 uM of Fatty Acid Synthase (FASN) inhibitor TVB-3166 for three days. Untargeted global proteomics (Tryp\/Lys-C; Lumos) was performed on the whole cell lysates, as well as isolated lipid droplet fractions from each lysate. All samples were prepared in the same manner, including lipid extraction prior to protein digestion.","fileCount":"14","fileSizeKB":"10371766","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"breast cancer;lipid metabolism;fatty acid synthase;FASN;TVB-3166;cancer metabolism;MCF10CA1a;lipid droplet;fatty acid synthesis","pi":[{"name":"Chaylen J Andolino","email":"candolin@purdue.edu","institution":"Purdue University","country":"United States"},{"name":"Dorothy Teegarden","email":"dteegard@purdue.edu","institution":"Purdue University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"932cd20547af4a18b34a3a0948395ec2","id":"1858"}, {"dataset":"MSV000095939","datasetNum":"95939","title":"Unveiling signaling pathways inducing MHC class II expression in neutrophils","user":"trendsetter","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727190541000","created":"Sep. 24, 2024, 8:09 AM","description":"Gram-negative bacillary bacteremia poses a significant threat, ranking among the most severe infectious diseases capable of triggering life-threatening sepsis. Despite the unambiguous involvement of neutrophils in this potentially fatal disease, there are limited data about the molecular signaling mechanisms, phenotype, and function of human neutrophils during the early phase of gram-negative bacillary bacteremia. By using an unbiased proteomics and flow cytometry approach, we identified an antigen-presenting cell (APC)-like phenotype in human peripheral blood neutrophils (PMN) with MHC class II molecule expression in the early phase of bacteremia. Using an in-vitro model of GM-CSF-mediated induction of APC-like phenotype in PMN, we investigated downstream signaling pathways leading to MHC class II expression. GM-CSF stimulation of neutrophils leads to the activation of three major signaling pathways, the JAK-STAT, the mitogen-activated protein kinase (MAPK), and the phosphoinositide 3-kinase (PI3K)-Akt-mTOR pathways, while MHC class II induction is mediated by a MAPK-p38-MSK1-CREB1 signaling cascade and the MHC class II transactivator CIITA in a strictly JAK12 kinase-dependent manner. Our data describing details of signaling pathways inducing MHC class II expression in neutrophils open new possibilities of therapeutic targeting of JAK12 signaling during different stages of gram-negative bacteremia and sepsis.","fileCount":"49","fileSizeKB":"29056955","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"MHC;Phosphoproteomics;neutrophils","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD056178","task":"655ebb43e679475a9764d1625791fc30","id":"1859"}, {"dataset":"MSV000095937","datasetNum":"95937","title":"Pseudomonas_aeruginosa_supernatants_LC-HRMS analysis - UniGE","user":"Abory","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727176552000","created":"Sep. 24, 2024, 4:15 AM","description":"In this study, we used untargeted metabolomics to analyze and compare the exo-metabolome of wild type P. aeruginosa strain PA14, as well as a mutant (PA14_D4mex) lacking the four clinically relevant efflux pumps (EPs), in which we overexpressed individually the four clinically relevant Mex EPs from an inducible promoter. The supernatants were extracted and analyzed by LC-HRMS.","fileCount":"85","fileSizeKB":"2540199","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa (NCBITaxon:287)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomic;Pseudomonas;natural substrates;antibiotic resistance;multidrug efflux","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"53017db3ce874e2daba3813d7e306cf7","id":"1860"}, {"dataset":"MSV000095935","datasetNum":"95935","title":"Ion Mobility-Assisted Free Radical Initiated Peptide Sequencing","user":"nborotto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727134259000","created":"Sep. 23, 2024, 4:30 PM","description":"Free radical-initiated peptide sequencing (FRIPS), a TEMPO-assisted mass spectrometry, has shown potential as a peptide tandem mass spectrometry (MS\/MS) tool that can be an alternative to electron-based mass spectrometry and the traditional collision-based methods. However, a couple of instrumentation barriers need to be overcome before this approach can be a practical tool. One of the barriers is the limitation of the FRIPS-based technique to ion trap mass spectrometry or an orbitrap due to the MS3 workflow. To overcome this challenge, the work introduces a recently developed activation within the trapped ion mobility mass spectrometry (TIMS) device that was found to initiate the radical species. More importantly, the generated product ion was mobility separated, which increased the sequence coverage. Overall, coupling the activation within the TIMS cell with the para-TEMPO-Bz-based FRIPS mass spectrometry offers another practical approach that can be utilized for peptide MS\/MS analysis","fileCount":"47","fileSizeKB":"279180","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mass spectrometry;tandem mass spectrometry","pi":[{"name":"Nicholas Borotto","email":"nborotto@unr.edu","institution":"University of Nevada","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a47e70c00ed24e319fc3badf70a5409c","id":"1861"}, {"dataset":"MSV000095932","datasetNum":"95932","title":"A comprehensive multi-omics signature of doxorubicin-induced cellular senescence in the postmenopausal human ovary","user":"JoannaBons","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727108394000","created":"Sep. 23, 2024, 9:19 AM","description":"A major aging hallmark is the accumulation of cellular senescence burden. Over time senescent cells contribute to tissue deterioration through chronic inflammation and fibrosis driven by the Senescence-Associated Secretory Phenotype (SASP). The human ovary is one of the first organs to age, and prominent age-related fibroinflammation within the ovarian microenvironment is consistent with the presence of senescent cells. However, bona fide senescent cells have not been validated in the human ovary. Therefore, we established a doxorubicin-induced model of cellular senescence to define a signature of ovarian senescent cells. Explants of human postmenopausal ovarian cortex and medulla were treated with doxorubicin for 24 hours followed by culture for up to 10 days in doxorubicin-free medium. Tissue viability was confirmed by histology, lack of apoptosis, and continued glucose consumption by explants. Single nuclei sequencing and proteomics revealed an unbiased signature of ovarian senescence. We identified distinct senescence profiles for the cortex and medulla, driven predominantly by epithelial and stromal cells. Proteomics uncovered subregional differences in addition to 120 proteins common to the cortex and medulla SASP. Integration of transcriptomic and proteomic analyses revealed 26 shared markers, defining a robust senotype of doxorubicin-induced senescence unique to the postmenopausal ovary. A subset of these proteins - Lumican, SOD2, MYH9 , and Periostin - were mapped onto native tissue to reveal compartment-specific localization. This senotype will help determine the role of cellular senescence in ovarian aging and inform the development of biomarkers to identify and therapeutic applications to slow or reverse ovarian aging, senescence, and cancer.","fileCount":"36","fileSizeKB":"54029136","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cellular senescence;Doxorubicin;Ovarian aging;Senescence-Associated Secretory Phenotype (SASP);Data-independent acquisition;Quantitative proteomics;Reproductive aging","pi":[{"name":"Birgit Schilling","email":"bschilling@buckinstitute.org","institution":"Buck Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD056100","task":"f12d75c8d2d441d18d666f4f59098238","id":"1862"}, {"dataset":"MSV000095931","datasetNum":"95931","title":"Proteomics corresponding to structural analysis of model Alzheimers brain","user":"mrwaas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727106318000","created":"Sep. 23, 2024, 8:45 AM","description":"Fractions prepared from a lysed Alzheimer's model rat were used as a basis for cryo EM. Mass spectrometry was used to investigate whether there is orthogonal evidence for proteins with matched densities.","fileCount":"22","fileSizeKB":"10528827","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:34 - \\\"Methylation.\\\"","keywords":"Alzheimers;structure","pi":[{"name":"Mohammad Mazhab-Jafari","email":"Mohammad.Mazhab-Jafari@uhn.ca","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"06b88640dd704a30aacfd4333e92696b","id":"1863"}, {"dataset":"MSV000095928","datasetNum":"95928","title":"Protective Effects of FXI Inhibition by Abelacimab in a Baboon Model of live Staphylococcus aureus Sepsis","user":"sbyrum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727097443000","created":"Sep. 23, 2024, 6:17 AM","description":"Sepsis remains a major clinical challenge characterized by dysregulated immune response, coagulation abnormalities, and multi-organ failure, leading to high morbidity and mortality. This study investigates the therapeutic potential of Abelacimab, a novel monoclonal antibody targeting the plasma zymogen coagulation fFactor XI\/XIa (FXI\/XIa), in a baboon model of live Staphylococcus aureus sepsis.\nHealthy Papio anubis baboons were randomly assigned to either a control or a treatment group receiving Abelacimab. Both groups (n=6, each) were intravenously infused with a LD50 dose of live S. aureus. The treatment group was administered Abelacimab, 30 minutes after bacterial infusion. Hematologic, coagulation, inflammatory, and organ function parameters were monitored for 7 days or until the animals exhibited signs of irreversible organ failure. Proteomic analysis was conducted to elucidate the underlying mechanisms by which Abelacimab offered protection.\nAll six Abelacimab-treated baboons survived to the 7-day endpoint, while three out of six untreated controls succumbed to sepsis within 102 hours. Abelacimab significantly attenuated sepsis-induced consumptive coagulopathy, as evidenced by coagulation and fibrinolysis markers. Treated animals showed decreased levels of pro-inflammatory cytokines, reduced neutrophil activation, and preservation of endothelial integrity, leading to reduced organ damage. Proteomic analysis revealed that Abelacimab modulated pathways related to coagulation, inflammation, and tissue injury, contributing to improved survival outcomes.\nWe found that FXI\/XIa inhibition by Abelacimab offers significant protection in a model of live S. aureus sepsis by attenuating activation of coagulation factors, reducing inflammation, and preventing organ failure. These findings suggest that targeting FXI may be a promising therapeutic strategy for managing sepsis, addressing multiple facets of its complex pathophysiology.\n","fileCount":"58","fileSizeKB":"40634428","spectra":"1673251","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Papio anubis (NCBITaxon:9555)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Abelacimab;sepsis;baboon model;Staphylococcus aureus;organ failure","pi":[{"name":"Florea Lupu","email":"Lupu@omrf.org","institution":"Oklahoma Medical Research Foundation","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD056090","task":"c24e4e695abe4803a7f718730c9002f6","id":"1864"}, {"dataset":"MSV000095925","datasetNum":"95925","title":"Klebsiella oxytoca Pyrazine vs Pyrazinone Eliciting Conditions","user":"Hamchand","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727072999000","created":"Sep. 22, 2024, 11:29 PM","description":"These datasets describe the eliciting conditions for the leup operon in K. oxytoca and the metabolites of the pyr gene in K. oxytoca \n\nFile descriptions: 16495_KO1-3: ESI+ runs of the pyr KO K. oxytoca strain in M9+CAS+Gal KOx_WT1-3: ESI+ runs of K. oxytoca WT in M9+CAS+Gal \nThese files should be compared to each other. \n\nKOxy_M9CASGAL_MSMS_Pyrazine files are targeted MS2 Qtof runs of compounds from Klebsiella oxytoca that have the pyrazine-like UV-Vis spectrum.\n\nKoxNeu5Ac_1-3_AutoMSMS: ESI+ MS2 runs of WT K. oxytoca in M9+CAS+Neu5AC \nKoxWT_1-3_AutoMSMS: ESI+ MS2 runs of WT K. oxytoca in M9+CAS \nThese files should be compared to each other.","fileCount":"15","fileSizeKB":"1022334","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Klebsiella oxytoca KCTC 1686 (NCBITaxon:1006551)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Klebsiella oxytoca ","pi":[{"name":"Jason Crawford","email":"jason.crawford@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7720d6f13cc449c483a3d22f1e0d0d85","id":"1865"}, {"dataset":"MSV000095923","datasetNum":"95923","title":"An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions","user":"Arminja","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1727026640000","created":"Sep. 22, 2024, 10:37 AM","description":"Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins (RBPs), which can modulate the fate of the RNA molecules from transcription to degradation. Vice versa, RNA can regulate the interactions and functions of the associated proteins. Dysregulation of RBPs is linked to diseases such as cancer and neurological disorders. RNA and RBPs are present in mitotic structures like the centrosomes and spindle microtubules, but their influence on mitotic spindle integrity remains unknown. Thus, we applied the R-DeeP strategy for the proteome-wide identification of RNA-dependent proteins and complexes to cells synchronized in mitosis versus interphase. The resulting atlas of RNA-dependent proteins in cell division can be accessed through the R-DeeP 3.0 database (R-DeeP3.dkfz.de). It revealed key mitotic factors as RNA-dependent such as AURKA, KIFC1 and TPX2 that were linked to RNA despite their lack of canonical RNA-binding domains. KIFC1 was identified as a new interaction partner and phosphorylation substrate of AURKA at S349 and T359. In addition, KIFC1 interacted with both, AURKA and TPX2, in an RNA-dependent manner. Our data suggest a riboregulation of mitotic protein-protein interactions during spindle assembly, offering new perspectives on the control of cell division processes by RNA-protein complexes.","fileCount":"202","fileSizeKB":"45980722","spectra":"0","psms":"1546497","peptides":"435997","variants":"558346","proteins":"19703","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RNA, protein complex, mitosis, interphase","pi":[{"name":"Arminja Nadine Kettenbach","email":"Arminja.N.Kettenbach@Dartmouth.edu","institution":"Dartmouth Medical School","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD056068","task":"46b801f9c62549db86bc4cd5ad04567c","id":"1866"}, {"dataset":"MSV000095922","datasetNum":"95922","title":"GNPS - Metabolite-Driven Mechanisms Reveal Chemical Ecology of Lehmann Lovegrass Invasion in North American Semi-Arid Ecosystems","user":"benyang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726953101000","created":"Sep. 21, 2024, 2:11 PM","description":"This dataset comprises raw LC-MS data generated from a study examining the root and rhizosphere metabolomes of of Lehmann lovegrass (Eragrostis lehmanniana) and Arizona cottontop (Digitaria californica) in both canopy and inter-canopy regions under velvet mesquite trees (Prosopis velutina) at the Santa Rita Experimental Range (SRER) in Arizona. Samples were collected from twelve 1m x 1m plots representing two dominant plant species (Lehmann lovegrass and Arizona cottontop) across two canopy conditions (closed and open), resulting in 36 root and rhizosphere samples.","fileCount":"568","fileSizeKB":"28353660","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":" Eragrostis lehmanniana;Digitaria californica","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plant;Rhizosphere","pi":[{"name":"Malak M. Tfaily","email":"tfaily@arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"e439d8879ed44c83822512fd035f7889","id":"1867"}, {"dataset":"MSV000095917","datasetNum":"95917","title":"CSF protein biomarkers predict response to multi-agent intraventricular chemotherapy in patients with CNS lymphoma","user":"TKislinger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726845848000","created":"Sep. 20, 2024, 8:24 AM","description":"Raw mass spectrometry data from cerebrospinal fluid (CSF) proteomics analysis of central nervous system lymphoma (CNSL) patients undergoing multi-agent intraventricular chemotherapy (MAIVC). The study aimed to identify CSF-based proteomic biomarkers for treatment response and outcome prediction in CNSL, analyzing 117 CSF samples from 59 patients.","fileCount":"128","fileSizeKB":"140498076","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"cerebrospinal fluid;CNS lymphoma;proteomics","pi":[{"name":"Dr. Thomas Kislinger","email":"thomas.kislinger@utoronto.ca","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ca4a1a7acc304ff8b2e6d08961a64390","id":"1868"}, {"dataset":"MSV000095916","datasetNum":"95916","title":"Mass Spectrometry of T47D cells treated with PTK6 PROTAC ","user":"criseydam","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726838343000","created":"Sep. 20, 2024, 6:19 AM","description":"PTK6 PROTAC treatment of T47D breast cancer cells were analyzed with mass spectrometry for determining PTK6 PROTAC specificity and global proteomic changes.","fileCount":"27","fileSizeKB":"31465689","spectra":"1185683","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PTK6, BRK, PROTAC, Breast Cancer, degraders","pi":[{"name":"Hanna Irie","email":"hanna.irie@mssm.edu","institution":"Icahn School of Medicine at Mount Sinai","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056058","task":"6c9734cf106f42b5913751f28a634782","id":"1869"}, {"dataset":"MSV000095914","datasetNum":"95914","title":"Mass spectrometry-based workflow for the identification and quantification of alternative and canonical proteins in pancre-atic cancer cells.","user":"bertrandfabre31","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726818686000","created":"Sep. 20, 2024, 12:51 AM","description":"Samples from a panel of pancreatic cancer cell lines and HeLa and HEK293T cells were lysed in a buffer containing sodium deoxycholate and digested with trypsin. A fraction of the sample was analysed using data dependent analysis on a Thermofischer scientific Exploris 480 and the rest of the sample was fractionated using high pH reverse phase. Peptides from each fraction were injected on a Thermofischer scientific Exploris 480 in data independent acquisition.","fileCount":"90","fileSizeKB":"59005168","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Alternative proteins;Microproteins;Short open reading frame-encoded peptides;Pancreatic ductal adenocarcinoma;Data independent acquisition","pi":[{"name":"Bertrand Fabre","email":"bertrand.fabre@univ-tlse3.fr","institution":"LRSV (CNRS)","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9c3137485504451083244eedd601988d","id":"1870"}, {"dataset":"MSV000095912","datasetNum":"95912","title":"Heart surfaceome profiling using biotin capture","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726801965000","created":"Sep. 19, 2024, 8:12 PM","description":"Cell surface proteins (surfaceome) represent key signalling and interaction molecules for therapeutic targeting, biomarker profiling, and cellular phenotyping. Understanding the surfaceome of complex tissues including the heart is essential to investigate membrane composition and function in physiological and pathological states. Here, we present a protein-centric workflow that enables the labelling, capture and detection of the cardiac cell surfaceome using ultra-high-sensitivity mass spectrometry-based proteome analysis in individual murine hearts. By preserving cardiac cell architecture of the neo-native heart, this workflow combines coronary artery perfusion using cleavable biotin and unbiased capture of the surface-accessible heart proteome.","fileCount":"19","fileSizeKB":"11445053","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"heart;cell surface;plasma membrane","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b614f9a880e44d2d9103f2f4921a2fef","id":"1871"}, {"dataset":"MSV000095911","datasetNum":"95911","title":"Bunodosoma proteins thermal stress","user":"mapabeam","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726800045000","created":"Sep. 19, 2024, 7:40 PM","description":"Protein analysis of Bunodosoma sea anemone by thermal stress","fileCount":"38","fileSizeKB":"1218864","spectra":"0","psms":"4228","peptides":"547","variants":"678","proteins":"113","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actiniaria (NCBITaxon:6103);Bunodosoma (NCBITaxon:31163)","instrument":"Dionex instrument model","modification":"UNIMOD:894 - \\\"Carboxymethylated DTT modification of cysteine.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"sea anemone;Gulf of Mexico","pi":[{"name":"Mayra Pamela Becerra Amezcua","email":"mayrapame@gmail.com","institution":"Universidad Autonoma Metropolitana","country":"Mexico"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"569d1fe89adf4180953402a739e2a314","id":"1872"}, {"dataset":"MSV000095910","datasetNum":"95910","title":"A quantitative, proteome wide approach reveals general correlates of antigen presentation and immunogenicity for antiviral CD8+ T cell epitopes","user":"NathanC","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726796695000","created":"Sep. 19, 2024, 6:44 PM","description":"Quantification of MHC-peptide abundance (and source protein expression) during timecourse of infection of various cell lines (primary (BMDC) and immortalised (DC2.4) dendritic cells; primary (PMF) and immortalised fibroblasts (MC57G)) with vaccinia virus strain Western Reserve.","fileCount":"182","fileSizeKB":"59326113","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Vaccinia virus Western Reserve (NCBITaxon:696871)","instrument":"QTRAP 5500;QTRAP 6500+;Q Exactive Plus","modification":"MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Vaccinia virus;Antigen processing and presentation;MHC;Epitope;CD8 T cell","pi":[{"name":"Anthony Purcell","email":"anthony.purcell@monash.edu","institution":"Monash University","country":"Australia"},{"name":"Nathan Croft","email":"nathan.croft@monash.edu","institution":"Monash University","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4e2a2a82a8c94e40a59292218c1f82d0","id":"1873"}, {"dataset":"MSV000095907","datasetNum":"95907","title":"IRF4 mediates nonenzymatic dependency on IRE1 in Multiple 1 Myeloma cells","user":"vpham","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726776772000","created":"Sep. 19, 2024, 1:12 PM","description":"Multiple Myeloma (MM) arises through oncogenic transformation of immunoglobulin-secreting\nplasma cells. MM often co-opts the endoplasmic-reticulum (ER) stress mitigator, inositol\nrequiring enzyme 1 (IRE1), to sustain malignant growth. While certain MMs require enzymatic\nIRE1-dependent activation of the ER-homeostatic transcription factor XBP1s, others display\nnonenzymatic dependency on IRE1 that is not yet mechanistically understood. Interferon\nregulatory factor 4 (IRF4) stimulates gene programs that promote immune-cell proliferation and cell cycle control by IRE1 in MM. Here we show that IRF4 acts as a key conduit of nonenzymatic cell cycle control by IRE1 in MM. IRE1 silencing increased inhibitory phosphorylation of IRF4, disrupting its chromatin-binding activity and mRNA transcription. IRF4 knockdown recapitulated, whereas IRF4 repletion reversed the anti-proliferative phenotype of IRE1 silencing. Functional studies revealed that IRF4 engages the E2F1 and CDC25A genes and promotes CDK2 activation to drive cell cycle progression. Our results advance mechanistic understanding of IRE1 and IRF4 in MM.","fileCount":"48","fileSizeKB":"16163736","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"Fixed mod: C (+57.0215), K (+304.2071), peptide N-term (+304.2071). Variable mod: M (+15.994), Y(+304.2071), STY (+79.9663)","keywords":"IRE1 nonenzymatic activity, IRF4, IRF4 activity, E2F1, cell cycle regulation","pi":[{"name":"Avi Ashkenazi","email":"aa@gene.com","institution":"Genentech, Inc.","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b90a490271814221a2cd75d9f2b288a6","id":"1874"}, {"dataset":"MSV000095905","datasetNum":"95905","title":"GNPS - Microbiome Reciprocal Transfer Experiment 2023 - Investigating the effect on the host of `mismatched` microbiomes","user":"mcmk3","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726769197000","created":"Sep. 19, 2024, 11:06 AM","description":"Full reciprocal transfer of microbiomes between nine host strains of phytoplankton and microbe-free controls (Kuijpers et al unpublished). Microbiomes were naturally recruited from lake and stream water in an assembly experiment (Broe et al unpublished). Transferred microbiomes were added to axenic hosts and grown for 7 or 14 days before control or heat shock treatment. ","fileCount":"4692","fileSizeKB":"234269873","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Desmonostoc muscorum (NCBITaxon:1179);Chlorella sorokiniana (NCBITaxon:3076);Chlorella vulgaris (NCBITaxon:3077);Chlamydomonas reinhardtii (NCBITaxon:3055);Porphyridium aerugineum (NCBITaxon:2792);Vischeria (NCBITaxon:44431);Nannochloris (NCBITaxon:3187)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"host microbe interactions;host microbiome interactions;aquatic;freshwater;phytoplankton;reciprocal transfer design;MSCollaboratory","pi":[{"name":"Sara Jackrel","email":"sjackrel@ucsd.edu","institution":"University of California, San Diego","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"be3f823ad3564f1fa1556667ed3c185d","id":"1875"}, {"dataset":"MSV000095902","datasetNum":"95902","title":"Secretome Analysis of Time- and Passage-Dependent of Wharton's Jelly Mesenchymal Stem Cells Using Quantitative Proteomic ","user":"Anastasha97","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726703819000","created":"Sep. 18, 2024, 4:56 PM","description":"This dataset contains proteins from the secretomes (Conditioned Media) of Wharton's Jelly Mesenchymal Stem Cells (WJMSC) harvested at different time points (24, 48, and 72 hours) and cell passages (Passage 3, Passage 5, and Passage 10). 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This research seeks to enhance the clinical efficiency of WJMSCs for regenerative medicine applications by revealing the dynamic nature of their secretome.","fileCount":"163","fileSizeKB":"66671940","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Secretomes;Wharton's Jelly;Mesenchymal Stem Cells;Time Dependent Harvest;Passage Dependent Harvest","pi":[{"name":"Wan Safwani Wan Kamarul Zaman","email":"wansafwani@um.edu.my","institution":"Universiti Malaya","country":"Malaysia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD056000","task":"9d6d3009be514a2d9906f22aed0a18fc","id":"1876"}, {"dataset":"MSV000095899","datasetNum":"95899","title":"GNPS - 2024 - Northen \/ Floge - Early stage viral infection of cyanobacteria drives marine bacterial chemotaxis","user":"smkosina","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726690661000","created":"Sep. 18, 2024, 1:17 PM","description":"Synechococcus WH8102 axenic infected with lytic phage S-SSM5. 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Computational meta-analysis of human interstitial lung disease single-cell RNA sequencing datasets confirmed these genes are highly expressed in disease samples and strongly correlate with mechanotransduction and senescence-related pathways. 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Thackray","email":"vthackray@health.ucsd.edu","institution":"University of California San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"98214c8c40d24dc89983b77e5149962b","id":"1893"}, {"dataset":"MSV000095867","datasetNum":"95867","title":"GNPS - Dataset Creation from GNPS Molcular Networking - 0d462f743d4943e584fb93e177c62d40","user":"tehanr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726446533000","created":"Sep. 15, 2024, 5:28 PM","description":"LC-HR-MS\/MS data for culture extracts of the fungi Paraisaria cascadensis, P. insignis, and P. pseudoheteropoda.","fileCount":"4","fileSizeKB":"207078","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Paraisaria cascadensis;Paraisaria pseudoheteropoda;Paraisaria insignis","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fungi","pi":[{"name":"Kerry McPhail","email":"kerry.mcphail@gmail.com","institution":"Oregon State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"450f079fd3de41449109e969e2c2e0d0","id":"1894"}, {"dataset":"MSV000095866","datasetNum":"95866","title":"GNPS-Passive accumulation of alkaloids in non-toxic frogs challenges paradigms of the origins of acquired chemical defenses","user":"rfitch","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726429910000","created":"Sep. 15, 2024, 12:51 PM","description":"Paper Title: Passive accumulation of alkaloids in non-toxic frogs challenges paradigms of the origins of acquired chemical defenses.\nAuthor List; Rebecca D Tarvin, Jeffrey L Coleman, David A Donoso, Mileidy Betancourth-Cundar, Karem Lopez-Hervas, Kimberly S Gleason, J Ryan Sanders, Jacqueline M Smith, Santiago R Ron, Juan C Santos, Brian E Sedio, David C Cannatella, Richard Fitch\n\nRAW files used for alkaloid identification in crude skin extracts.\nCitation: eLife August 2, 2024 DOI: 10.7554\/eLife.100011.1\n","fileCount":"277","fileSizeKB":"17605977","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Multiple Frog Species","instrument":"ITQ 1100","modification":"NA","keywords":"amphibians, toxin sequestration, lipophilic alkaloids, toxin resistance, bioaccumulation, adaptive landscape","pi":[{"name":"Rebecca D. Tarvin","email":"rdtarvin@berkeley.edu","institution":"University of California, Berkeley","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d51d3e92c5574164934507a642c56512","id":"1895"}, {"dataset":"MSV000095862","datasetNum":"95862","title":"The co-chaperone DNAJA2 buffers proteasomal degradation of cytosolic proteins with missense mutations","user":"bakerha","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726266514000","created":"Sep. 13, 2024, 3:28 PM","description":"MS experiment to look at KO efficiency using CRISPR KO with a puromycin selection plasmid with sgRNAs targeting DNAJA2, USP11 and SUGT1.","fileCount":"1915","fileSizeKB":"190794142","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:1060 - \\\"Cys->Lys substitution.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"chaperone;DNAJA2;cytosolic proteins;USP11;SUGT1","pi":[{"name":"Thibault Mayor","email":"mayor@msl.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d801be08bc9f4fc28d940d09269143f4","id":"1896"}, {"dataset":"MSV000095861","datasetNum":"95861","title":"Acquisition of embryogenic competence during protoplast development of Fagopyrum","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726237263000","created":"Sep. 13, 2024, 7:21 AM","description":"Reprogramming in protoplast cultures is a key step for acquiring embryogenic competence by dedifferentiated cells, thus leading to plant regeneration. Therefore, to better understand factors trigging the processes, this work focuses on analysing proteomes, cell wall composition and changes in the expression profile of selected genes. The results demonstrate a significant accumulation of somatic embryogenesis related proteins like late embryogenesis abundant proteins (embryogenic protein-DC-8-like, seed biotin-containing protein) and endochitinases during the developmental path of protoplast cultures supporting somatic embryogenesis events. Additionally, there is an increase in seed storage proteins like vicilin, oleosins, and seed biotin-containing proteins in the cultures. Investigation of somatic embryogenesis-associated transcription factors revealed intensive up-regulation of LEC1 for 50th day of F. tataricum protoplast cultures. Furthermore, we demonstrated the variable distribution of cell wall components like pectin side chains, arabinogalactan proteins (AGP) and extansin (EXT), indicating the acquisition of competence and cellular differentiation. ","fileCount":"28","fileSizeKB":"104829998","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fagopyrum tataricum (NCBITaxon:62330);Fagopyrum esculentum (NCBITaxon:3617)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"differentiation;embryogenic competence;Fagopyrum;oleosins;protoplast cultures;somatic embryogenesis;vicilins","pi":[{"name":"Alexander Betekhtin","email":"alexander.betekhtin@us.edu.pl","institution":"Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice","country":"Poland"},{"name":"Artur Pinski","email":"artur.pinski@us.edu.pl","institution":"Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice","country":"Poland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD055850","task":"d96b03d7eb8d40e2bf2105b1f69c6f6e","id":"1897"}, {"dataset":"MSV000095860","datasetNum":"95860","title":"HLA-B14 and HLA-B27 peptide repertoire","user":"e_lorente","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726222326000","created":"Sep. 13, 2024, 3:12 AM","description":"we have used large-scale mass spectrometry-based peptide sequencing to analyze the peptidomes of HLA-B*14:03, HLA-B*14:02, and HLA-B*27:05","fileCount":"33","fileSizeKB":"67078858","spectra":"513190","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive-Plus mass spectrometer","modification":"UNIMOD:1267 - \\\"Oxidised 13C4 labelled Methionine.\\\"","keywords":"HLA;Peptide","pi":[{"name":"Elena Lorente","email":"elorente@isciii.es","institution":"Instituto de Salud Carlos III","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055841","task":"6d484512e2d742d7b4a829353bb84efc","id":"1898"}, {"dataset":"MSV000095859","datasetNum":"95859","title":"GNPS - Myxococcus xanthus DZ2 metabolome","user":"Mathieu_Sourice","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726217796000","created":"Sep. 13, 2024, 1:56 AM","description":"Project title : Combining culture optimization and synthetic biology to improve production and detection of secondary metabolites in Myxococcus xanthus: application to myxoprincomide.","fileCount":"90","fileSizeKB":"10047254","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Myxococcus xanthus DZ2 (NCBITaxon:1198133)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Myxobacteria;Secondary metabolites;Chassis strain","pi":[{"name":"Beatrice PY","email":"py@imm.cnrs.fr","institution":"LCB CNRS UMR7283","country":"France"},{"name":"Corinne AUBERT","email":"aubert@imm.cnrs.fr","institution":"LCB CNRS UMR7283","country":"France"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c6d1791557264737b9e1c295649625b7","id":"1899"}, {"dataset":"MSV000095855","datasetNum":"95855","title":"GNPS - Cardiolipin from bovine heart authentic standard analysed in negative mode","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726179954000","created":"Sep. 12, 2024, 3:25 PM","description":"Cardiolipin from bovine heart authentic standard analysed in negative mode C18-ESI-HRMS with water and acetonitrile bot 0.05% ammonium hydroxide","fileCount":"19","fileSizeKB":"1688175","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mammalia (NCBITaxon:40674)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cardiolipin;bovine heart;LOD","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4cd9f724b9fb4299827275b034f50c93","id":"1900"}, {"dataset":"MSV000095853","datasetNum":"95853","title":"GNPS - RiPP Low pH metal Competition_09122024 ","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726167242000","created":"Sep. 12, 2024, 11:54 AM","description":"Microbulbifer RiPP has the ability to bind strongly with Copper even in competitive metal binding experiments","fileCount":"11","fileSizeKB":"375111","spectra":"16227","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"none","instrument":"Qexactive MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RiPP;Metal;Competition","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"910a48a3b04842909a901b78ec19b5f7","id":"1901"}, {"dataset":"MSV000095850","datasetNum":"95850","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726154663000","created":"Sep. 12, 2024, 8:24 AM","description":"Whole proteome data from heart tissue of young and old killifish.","fileCount":"36","fileSizeKB":"28212957","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"heart;aging;killifish","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD055822","task":"8c32b4bbbd2b4669bc385a965da23893","id":"1902"}, {"dataset":"MSV000095847","datasetNum":"95847","title":"GNPS - Fasting is required for many benefits of calorie restriction ","user":"babygirija","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726149627000","created":"Sep. 12, 2024, 7:00 AM","description":"Targeted metabolomics of brain after feeding regimens","fileCount":"122","fileSizeKB":"24191840","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics","pi":[{"name":"John Denu","email":"john.denu@wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"af56c74535574094bee28443e455c78b","id":"1903"}, {"dataset":"MSV000095846","datasetNum":"95846","title":"Specialized metabolome from developing Arabidopsis thaliana seeds under warm temperatures","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726132310000","created":"Sep. 12, 2024, 2:11 AM","description":"Seed development, which depends on mother plant genetic background and environmental conditions, is a major component determining seed composition. Seed quality is a main agricultural concern, impacting both food and non-food applications, while also playing a central role in biodiversity conservation and environment protection. Climate change, characterized, among other stresses, by the emergence of extremely high temperatures, constitute a critical global threat to agriculture. Specialized metabolites (SMs) play crucial roles in the interactions of plants and seeds with their environments. Several SMs are known to be protective compounds involved in seed stress responses, thus impacting directly or indirectly their quality. In this study, we performed untargeted metabolomic (LC-MS\/MS) and transcriptomic (RNA-Seq) analyses of Arabidopsis thaliana seeds harvested at six developmental stages (Globular, Transition, Torpedo, Bent cotyledon, Mature green and Dry seed), and developed under control and warm temperature conditions. Those data provide an original and valuable resource for future studies on the role of SMs and genes involved in seed warm thermic stress responses and for the study of their regulation and functions during seed development.","fileCount":"163","fileSizeKB":"34350328","spectra":"869253","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II;Ultimate 3000 (Thermo Fischer Scientific - HPLC)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Untargeted metabolomics;Arabidopsis thaliana;Seed development;Warm temperatures","pi":[{"name":"Massimiliano CORSO","email":"massimiliano.corso@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c8a80991385a41f689eaf5c414fee652","id":"1904"}, {"dataset":"MSV000095845","datasetNum":"95845","title":"Unraveling proteomic chaos - ClpX deficiency in Staphylococcus aureus impacts bacterial virulence and stress-specific bacterial fitness under infection-modeling conditions","user":"buschl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726129350000","created":"Sep. 12, 2024, 1:22 AM","description":"Host-mediated stressors affect bacterial pathogens during infection processes. In response to those stressors, bacteria adapt their gene expression as well as ultimately proteome profile and activity. In Staphylococcus aureus protein homeostasis is largely mediated by the Clp system consisting of the ClpP peptidase, the unfoldases ClpX and ClpC, and the chaperones ClpB and ClpL. The proteases ClpXP and ClpCP are crucial for general and targeted proteolysis, which rely on the unfoldases interacting with specific targets. ClpX is particularly involved in overall regulation of bacterial virulence and fitness and it is the most conserved Clp unfoldase. However, the majority of S. aureus ClpX targets remains elusive. \nFor investigation of the effect of ClpX deficiency the S. aureus mutant strain HG001 clpX::km and the complemented strain HG001 clpX::km pTripleTREP_clpX were constructed using the newly developed plasmid systems pSauSE (allele exchange plasmid) and pTripleTREP (controllable expression plasmid). When tracking infection processes, the S. aureus clpX mutant revealed a less virulent phenotype in a Galleria model compared to the HG001 wild type and drastically low intracellular replication in in-vitro HBE cell culture infection experiments.\nThe effect of ClpX deficiency under infection-relevant conditions was recorded after cultivating HG001 wild type, the HG001 clpX mutant and the complemented HG001 clpX mutant with pTripleTREP_clpX under iron limitation and microaerobic conditions by mass spectrometry in data independent mode. To address differences in proteome composition caused by the strain background and growth conditions, a normalization strategy based on an external standard was employed. The standard consists of 15N-labeled Bacillus subtilis proteins enabling reliable distinction between standard and sample proteins and providing robust relative quantification of sample proteins.\nThe proteomic profiles revealed specific ClpX- and condition-dependent changes as well as entanglement of those. An iModulon-inspired analysis resulted in 36 independent components, unravelling the different influences. Known ClpX-targets such as Spx and Sle1 were confirmed as robust targets and new targets such as NikA and SAOUHSC_00671 were suggested. Out of the two investigated infection-relevant conditions, iron limitation generally induced the Fur regulon, and under microaerobic condition the Rex regulon was induced. Moreover, ClpX-dependent condition-specific effects, such as a subregulon of the known Fur regulon, which is less responsive to the provoked iron limitation in the clpX mutant, were also observed.\nWith our proteomics data, we provide a global insight into ClpX-dependent adaptation of S. aureus physiology under infection-relevant conditions.\n","fileCount":"78","fileSizeKB":"177927888","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus aureus (NCBITaxon:1280)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"S. aureus;ClpX;protein homeostasis;infection mimicking;iron limitation;oxygen limitation","pi":[{"name":"Prof. Uwe Voelker","email":"voelker@uni-greifswald.de","institution":"Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald","country":"germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055808","task":"997e5c00220e4544b472cc516ebcb353","id":"1905"}, {"dataset":"MSV000095844","datasetNum":"95844","title":"GNPS - Specialized metabolome seed coat\/endosperm and seed embryo of Arabidopsis thaliana","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726128642000","created":"Sep. 12, 2024, 1:10 AM","description":"Untargeted metabolomic analyses were carried out on seed coat\/endosperm and seed embryo (dry seeds) of Arabidopsis thaliana Columbia-0 genotype. Three biological replicates were analyzed for each sample.","fileCount":"24","fileSizeKB":"10222947","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II;Ultimate 3000 (Thermo Fischer Scientific - HPLC)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis thaliana;Seed coat and endosperm;Seed embryo;Untargeted metabolomics","pi":[{"name":"Massimiliano CORSO","email":"massimiliano.corso@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"79c27d5be8b6433cbbcf888b746a6432","id":"1906"}, {"dataset":"MSV000095843","datasetNum":"95843","title":"GNPS - Untargeted metabolomic analysis in Brassica napus seed coat\/endosperm and embryo - GNPS","user":"macorso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726128639000","created":"Sep. 12, 2024, 1:10 AM","description":"Untargeted metabolomic analyses were carried out on seed coat\/endosperm and seed embryo (dry seeds) of two Brassica napus genotypes (Aviso and Major). Four biological replicates were analyzed for each sample.","fileCount":"42","fileSizeKB":"8651269","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brassica napus (NCBITaxon:3708)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Specialized metabolites;seed tissues;Seed development;Brassciaceae","pi":[{"name":"Massimiliano Corso","email":"massimiliano.corso@inrae.fr","institution":"INRAE","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"1f7e4c16a68041edb49d43e8f5e125c7","id":"1907"}, {"dataset":"MSV000095842","datasetNum":"95842","title":"GNPS - Specific redox and iron homeostasis responses in the root tip of Arabidopsis upon zinc excess","user":"stephINRAE","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726125690000","created":"Sep. 12, 2024, 12:21 AM","description":" Zinc (Zn) excess negatively impacts primary root growth in Arabidopsis. The effects of Zn excess on root growth processes in the root tip are not well understood. \r\n Transcriptomics, ionomics and metabolomics were used to examine the specific impact of Zn excess on the root tip (RT) compared to the remaining root (RR). \r\n Zn excess exposure resulted in shortened root apical meristem and elongation zone, with differentiation initiating closer to the tip of root. Zn accumulated at a lower concentration in the RT than in RR. \r\n","fileCount":"1269","fileSizeKB":"61389658","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"impact II","modification":"no","keywords":"Arabidopsis thaliana;specialized metabolism;root apical meristem;zinc excess","pi":[{"name":"Stephanie Boutet","email":"stephanie.boutet@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"26b6dbc1aab84d95a2454a87b2967352","id":"1908"}, {"dataset":"MSV000095830","datasetNum":"95830","title":"MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation","user":"lfields","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726062160000","created":"Sep. 11, 2024, 6:42 AM","description":"Mass spectrometry imaging (MSI) has gained popularity in large-scale clinical analyses due to its high sensitivity, specificity and throughput. However, global profiling experiments are often still restricted to LC-MS\/MS analyses that lack spatial localization due to low throughput methods for on-tissue peptide confirmation. Parallel LC-MS\/MS confirmation of extracted peptides is often utilized with MALDI-MSI; however, integration and analysis of the two data sets once again presents a bottleneck in throughput. Further, the incorporation of histological stains is critical for mapping identified peptides of interest back to relevant tissue regions, yet many software generated for this are not readily accessible to those lacking coding capabilities. Here, we present a novel platform termed MSIght, which automates the integration of these multiple modalities into an accessible and modular platform. Histological stains of tissue sections are co-registered to their respective MSI data sets to improve spatial localization and resolution of identified peptides. LC-MS\/MS data of extracted peptides is used to confirm putative MSI identifications and generate confident MS images in an untargeted manner. This platform enables large-scale clinical cohorts to utilize MSI for global proteomic profiling to uncover novel biomarkers in a spatial manner, thus widely expanding the utility of MSI in clinical discovery. ","fileCount":"1479","fileSizeKB":"67607702","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"rapifleX;Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"MALDI;multimodal imaging;mass spectrometry imaging;histology","pi":[{"name":"Lingjun Li","email":"lingjun.li@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055780","task":"08b12b13a622433782b6f82366e40869","id":"1909"}, {"dataset":"MSV000095829","datasetNum":"95829","title":"GNPS - GC-MS files for modeling bacterial interactions in coastal lignin degrading consortium","user":"Qiannan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726036699000","created":"Sep. 10, 2024, 11:38 PM","description":"GC-MS files for modeling bacterial interactions in coastal lignin degrading consortium","fileCount":"37","fileSizeKB":"879718","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"GCMS-QP2020NX (Shimadzu Scientific Instruments instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"GC-MS","pi":[{"name":"Peng qiannan","email":"pqiannan1029@163.com","institution":"Shandong University","country":"China "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ae06dfaad28342c0be522e493f7b7f6e","id":"1910"}, {"dataset":"MSV000095828","datasetNum":"95828","title":"GNPS - LC-MSMS files for modeling bacterial interactions in coastal lignin degrading consortium","user":"Qiannan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726032632000","created":"Sep. 10, 2024, 10:30 PM","description":"LC-MSMS files for modeling bacterial interactions in coastal lignin degrading consortium","fileCount":"73","fileSizeKB":"1476360","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"LTQ Orbitrap velos pro ETD (Thermo Scientific Instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MSMS","pi":[{"name":"Peng qiannan","email":"pqiannan1029@163.com","institution":"Shandong University","country":"China "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"45dfc992b98242f1a620a8f88ab7d8e4","id":"1911"}, {"dataset":"MSV000095826","datasetNum":"95826","title":"GNPS - IQ-1687 10\/SEPT\/2024 Aspergillus spp","user":"albertopardo97","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1726014157000","created":"Sep. 10, 2024, 5:22 PM","description":"MS\/MS spectra of the extract of the possible fungal species aspergillus endophyte of seaweed","fileCount":"2","fileSizeKB":"23482","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus (NCBITaxon:5052)","instrument":"Xevo G2-S QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Aspegillus, Psaudaboydin","pi":[{"name":"Dr. Jose Alberto Rivera Chavez","email":"jrivera@iquimica.unam.mx","institution":"Insituto de Quimica, UNAM","country":"Mexico"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c47b63468c749ce80ec46731e7160fe","id":"1912"}, {"dataset":"MSV000095824","datasetNum":"95824","title":"Proteome-wide Investigation of Proline Hydroxylation in Pancreatic Ductal Adenocarcinoma Using DiLeu Isobaric Labeling Strategy","user":"Feixuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725994798000","created":"Sep. 10, 2024, 11:59 AM","description":"Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer marked by a dense, collagen-rich extracellular matrix that promotes tumor progression. In this study, we developed a high-throughput method combining enhanced hydrophilic interaction chromatography (HILIC) and 12-plex N,N-dimethyl leucine (DiLeu) isobaric tags for efficient quantitative analysis of hydroxyproline. Applied to human pancreatic tissues, this approach identified the largest hydroxyproline dataset reported for the pancreas. Our analysis reveals significant changes in proline hydroxylation in benign tumors, PDAC, and adjacent normal tissues, highlighting key proteins like collagen and GAPDH as potential targets for further investigation into PDAC progression.","fileCount":"135","fileSizeKB":"120529567","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;Orbitrap Fusion Lumos","modification":"Proline hydroxylation","keywords":"PDAC, proline hydroxylation, high-throughput, multiplex, DiLeu, HILIC","pi":[{"name":"Lingjun Li","email":"lingjun.li@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ddede807f6a4404bbc56bec0caaa5ff5","id":"1913"}, {"dataset":"MSV000095822","datasetNum":"95822","title":"Coronary Event Risk Test as a Potential Tool to Predict Cardiovascular Risk in Gout and Hyperuricemia","user":"AlesKvasnicka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725953920000","created":"Sep. 10, 2024, 12:38 AM","description":"Objective. Gout is linked with an excess risk of cardiovascular disease (CVD) and there is a need for new tests to assess and stratify high-risk patients. The Coronary Event Risk Test (CERT) based on the determination of plasma ceramides is an efficient event and death risk prediction tool. In this brief report, we focused on the application of the CERT score on hyperuricemia and gout patients for the first time.\n\nMethods. Plasma was collected in a single center from 94 hyperuricemic patients, 196 gout patients and 53 controls. Liquid chromatography coupled with mass spectrometry was used to determine the ceramide levels. The CERT score was calculated based on the conventionally used algorithm which provides a 12-point scale that classifies patients from low-risk (score 0-2) to high-risk groups (score 10-12).\n\nResults. We found significantly elevated CERT score in patients with gout and hyperuricemia compared to healthy controls. Increased and high-risk CERT score (>7) was 2-fold (11.7%, p-value<0.01) and 5.5-fold (31.12%, p-value<0.001) more frequent in hyperuricemic (median = 3) and gout (median = 5) patients, respectively, compared with controls (median = 2).\n\nConclusion. Our findings show that the CERT score can be used to stratify high-risk gout patients independently on conventional CVD markers. Additionally, we found that patients with hyperuricemia also showed increased CERT score and CVD risk. These results show for the first time how the CERT score can be used in rheumatology practice to stratify and manage gout and hyperuricemic patients by this novel predictive tool.","fileCount":"7","fileSizeKB":"252183","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QTRAP 6500+;ExionLC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ceramides;hyperuricemia;gout;Coronary Event Risk Test;CERT;cardiovascular disease;CVD","pi":[{"name":"Blanka Stiburkova","email":"stiburkova@revma.cz","institution":"Institute of Rheumatology, Prague","country":"Czech Republic"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"","task":"c7448382fb3e4b83aa128ffbcef61c17","id":"1914"}, {"dataset":"MSV000095821","datasetNum":"95821","title":"GNPS - LC-MS files for modeling bacterial interactions in coastal lignin degrading consortium","user":"Qiannan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725944985000","created":"Sep. 9, 2024, 10:09 PM","description":"LC-MS files for modeling bacterial interactions in coastal lignin degrading consortium","fileCount":"1212","fileSizeKB":"8828419","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS","pi":[{"name":"Peng qiannan","email":"pqiannan1029@163.com","institution":"Shandong University","country":"China "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"87fa0b51cc144794b7d15f313f88c670","id":"1915"}, {"dataset":"MSV000095820","datasetNum":"95820","title":"CMMC_Foodbiomarker_standards_Dietary_readouts","user":"JAGONGO_1994","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725929350000","created":"Sep. 9, 2024, 5:49 PM","description":"MS\/MS fragmentation data of foodbiomarker standards acquired on Q Exactive - with\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"2382","fileSizeKB":"147841317","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"No species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CMMC;Foodbiomarkers;standards","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ad5e5c13c62d4ea9b39e566797a1ed49","id":"1916"}, {"dataset":"MSV000095819","datasetNum":"95819","title":"GNPS - 20240909_piperamides_standards","user":"Tito_Damiani","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725915676000","created":"Sep. 9, 2024, 2:01 PM","description":"Analytical standards of Piper alkaloids, both synthetized and commercially-available","fileCount":"16","fileSizeKB":"1121681","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Analytical standards","instrument":"Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"piperamides;standards;alkaloids","pi":[{"name":"Tomas Pluskal","email":"tomas.pluskal@uochb.cas.cz","institution":"Institute of Organic Chemistry and Biochemistry of the CAS","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e0c34d8f4c5e4ba0a926bb9cdb175db4","id":"1917"}, {"dataset":"MSV000095818","datasetNum":"95818","title":"Treponema pallidum SS14 global proteomics","user":"spirochete","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725913322000","created":"Sep. 9, 2024, 1:22 PM","description":"Raw data files (RAW and mzML) and Scaffold search engine files corresponding to the whole proteome analyses of the syphilis spirochete, Treponema pallidum ssp. pallidum, strain SS14. ","fileCount":"51","fileSizeKB":"59102753","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Treponema pallidum subsp. pallidum SS14 (NCBITaxon:455434)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Treponema pallidum, syphilis, proteomics, outer membrane proteins, vaccine candidates","pi":[{"name":"Dr. Caroline Cameron","email":"caroc@uvic.ca","institution":"University of Victoria","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055753","task":"815a24b238e448c68584a42bd4761dd9","id":"1918"}, {"dataset":"MSV000095817","datasetNum":"95817","title":"A single centromeric nucleosome mediates attachments to a single microtubule in the thermotolerant yeast K. marxianus","user":"FHproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725910283000","created":"Sep. 9, 2024, 12:31 PM","description":"Kinetochores were purified from Kluyveromyces marxianus cell lysate after either being treated with benzonase (DB060424_061124_18150_Benzonase_1, DB060424_061124_18150_Benzonase_2, DB032421_033021_B) or with no treatment (DB060424_061124_18150_control_1, DB060424_061124_18150_control_2, DB032421_033021_C). The endogenous DSN1 kinetochore gene was C-terminally tagged with 6xHis and 3xM3DK. Harvested yeast were resuspended in Buffer H (25 mM HEPES pH 8.0, 150 mM KCl, 2 mM MgCl2, 0.1 mM EDTA pH 8.0, 0.1% NP-40, 15% glycerol) supplemented with protease inhibitors, phosphatase inhibitors, and 2 mM DTT. After resuspension and re-spinning, yeast pellets were frozen in liquid nitrogen and lysed using a Freezer Mill (SPEX, Metuchen NJ). Lysate was clarified via ultracentrifugation at 24,000 RPM (98,000 x g) for 90 minutes and the protein layer was extracted with a syringe. This extract was incubated with magnetic a-M3DK antibody conjugated Dynabeads (Invirtrogen, Waltham MA) for 3 hours at 4 C with rotation. For benzonase treated samples, 300 units of benzonase per milliliter of lysate were added during this incubation step. Dynabeads were washed with 10x bead volume of Buffer H 5 times (the last 3 washes omitting DTT and phosphatase inhibitors). For mass spectrometry, kinetochores were eluted from Dynabeads with 0.2% RapiGest (Waters Corporation, Milford MA) in 50 mM HEPES pH 8.0. For all experiments, the total protein concentration was determined by NanoDrop measurement and the relative purity by silver stain gel analysis.","fileCount":"36","fileSizeKB":"23935963","spectra":"0","psms":"80536","peptides":"15123","variants":"20548","proteins":"2030","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Kluyveromyces marxianus (NCBITaxon:4911)","instrument":"Orbitrap Fusion ETD;Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mitosis, kinetochore, centromere, cell division, Kluyveromyces marxianus","pi":[{"name":"Susan Biggins","email":"sbiggins@fredhutch.org","institution":"Fred Hutchinson Cancer Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"39a41e7265684e05ad04070428284442","id":"1919"}, {"dataset":"MSV000095816","datasetNum":"95816","title":"Phaeodactylum tricornutum laboratory culture extracts","user":"lbabocckadams","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725909754000","created":"Sep. 9, 2024, 12:22 PM","description":"Solid phase extracted laboratory culture of Phaeodactylum tricornutum, analyzed via LC-ICP MS, LC-Orbitrap, and LC-FT-ICR MS, and LC-ICP MS analysis of media with no culture inoculum.","fileCount":"9","fileSizeKB":"6494788","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phaeodactylum tricornutum (NCBITaxon:2850)","instrument":"Orbitrap Fusion;Hybrid linear ion trap FT-ICR MS at 21T (National High Magnetic Field Laboratory);iCap Q (Thermo Scientific)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"copper ligand;diatom","pi":[{"name":"Daniel Repeta","email":"drepeta@whoi.edu","institution":"Woods Hole Oceanographic Institution","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"99becab21cf544018a38b872ab5c2a3a","id":"1920"}, {"dataset":"MSV000095815","datasetNum":"95815","title":"nAchR interactome in adult brain of subunit mutant","user":"JSRosenthal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725907365000","created":"Sep. 9, 2024, 11:42 AM","description":"Proteins interacting with the nicotinic acetylcholine receptor in the adult brain of nAchR subunit mutants. ","fileCount":"47","fileSizeKB":"69168353","spectra":"0","psms":"281685","peptides":"16459","variants":"21784","proteins":"2577","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"label-free quantitation, mass spectrometry","pi":[{"name":"Quan Yuan","email":"quan.yuan@nih.gov","institution":"National Institute of Neurological Disorders and Stroke","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD055751","task":"41301833f1024b588b2f714048bc2141","id":"1921"}, {"dataset":"MSV000095813","datasetNum":"95813","title":"Burger_et_al_ilicicolin_metabolomics","user":"iburger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725889115000","created":"Sep. 9, 2024, 6:38 AM","description":"In this study, the ilicicolin biosynthetic gene cluster (BGC) in Trichoderma reesei was genetically activated, and a series of gene cluster enzyme deletions were performed. Mycelia were harvested and subjected to polar extraction. The resulting polar extracts were analyzed using an untargeted lipidomics workflow in positive ionization mode (for further methodological details, refer to the publication).\n\nThe dataset includes:\nMetabolomics data: 16 raw files (4 experimental conditions, in quadruplicates) measured using trapped ion mobility spectrometry (TIMS).\nMolecular networking data: 2 raw files (from 2 conditions) measured without TIMS to obtain improved fragmentation spectra. Molecular networking analysis was conducted with MZmine 4, and the corresponding batch file is included as supplementary data.","fileCount":"736","fileSizeKB":"2668073","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichoderma reesei (NCBITaxon:51453)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fungi;natural products;metabolomics","pi":[{"name":"Matthias Schittmayer","email":"matthias.schittmayer@tuwien.ac.at","institution":"TU Wien","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d3a4caa6ec9f4d4f81ba235984d054c7","id":"1922"}, {"dataset":"MSV000095811","datasetNum":"95811","title":"GNPS - Chesneau_et_al_MetaFlowTrain_Exometabolites","user":"sperin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725877875000","created":"Sep. 9, 2024, 3:31 AM","description":"Description: Bacterial and fungal exometabolites were harvested from MetaFlowTrain. Bacteria and fungi were grown in various peat washes within the MetaFlowTrain system. Two milliliters of exometabolites were collected at two different timepoints 24 hours and 62 hours from the MetaFlowTrain output and subsequently extracted (for more details, see publication). \r\nThere are four folders:\r\n - \"221208_Guillaume_Chambers_AA\"\r\n - \"221208_Guillaume_Chambers_TCA&Gly\"\r\n - \"230530_Guillaume_Chambers_AA\"\r\n - \"230530_Guillaume_Chambers_TCA&Gly\".\r\nData in the folders from 221208 were used to build Figure 2, while data from 230530 were used for Figures 3 and 4. \r\nFilenames depict, in order: the sample number, the microbial inoculum in the first chamber, the microbial inoculum in the second chamber, and the peat wash used. F stands for fungi, B for bacteria, and X for mock (e.g., \"01_F_B_Peat1\" indicates sample number 1, fungi in the first chamber, bacteria in the second chamber, and peat wash 1).","fileCount":"705","fileSizeKB":"87333724","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Communities of Bacterial and Fungal strains","instrument":"QExactive","modification":"none","keywords":"Microbial Exometabolites","pi":[{"name":"Guillaume Chesneau","email":"gchesneau@mpipz.mpg.de","institution":"Max Planck for Plant Breeding","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"30de441f5b364a9fa99feffe9b949ed7","id":"1923"}, {"dataset":"MSV000095810","datasetNum":"95810","title":"Persistent IgG1 clones dominate and personalize the plasma antibody repertoire","user":"DaniquevanRijswijck","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725872108000","created":"Sep. 9, 2024, 1:55 AM","description":"Antibodies play a pivotal role in the immune defense and long-term immunity. Yet, while several studies have highlighted the long durability of antigen-specific antibody responses, it is unclear whether this durability stems from the continuous production of the same clones or the recurrent activation of B cells generating new clones over time. To gain insights into the long-term stability of the human antibody repertoire, we monitored the concentrations of hundreds of the most abundant IgG1 antibody clones in plasma samples of 11 healthy donors at 9 sampling points over a year. During this year, each donor received 3 doses of a COVID-19 vaccine. Notwithstanding these vaccinations, the concentrations of the most abundant individual IgG1 clones remained extraordinarily constant throughout the year. Given the 2-3 week turn-over of IgG1 molecules in blood, our data suggest that these abundant clones are primarily associated with long-term immunity rather than being induced by acute infections or vaccinations. These dominant clones do not undergo further somatic hypermutation over the year and are therefore likely produced consistently by long-lived plasma cells. The long-term stability of dominant IgG1 clones was observed in all donors, although there was no overlap in any of the detected clones when comparing IgG1 repertoires across donors. While most dominant IgG1 clones remained constant throughout the year, a small subset emerged later and remained stable thereafter, whereas another subset decreased in concentration. Overall, our data suggests that the vast majority of abundant IgG1 clones in plasma are persistently produced by long-lived plasma cells. 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Two-point COOKIE-Pro data are searched with dynamic modification of unimod:1 (Carbamidomethyl) and unimod:2062 (DBIA) on cysteine.","fileCount":"62","fileSizeKB":"59922728","spectra":"128481","psms":"134142","peptides":"22312","variants":"36638","proteins":"7412","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;Orbitrap Ascend","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"covalent inhibitor;BTK;ibrutinib;spebrutinib;ABPP","pi":[{"name":"Jin Wang","email":"wangj@bcm.edu","institution":"Baylor College of Medicine, Houston TX","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"73e24ac0d5444635be540238c18fce71","id":"1927"}, {"dataset":"MSV000095803","datasetNum":"95803","title":"GNPS - Plant extracts received from Malaga and run in August 2024","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725748767000","created":"Sep. 7, 2024, 3:39 PM","description":"Organic Plant extracts resuspended in 8\/2 MeOH\/H2O and analysed in positive ESI DDA mode using C18 RP chromatography","fileCount":"165","fileSizeKB":"17340413","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plant;organic extract;nontargeted","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1324ab567d354ec7b7db42103e212757","id":"1928"}, {"dataset":"MSV000095802","datasetNum":"95802","title":"Using conserved protein to mRNA ratios across kingdoms to enhance microbial functional predictions","user":"Mengshi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725729262000","created":"Sep. 7, 2024, 10:14 AM","description":"Understanding the biology of native microbial communities is hindered by the lack of robust functional data for the microbes within these communities. Quantifying mRNA levels via transcriptomics to infer function has proven successful in these communities. However, this requires the ability to accurately predict protein levels, which are the primary functional units, from mRNA levels. While a positive correlation exists between mRNA and protein levels, for certain genes, mRNA is not a predictor of protein. To address this challenge, studies have quantified the protein-to-RNA (PTR) ratios of all genes, including those in which mRNA levels are not predictive of protein levels. These data enabled the calculation of RNA-to-protein (RTP) conversion factors for some of these genes that, when applied to mRNA levels, enhance the predictivity for protein levels. Despite the potential of RTP conversion factors, their calculation requires extensive datasets, which are costly and not available for most microbes. Here, we generated and analyzed comprehensive datasets from seven bacterial strains and one archaeon and identified orthologous genes in which mRNA was not predictive of protein but had consistent PTR ratios. Calculation and application of conversion factors for these genes improved protein prediction from mRNA, even when the conversion factors were derived from distantly-related bacteria. RTP conversion factors derived from bacteria also improved protein predictivity from mRNA in an archaeon, indicating that this approach is robust across domains of life. Ultimately, this approach improves protein prediction from mRNA without the need for paired transcriptomic\/proteomic data from a microbe of interest. 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CH1 (NCBITaxon:467705);Aggregatibacter actinomycetemcomitans (NCBITaxon:714);Aggregatibacter actinomycetemcomitans Y4 (NCBITaxon:1035194);Sulfolobus islandicus M.16.4 (NCBITaxon:426118);Staphylococcus aureus subsp. aureus USA300 (NCBITaxon:367830)","instrument":"Dionex instrument model","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Pseudomonas aeruginosa;RNA to protein ratio;transcriptomics;proteome;translation","pi":[{"name":"Marvin Whiteley","email":"mwhiteley3@gatech.edu","institution":"Georgia Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055700","task":"14fda9e4f1d44f25a5f82f65c4503a9e","id":"1929"}, {"dataset":"MSV000095801","datasetNum":"95801","title":"GNPS - 2024 09 04 Alexandre TRONEL PAPER 1","user":"alegouellec","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725709438000","created":"Sep. 7, 2024, 4:43 AM","description":"The gut microbiome is a complex ecosystem stratified that varies along different sections of the gut. It comprises a wide array of metabolites originating from both food, host, and microbes. Microbially-derived metabolites, such as bile acids, short-chain fatty acids, and indole derivatives, are of significant interest due to their direct interactions with host physiology and regulating function. Most current studies on the gut microbiome focus on fecal samples, which do not fully represent the upper parts of the gut due to its stratification. To collect microbiome samples from the proximal gut microbiome, endoscopic methods or new non-invasive medical devices can be used. To enable comprehensive profiling of the gut metabolome and analyze key metabolites, we developed a combined approach combining untargeted and semi-targeted metabolomics using a Q-Exactive Plus Orbitrap mass spectrometer. Initially, we selected 49 metabolites of interest for the gut metabolome based on four distinct criteria. We validated these metabolites through repeatability and linearity tests and created a compound database using the software TraceFinder (ThermoFisher Scientific). For untargeted metabolomics, we established a workflow for the annotation and discovery of molecules. Finally, 37 metabolites were validated for semi-targeted metabolomics, and we conducted a proof of concept on small intestinal and fecal samples form a clinical trial (NCT05477069). Our combined approach, facilitated by molecular networking, demonstrated the potential to discover new metabolites. 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\\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:199 - \\\"DiMethyl-CHD2.\\\";UNIMOD:193 - \\\"O18 label at both C-terminal oxygens.\\\"","keywords":"comamonas;plastic;biodegradation;iptl","pi":[{"name":"Jacob Waldbauer","email":"jwal@uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055638","task":"f5952bf198094e92b901ea870a1bdab2","id":"1933"}, {"dataset":"MSV000095791","datasetNum":"95791","title":"GNPS - Cempasuchil_(Tagetes_erecta)_Root_Extract_Mexico","user":"Lucho","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725591828000","created":"Sep. 5, 2024, 8:03 PM","description":"data Cempasuchil_(Tagetes_erecta)_Root_Extract_Mexico. 6530A Q-TOF LC\/MS (Agilent instrument model) ESI+ and ESI-","fileCount":"422","fileSizeKB":"1817540","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"'Tagetes erecta' phytoplasma (NCBITaxon:2304446)","instrument":"6530A Q-TOF LC\\\/MS","modification":"no","keywords":"tagetes","pi":[{"name":"Luis Alberto Gonzalez Lopez ","email":"laglgonzalez@gmail.com","institution":"UdeA","country":"Colombia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"851f9d756a5245ea97508dcee456fa6b","id":"1934"}, {"dataset":"MSV000095790","datasetNum":"95790","title":"GNPS - MS MS MS for Liu group jingjie","user":"huzhijuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725591485000","created":"Sep. 5, 2024, 7:58 PM","description":"Mass spectrometry data of mitochondrial precipitation and cellular precipitation","fileCount":"17","fileSizeKB":"10131080","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Scientific Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MS data cell","pi":[{"name":"xingguo liu","email":"liu_xingguo@gibh.ac.cn","institution":"Guangzhou Institutes of Biomedicine and Health Chinese Academy of Science","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0156d930e4c742d4ab59e1a6a149770a","id":"1935"}, {"dataset":"MSV000095789","datasetNum":"95789","title":"GNPS - Pooled Chemical Standard (DDA & Full-scan)","user":"spxing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725577522000","created":"Sep. 5, 2024, 4:05 PM","description":"LC-MS data of pooled chemical standards. Data were collected using DDA and full-scan (0eV, 10eV and 20 eV isCID).\nBile acid pool: glycocholic acid (GCA), glycochenodeoxycholic acid (GCDCA), taurodeoxycholic acid (TDCA), taurocholic acid (TCA), taurolithocholic acid (TLCA), and tauro-3alphahydroxy-12ketocholanoic acid.\nDrug pool: sertraline, venlafaxine, ritonavir, darunavir, losartan, quetiapine, sulfasalazine, and abacavir.\n","fileCount":"25","fileSizeKB":"2315731","spectra":"5475","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chemical standard","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Chemical standards","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"361b126b35f64bb89a99e7a9974cf8a7","id":"1936"}, {"dataset":"MSV000095788","datasetNum":"95788","title":"nAchR interactome in adult brain","user":"JSRosenthal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725575072000","created":"Sep. 5, 2024, 3:24 PM","description":"Proteins interacting with the nicotinic acetylcholine receptor in adult brain","fileCount":"42","fileSizeKB":"59942173","spectra":"0","psms":"340127","peptides":"19811","variants":"26171","proteins":"2029","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"label-free quantitation, mass spectrometry","pi":[{"name":"Quan Yuan","email":"quan.yuan@nih.gov","institution":"National Institute of Neurological Disorders and Stroke","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD055602","task":"ae123c6080cc45488dd25ddaa880c15f","id":"1937"}, {"dataset":"MSV000095787","datasetNum":"95787","title":"GNPS - NIST Reference Human Feces","user":"spxing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725574670000","created":"Sep. 5, 2024, 3:17 PM","description":"NIST reference human feces (omnivore, vegan and pooled samples) collected in DDA and full-scan modes. 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These samples are negative ionization mode, organic matter metabolomics datasets from many distinct environments, including global cropland; dryland; late Pleistocene-aged permafrost; temperate and tropical forest soils; rivers and lakes; and ocean DOM. ","fileCount":"416","fileSizeKB":"22333607","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;DOM;Organic matter;Environmental","pi":[{"name":"Ben Bowen","email":"bpbowen@lbl.gov","institution":"Lawrence Berkeley National Lab","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4d8c5f978c604ddb80857c01e68c08a9","id":"1940"}, {"dataset":"MSV000095784","datasetNum":"95784","title":"GNPS - Linking Ecology, Behavior, and Immunology to Spatio-Temporal Variation in Helminth Transmission - PRJ5","user":"marwa38","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725556735000","created":"Sep. 5, 2024, 10:18 AM","description":"Samples of livers from stickleback fish captured from 47 lakes on Vancouver Island, with associated data on parasite infection status, immune traits, diet, and morphology. 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RPA-binding by WRN\r\nand its helicase activity are crucial for countering the persistence of G4 structures after fork stalling.\r\nAbsence of WRN-RPA binding hampers fork recovery, causing single-strand DNA gaps, enlarged\r\nby MRE11, and triggering MUS81-dependent double-strand breaks which requires efficient repair\r\nby RAD51 to prevent excessive DNA damage.","fileCount":"31","fileSizeKB":"7490987","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"WERNER PHOSPHOSITES","pi":[{"name":"FEDERICA FRATINI","email":"federica.fratini@iss.it","institution":"ISS","country":"Italia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD059007","task":"49c19e8415f646d1b23425dad98602d2","id":"1961"}, {"dataset":"MSV000095748","datasetNum":"95748","title":"Proteomic Characterization of Venom from Scorpio fuscus ","user":"ufukcelebioglu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725362917000","created":"Sep. 3, 2024, 4:28 AM","description":"Proteomic Characterization of Venom from Scorpio fuscus (Scorpiones: Scorpionidae) with Perspectives for Therapeutic Applications","fileCount":"44","fileSizeKB":"5855432","spectra":"0","psms":"3996","peptides":"1823","variants":"2533","proteins":"105","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Scorpio fuscus (NCBITaxon:1662104)","instrument":"Q Exactive","modification":"UNIMOD:35 - 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During LC-MS acquisition, the 5 DRs are run at the beginning of each batch.","fileCount":"19","fileSizeKB":"10081982","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Quality Control;DIA;Digestion Replicates;Whole Blood","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055482","task":"628d70c002d54dd9a712028c9d89a6b1","id":"1967"}, {"dataset":"MSV000095742","datasetNum":"95742","title":"QCeltis Case Study 1: Depleted Plasma QC Dataset","user":"vegesnam","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1725308871000","created":"Sep. 2, 2024, 1:27 PM","description":"A dataset containing depleted plasma samples used as quality control technical replicates (TR) and digestion replicates (DR). Plasma aliquot was shunted to Top14 Abundant Protein Depletion Resin (A36372) based depletion. Depleted plasma samples were processed on a i7 automated liquid handling system (Beckman Coulter) in a 96-well plate for protein denaturation, cysteine reduction and alkylation, and trypsin digestion. Healthy control pooled samples were used as DRs and embedded between samples during digestion. Depleted plasma tryptic peptides were separated by EVOSEP One LC System (Evosep) over a 45-minute gradient injected into an Orbitrap Exploris 480 MS (Thermo Fisher) using DIA-MS settings as described by McArdle and Binek et. al. During MS acquisition, the 4 DRs are run at the beginning of each batch. In addition, pooled, bulk digested plasma samples from Parkinsons Disease patients are included as technical replicates (TRs) at the beginning and middle of every MS batch, with the goal of assessing LC-MS performance. 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Postprandial urine samples from 17 subjects were collected\r\nsequentially after each meal up to 24 hr and analyzed by untargeted metabolomics\r\nthrough an UHPLC-qTOF. 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Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"683","fileSizeKB":"52385974","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gasterosteus aculeatus (NCBITaxon:69293)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"stickleback;genotypes;chromosomal inversions;lab;environmental;MSCollaboratory","pi":[{"name":"Daniel Bolnick","email":"daniel.bolnick@uconn.edu","institution":"University of Connecticut","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"daf65d6425ef4d4991de869bfecd06d0","id":"1973"}, {"dataset":"MSV000095729","datasetNum":"95729","title":"Laboratory evolution in Novosphingobium aromaticivorans enables rapid catabolism of a model lignin-derived aromatic dimer","user":"dlcarper","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724970626000","created":"Aug. 29, 2024, 3:30 PM","description":"Lignin contains a variety of interunit linkages, which leads to a range of potential decomposition products that can be used as carbon and energy sources by microbes. B-O-4 linkages are the most common in native lignin and associated catabolic pathways have been well characterized. However, the fate of the mono-aromatic intermediates that result from B-O-4 dimer cleavage has not been fully elucidated. Here, we used experimental evolution to identify mutant strains of Novosphingobium aromaticivorans with improved catabolism of a model aromatic dimer containing a B-O-4 linkage, guaiacylglycerol-b-guaiacyl ether (GGE). We identified several parallel causal mutations, including a single nucleotide polymorphism in the promoter of an uncharacterized gene that roughly doubled the growth yield with GGE. We characterized the associated enzyme and demonstrated that it oxidizes an intermediate in GGE catabolism, B-hydroxypropiovanillone, to vanilloyl acetaldehyde. Identification of this enzyme and its key role in GGE catabolism furthers our understanding of catabolic pathways for lignin-derived aromatic compounds.","fileCount":"133","fileSizeKB":"77420342","spectra":"946949","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Novosphingobium aromaticivorans (NCBITaxon:48935)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Novosphingobium aromaticivorans;Lignin;Laboratory evolution","pi":[{"name":"Richard J. Giannone","email":"giannonerj@ornl.gov","institution":"Oak Ridge National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055367","task":"ba59d42dbda040a7947d33f0f05bbabe","id":"1974"}, {"dataset":"MSV000095726","datasetNum":"95726","title":"GNPS - Urobiome Duke Burnett 220 ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724964054000","created":"Aug. 29, 2024, 1:40 PM","description":"220 Urine samples for Lindsey Burnett in collaboration with Duke. ","fileCount":"554","fileSizeKB":"23079122","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"urine;metabolomics","pi":[{"name":"Lindsey Burnett","email":"liburnett@health.ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"db6b64407c0d49689e5e8f689b698d88","id":"1975"}, {"dataset":"MSV000095724","datasetNum":"95724","title":"mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase","user":"aordureau","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724951793000","created":"Aug. 29, 2024, 10:16 AM","description":"Supporting MS data for paper (DOI:10.1016\/j.celrep.2024.115179) by Pham, B. et al., titled \"mTORC1 regulates the pyrimidine salvage pathway by controlling UCK2 turnover via the CTLH-WDR26 E3 ligase\". Related to Table S1 - HEK293 - degradomics (HA-2-165 | Unimod:35; 2016; 4 | 126 - Neg Ctrl (WT cells -AHA); 127n - MAEA-WT - UT_0h replicate 1; 127c - MAEA-WT - UT_0h replicate 2; 128n - MAEA-WT - UT_0h replicate 3; 128c - MAEA-WT - UT_10h replicate 1; 129n - MAEA-WT -UT_10h replicate 2; 129c - MAEA-WT - Tor1_10h replicate 1; 130n - MAEA-WT - Tor1_10h replicate 2; 130c - MAEA-WT - Tor1_10h replicate 3; 131n - MAEA[Y394A] - UT_0h replicate 1; 131c - MAEA[Y394A] - UT_0h replicate 2; 132n - MAEA[Y394A] - UT_0h replicate 3; 132c - MAEA[Y394A] - UT_10h replicate 1; 133n - MAEA[Y394A] - UT_10h replicate 2; 133c - MAEA[Y394A] - UT_01h replicate 3; 134n - MAEA[Y394A] - Tor1_10h replicate 1; 134c - MAEA[Y394A] - Tor1_10h replicate 2; 135n - MAEA[Y394A] - Tor1_10h replicate 3) ","fileCount":"25","fileSizeKB":"15804261","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"TMTpro;HEK293","pi":[{"name":"Alban Ordureau","email":"OrdureaA@mskcc.org","institution":"Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9fe7b8ead8884f37a8f26159870c3788","id":"1976"}, {"dataset":"MSV000095723","datasetNum":"95723","title":"Protein profile of extracellular vesicles derived from adult Parascaris spp.","user":"Vishnu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724945717000","created":"Aug. 29, 2024, 8:35 AM","description":"Proteomic analysis of extracellular vesicles released by adult males and females Parascaris spp.","fileCount":"7","fileSizeKB":"5722966","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Parascaris sp. (NCBITaxon:6255)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Extracellular vesicles, Proteome, Nematode, Parascaris","pi":[{"name":"Sriveny Dangoudoubiyam","email":"sdangoud@purdue.edu","institution":"Purdue University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0d57b08fc22843bd9a38a417c042a198","id":"1977"}, {"dataset":"MSV000095720","datasetNum":"95720","title":"The novel SCN5A-P1891A mutation is associated with left ventricular hypertrabeculation and links Nav1.5 to cardiomyocyte proliferation and disrupted 3D cardiac tissue formation","user":"XIOLIU","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724935893000","created":"Aug. 29, 2024, 5:51 AM","description":"Left ventricular hypertrabeculation (LVHT) is a heterogenous cardiac condition with a complex and poorly understood aetiology. We comprehensively characterised the effect of a novel P1891A mutation in the SCN5A gene, which encodes for the voltage gated sodium channel Nav1.5, identified in a Finnish family diagnosed with LVHT. ","fileCount":"33","fileSizeKB":"8807713","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"no","keywords":"protein protein interaction; SCN5A; Nav1.5","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b0c6f8b9d6874a20936a064a33b6495f","id":"1978"}, {"dataset":"MSV000095719","datasetNum":"95719","title":"GNPS - Japan waterproof products and sludge samples for PFAS analysis","user":"Bing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724919702000","created":"Aug. 29, 2024, 1:21 AM","description":"We included a dataset of environment samples from Japan, which includes HRMS data in negative mode in dda. The samples are collected in a variety of sources which may possess high concentration PFASs. detailed information on samples are given in metadata excel files.","fileCount":"88","fileSizeKB":"32186363","spectra":"1588286","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"PFAS;waterproof product;environmental samples (NCBITaxon:33858)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PFAS","pi":[{"name":"Weisi","email":"weisi@nju.edu.cn","institution":"Nanjing University","country":"China"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"78efa1621bb4458bae3b5d0cee6975b7","id":"1979"}, {"dataset":"MSV000095718","datasetNum":"95718","title":"GNPS - Refractory DOM Characterization","user":"ikoester","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724906145000","created":"Aug. 28, 2024, 9:35 PM","description":"5L PPL extracts from Eastern Tropical Norther Pacific and Station M for the structural characterization of refractory dissolved organic matter.","fileCount":"176","fileSizeKB":"21842714","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PPL;dissolved organic matter","pi":[{"name":"Lihini Aluwihare","email":"laluwihare@ucsd.edu","institution":"UCSD SIO","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7d20cf7a07ad44acae370b7578cf5239","id":"1980"}, {"dataset":"MSV000095717","datasetNum":"95717","title":"Proteomics analysis of endoplasmic reticulum(ER) enrichment","user":"yangyj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724894010000","created":"Aug. 28, 2024, 6:13 PM","description":"This study explores how cellular stress, particularly ER stress caused by ER-to-Golgi transport blockade, triggers unconventional protein secretion (UPS). The research identifies an ER tubulovesicular structure (ER-TB), shaped by the proteins ATL3 and RTN3L, as key to stress-induced UPS of transmembrane proteins like CFTR and SARS-CoV-2 spike protein. Knockdown of ATL3 and RTN3 disrupts ER-TB formation and UPS, while their combined presence promotes it. The findings suggest that ER-TB plays a crucial role in mitigating ER stress and may be involved in various physiological and pathological processes.","fileCount":"9","fileSizeKB":"2612769","spectra":"0","psms":"9560","peptides":"7609","variants":"8821","proteins":"1078","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"endoplasmic reticulum;proteomics;unconventional protein secretion;LC-MS\/MS","pi":[{"name":"Jin Young Kim","email":"jinyoung@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep. of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD055308","task":"33035e5a2496456abf03dd83126cc579","id":"1981"}, {"dataset":"MSV000095716","datasetNum":"95716","title":"Hepatic stellate cells isolated from PBS- or thioacetamide (TAA)-treated wild-type and Cyp1b1 knockout ","user":"haihaba","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724891931000","created":"Aug. 28, 2024, 5:38 PM","description":"Metabolomic analysis on hepatic stellate cells isolated from PBS- or thioacetamide (TAA)-treated wild-type and Cyp1b1 knockout mice was performed to determine the metabolic basis by which CYP1B1 ablation inhibits HSC activation and liver fibrosis.","fileCount":"61","fileSizeKB":"543380","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS;Hepatic stellate cells ;thioacetamide ;Cyp1b1 knockout ","pi":[{"name":"Wen Xie","email":"wex6@pitt.edu","institution":"University of Pittsburgs","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"80466dd5cd604f719c44658766bc39bd","id":"1982"}, {"dataset":"MSV000095715","datasetNum":"95715","title":"Multi-omics analysis of triple-negative breast cancers","user":"Arminja","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724891615000","created":"Aug. 28, 2024, 5:33 PM","description":"Abstract\nThe triple-negative breast cancer (TNBC) accounts for approximately 15% of all Breast Cancer (BC) cases. However, the prognosis and clinical outcomes of TNBC are worse than those of other BC subtypes due to a greater tumor and few therapeutically targetable oncogenic drivers. Numerous studies have employed genomic and transcriptomic approaches to identify clinically actionable TNBC subtypes in a comprehensive and unbiased manner using. While these analyses have advanced our knowledge of the molecular changes underlying TNBC, their clinical utility remains limited thus far. Given that proteins are the principal effector molecules of cellular signaling and function, we use a proteomic approach to quantitatively compare the abundances of 6,306 proteins across 55 formalin-fixed and paraffin-embedded (FFPE) TNBC tumors to reveal actionable pathways for anti-cancer treatment. We identified four major TNBC clusters by unsupervised clustering analysis of protein abundances. In addition, analyses of clinicopathological characteristics revealed associations between proteomic results and clinical phenotypes exhibited by each subtype. We validate the findings of our proteomics analysis, by inferring immune and stromal cell type composition from genome-wide DNA methylation profiles. Finally, quantitative proteomics on TNBC cell lines was conducted to identify representative in vitro models for each subtype. Collectively, our multi-omics data provide novel subtype-specific insights such as potential biomarkers, molecular drivers, and pharmacologic vulnerabilities for further investigations. \n","fileCount":"561","fileSizeKB":"157746005","spectra":"9009040","psms":"3279827","peptides":"1151452","variants":"1480378","proteins":"20163","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"TNBC, cancer, tumor, subtypes","pi":[{"name":"Arminja Kettenbach","email":"Arminja.N.Kettenbach@Dartmouth.edu","institution":"Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD055306","task":"3f0fdbffdefa4dcea091174acc77082f","id":"1983"}, {"dataset":"MSV000095714","datasetNum":"95714","title":"Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724888112000","created":"Aug. 28, 2024, 4:35 PM","description":"Proteomic analysis reveals translation-related proteins are significantly altered in\nresponse to stabilized G4s.\nIdentification of the importance of translation factors in overcoming G4s led to the\nquestion of how E. coli cells generally respond to chemicals that stabilize such\nstructures. As a first step in addressing this question, a proteomic analysis was carried\nout to measure the quantitative effects of NMM on the levels of individual proteins in E.\ncoli. Protein levels from early log-phase cultures of delta-tolC and delta-tolC tufA::kan strains\ngrown in the presence or absence of NMM were measured to assess how reduced EF-\nTu levels and NMM impacted expression.","fileCount":"27","fileSizeKB":"41294915","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Ascend","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Data-dependent acquisition (DDA);Bottom-up proteomics;E.coli;G-quadruplex;Orbitrap Ascend","pi":[{"name":"Joshua J. Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055304","task":"dec145bc38ee467b9e6f7bb1b13572de","id":"1984"}, {"dataset":"MSV000095712","datasetNum":"95712","title":"GNPS - Terrestrial DOM Indonesia peatland 2024","user":"ikoester","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724884100000","created":"Aug. 28, 2024, 3:28 PM","description":"Terrestrial DOM samples from Indonesia peatlands (PPL-extracted) from field expedition in 2024","fileCount":"299","fileSizeKB":"33481648","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"dissolved organic matter;terrestrial;Peatland;PPL","pi":[{"name":"Jennifer Bowen","email":"jbowen@ucsd.edu","institution":"UCSD SIO","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"180a4a52a3b944a5b8cadc036efb0ad5","id":"1985"}, {"dataset":"MSV000095709","datasetNum":"95709","title":"Identification and quantification of mediterrocin, a bacteriocin produced by Mediterraneibacter gnavus","user":"gcmingolelli","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724805494000","created":"Aug. 27, 2024, 5:38 PM","description":"Mediterraneibacter gnavus, a core member of the human gut microbiota, secretes mediterrocin, a broad-spectrum bacteriocin. Identification and quantification of mediterrocin produced by Mediterraneibacter [Ruminococcus] gnavus strains RJX1121, RJX1123, and ATCC29149 using intact protein analysis. ","fileCount":"73","fileSizeKB":"7076509","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"[Ruminococcus] gnavus (NCBITaxon:33038)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"intact protein analysis;bacteriocin","pi":[{"name":"Matt Henke","email":"mhenke3@uic.edi","institution":"University of Illinois Chicago Pharmaceutical Sciences","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"43fc9bb6871e4481a912124f85ba91a2","id":"1986"}, {"dataset":"MSV000095708","datasetNum":"95708","title":"GNPS - Bolnick Alaska Experimental Evolution (2023) - PRJ1","user":"marwa38","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724801913000","created":"Aug. 27, 2024, 4:38 PM","description":"Livers preserved in Ethanol from threespine stickleback (Gasterosteus aculeatus). Thirty per lake from 16 lakes in Alaska. Seven of the lakes are native populations, and nine of the lakes are experimentally introduced populations founded in 2019. Samples were collected by Dan Bolnick and colleagues in June 2023. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1302","fileSizeKB":"105694573","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gasterosteus aculeatus aculeatus (NCBITaxon:481459)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fish;stickleback;Alaska;MSCollaboratory","pi":[{"name":"Daniel Bolnick","email":"daniel.bolnick@uconn.edu","institution":"University of Connecticut","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8b2ff40d4b694adc85c4ea605b1a4622","id":"1987"}, {"dataset":"MSV000095706","datasetNum":"95706","title":"GNPS - Temperature induced lipidomic alterations","user":"VdL_VdL","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724789601000","created":"Aug. 27, 2024, 1:13 PM","description":"Lipidomic analysis of PDAC cells upon culturing at 38C compared to 37C for 10 days","fileCount":"40","fileSizeKB":"195143","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QTRAP 6500+","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipidomics","pi":[{"name":"Johannes V Swinnen","email":"j.swinnen@kuleuven.be","institution":"KU Leuven","country":"Belgium"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"821840b0f4674a748eb5f8f499268edf","id":"1988"}, {"dataset":"MSV000095705","datasetNum":"95705","title":"Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation mouse metabolome","user":"yousi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724786433000","created":"Aug. 27, 2024, 12:20 PM","description":"A collection of tissue, cecal, and fecal samples from mice.","fileCount":"114","fileSizeKB":"1739732","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"IBD; peanut butter feeding method ; microbially conjugated bile acid ; bile acid","pi":[{"name":"Robert Quinn","email":"quinnrob@Msu.edu","institution":"Michigan State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc9560044be8425da4721bda95d7d8e6","id":"1989"}, {"dataset":"MSV000095704","datasetNum":"95704","title":"GNPS - Long Island Sound PFAS Effects on Fish - PRJ2","user":"marwa38","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724774019000","created":"Aug. 27, 2024, 8:53 AM","description":"Samples of Fundulus fish from coastal freshwater with high and low levels of PFAS chemical pollution. Livers were dissected fresh from minnow-trapped fish and preserved in ethanol at room temperature. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"225","fileSizeKB":"18012533","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fundulus heteroclitus (NCBITaxon:8078)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PFAS;pollution;freshwater;Fundulus;fish;MSCollaboratory","pi":[{"name":"Daniel Bolnick","email":"daniel.bolnick@uconn.edu","institution":"University of Connecticut","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d0dbc39b506d422389d92ff2c49eeaf3","id":"1990"}, {"dataset":"MSV000095703","datasetNum":"95703","title":"GNPS - Integrated Omics-Based Discovery of Novel Genes, Secondary Metabolite Clusters, and Small Molecules in Penicillium spp. with Disparate Fungal Lifestyles","user":"cooperb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724766185000","created":"Aug. 27, 2024, 6:43 AM","description":"Four fungal strains, P. expansum R19, P. expansum Pe21, P. chrysogenum 404, and P. chrysogenum 413, were evaluated. Flasks containing 50 mL of potato dextrose broth (PDB) were individually inoculated with 100 uL of conidial suspensions of the fungi. Cultures were grown for 7 days, shaking at 25C. Filter-sterilized (0.2 um) spent growth medium (50 mL from three independent cultures) was centrifuged for 30 minutes at 15,000 x g. Chloroform was added to 3 mL medium at a 1:1 ratio before centrifuging again at 10,000 x g for 10 minutes. The supernatant was transferred to a tube containing 3 mL 60% methanol and vortexed for 2 minutes, then mixed with 5 mL of ethyl acetate. The top organic layer was transferred to a 15 mL conical tube and evaporated to dryness with continual flow of nitrogen gas. Sample residuals were resuspended in 100 uL 50% methanol\/0.1% formic acid. Twenty uL from each sample was pooled to make a quality control (QC) sample. Three samples of potato dextrose broth (PDB) without fungus were processed similarly but were not included in the QC. Five uL of the samples were separated on a 40 C heated, 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles coupled to a Vanquish HPLC pump controlling a 10-minute linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per minute. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1. The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was one and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from a blank sample consisting of 50% methanol\/0.1% formic acid and an inclusion ion list from the QC sample. Subsequently, five injections of QC were performed to generate MS2 spectra. After each of those injections, the resolved ions were appended to the exclusion list for the subsequent injection. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of m\/z 70-800. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, charge states were filtered to one and automated dynamic exclusion was enabled. Twenty precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Next, all test samples were analyzed alongside four intermittent injections of QC and blank consisting of 50% methanol\/0.1% formic acid. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of m\/z 70-800. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2.5 kV but with the same other settings.","fileCount":"57","fileSizeKB":"12494901","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Penicillium (NCBITaxon:5073)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"apple;blue mold;Penicillium expansum;Penicillium chrysogenum","pi":[{"name":"Bret Cooper","email":"bret.cooper@ars.usda.gov","institution":"USDA-ARS","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b77dc47001144ffe97fcc845e4a05513","id":"1991"}, {"dataset":"MSV000095697","datasetNum":"95697","title":"GNPS - DOM_SouthernOcean_NTA_LC-HRMS_DDA_Eclipse","user":"JessPat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724682415000","created":"Aug. 26, 2024, 7:26 AM","description":"Marine dissolved organic matter from Southern Ocean. Samples were analyzed by LC-MS\/MS in positive and negative electrospray ionization mode using DDA (Orbitrap Eclipse). ","fileCount":"165","fileSizeKB":"27764292","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DOM, non-targeted LC-HRMS, southern ocean","pi":[{"name":"Jordi Dachs","email":"jordi.dachs@idaea.csic.es","institution":"IDAEA-CSIC","country":"Spain"},{"name":"Maria Vila Costa","email":"maria.vila@idaea.csic.es","institution":"IDAEA-CSIC","country":"Spain"},{"name":"Pablo Gago Ferrero","email":"pablo.gago@idaea.csic.es","institution":"IDAEA-CSIC","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0e5d52dbd02a4f5da8861253784f4d6b","id":"1992"}, {"dataset":"MSV000095695","datasetNum":"95695","title":"Internalization of therapeutic antibodies into Dendritic cells as a risk factor for immunogenicity","user":"ducreta","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724669499000","created":"Aug. 26, 2024, 3:51 AM","description":"The appended raw files, csv files and other documents were deposited into the public domain in support for the publication \"Internalization of therapeutic antibodies into Dendritic cells as a risk factor for immunogenicity\" by Michel Siegel, Anna-Lena Bolender, Axel Ducret, Johannes Fraidling, Katharina Hartman, Cary M Looney, Olivier Rohr, Timothy Hickling, Martin Lechmann, Celine Marban-Doran and Thomas Kraft.\nThe abstract reads as follows: \"Immunogenicity, defined as the unwanted immune response triggered by the administration of therapeutic antibodies, leads to the production of anti-drug antibodies and is a significant risk factor for the development of therapeutic antibodies. Immunogenicity is a multifactorial phenomenon and risk factors influencing each and every step of the immune response may have major overall consequences. Previously, it has been observed that biophysical properties such as positive charge patches affect the biodistribution of therapeutic antibodies, pharmacokinetic properties like nonspecific clearance by altering their uptake into endothelial cells.\nThe internalization of therapeutic antibodies into dendritic cells plays a crucial role in immunogenicity. Cellular internalization is mainly facilitated by nonspecific endocytosis or fluid phase pinocytosis. It involves the cell engulfing surrounding fluid, leading to the internalization of its contents. The biophysical properties of therapeutic antibodies, such as positive charge patches, can influence this process as described for endothelial cells. We therefore hypothesize that internalization of therapeutic antibodies into dendritic cells is influenced by their biophysical properties. Investigating the link between charge patches and dendritic cells internalization using tool antibodies with large positive or negative charge patches, we observed that antibodies with large positive charge patches showed higher lysosomal accumulation and epitope presentation, an important risk factor for immunogenicity.\nTo understand the subsequent impact on T cell activation, we inserted a CD4+ T cell epitope from ovalbumin (a model antigen with well-characterized T cell epitopes) into the same tool compounds. This insertion led to no significant changes in dendritic cell internalization or T cell epitope presentation compared to wild-type antibodies, allowing for a direct comparison of the impact of internalization T cell epitope presentation on T cell activation. However, the insertion of the ovalbumin CD4+ T cell epitope into the tool antibodies increased the occurrence of a specific T cell response, coupled with enhanced internalization and epitope presentation. This increased activation is a key risk factor in immunogenicity, emphasizing the need for careful consideration during the development of biotherapeutics.\nIn conclusion, positive charge patches-mediated internalization and presentation significantly influence the immunogenicity of therapeutic antibodies.\"\ndoi: 10.3389\/fimmu.2024.1406643\nThe data deposited here supports the generation of Fig. 2 and 4 of this manuscript.","fileCount":"137","fileSizeKB":"69458511","spectra":"1825965","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:28 - \\\"Pyro-glu from Q.\\\";MOD:00412 - \\\"modification from UniMod artifact. OBSOLETE because UniMod entry 19 is now merged with UniMod 35 remap to MOD:00425 'monohydroxylated residue'.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":" monocyte-derived dendritic cell (moDC);immunogenicity;MAPPs;MHC-II peptides;internaiization assay;charge patches","pi":[{"name":"Axel Ducret","email":"axel.ducret@roche.com","institution":"Roche Innovation Center Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD055197","task":"ee74f3c27d5f4533955625dd97046977","id":"1993"}, {"dataset":"MSV000095691","datasetNum":"95691","title":"The Miniaturized Isolation of Neutrophil Granules (MING) method allowed a deep proteome mapping of human neutrophil granules","user":"Gabrielly_Alexandria","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724539061000","created":"Aug. 24, 2024, 3:37 PM","description":"Search files, Raw mass spectrum files in a non-standard (.raw) and standardized format (.mzML) for shotgun proteomics of the neutrophil granules using the MING method. \r\n\r\n","fileCount":"45","fileSizeKB":"22624789","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Neutrophil;Granules;Fractionation","pi":[{"name":"Gabrielly Alexandria","email":"gabriellyalexandria@gmail.com","institution":"University of Sao Paulo","country":"Brazil"},{"name":"Graziella Eliza Ronsein","email":"ronsein@iq.usp.br","institution":"University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ebb1b1d1913c48e5978b37abad954abc","id":"1994"}, {"dataset":"MSV000095690","datasetNum":"95690","title":"The Miniaturized Isolation of Neutrophil Granules (MING) method ","user":"Gabrielly_Alexandria","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724473932000","created":"Aug. 23, 2024, 9:32 PM","description":"Raw mass spectrum files for shotgun proteomics of the neutrophil granules using the MING method. NOT THE FINAL DATASET. VIEW MSV000095691\r\n\r\n","fileCount":"41","fileSizeKB":"22280994","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Neutrophil;Granules;fractionation","pi":[{"name":"Gabrielly Alexandria","email":"gabriellyalexandria@gmail.com","institution":"University of Sao Paulo","country":"Brazil"},{"name":"Graziella Eliza Ronsein","email":"ronsein@iq.usp.br","institution":"University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"147997ae6d714c9b97112ff64a5b2990","id":"1995"}, {"dataset":"MSV000095689","datasetNum":"95689","title":"Supporting raw MS data for paper (doi:10.1038\/s41589-025-01894-4) by Raiff A., Zhao Z. et al (2025), titled \"TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6\"","user":"aordureau","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724463656000","created":"Aug. 23, 2024, 6:40 PM","description":"Supporting raw MS data for paper (doi:10.1038\/s41589-025-01894-4) by Raiff A., Zhao Z. et al (2025), titled \"TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6\". Index of MS files and labels Supplementary Table 1 - HEK293T - Proteome (CZ-1-23 | Unimod:35; 737; 4 | 126 - HEK293T-WT; 127n - HEK293T-WT; 127c - HEK293T-WT; 128n - FEM1B-KO#1; 128c - FEM1B-KO#1; 129n - FEM1B-KO#1; 129c - FEM1B-KO#1; 130n - FEM1B-KO#2; 130c - FEM1B-KO#2; 131n - FEM1B-KO#2; 131c - FEM1B-KO#2)","fileCount":"25","fileSizeKB":"15050033","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"Proteome;TMT;FEM1B","pi":[{"name":"Alban Ordureau","email":"OrdureaA@mskcc.org","institution":"Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"90f18ecaa83245e6bc8ccc2d2200dd9b","id":"1996"}, {"dataset":"MSV000095687","datasetNum":"95687","title":" Multiomics Profiling of Extracellular Vesicles Supports Their Involvement in Endothelial Senescence-Associated Vascular Dysfunction","user":"gabrig","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724446627000","created":"Aug. 23, 2024, 1:57 PM","description":"Dysfunction of vascular endothelium is characteristic of many aging-related diseases, including Alzheimers disease (AD) and AD-related dementias (ADRD). While it is widely posited that endothelial cell dysfunction contributes to the pathogenesis and\/or progression of AD\/ADRD, it is not clear how. A plausible hypothesis is that intercellular trafficking of extracellular vesicles (EVs) from senescent vascular endothelial cells promotes vascular endothelial cell dysfunction. To test this hypothesis, we compared the expression of proteins and miRNAs in EVs isolated from early passage (EP) vs. senescent (SEN) primary human coronary artery endothelial cells (HCAECs) from the same donor. Proteomics and miRNA libraries constructed from these EV isolates were evaluated using FunRich gene ontology analysis to compare functional enrichment between EP and SEN endothelial cell EVs (ECEVs). Replicative senescence was associated with altered EV abundance and contents independent of changes in EV size. Unique sets of miRNAs and proteins were differentially expressed in SEN-ECEVs, including molecules related to cell adhesion, barrier integrity, receptor signaling, endothelial-mesenchymal transition and cell senescence. miR-181a-5p was the most upregulated miRNA in SEN-ECEVs, increasing >5-fold. SEN-ECEV proteomes supported involvement in several pro-inflammatory pathways consistent with senescence and the senescence-associated secretory phenotype (SASP). These data indicate that SEN-ECEVs are enriched in bioactive molecules implicated in senescence-associated vascular dysfunction, blood-brain barrier impairment, and AD\/ADRD pathology. These observations suggest involvement of SEN-ECEVs in the pathogenesis of vascular dysfunction associated with AD\/ADRD. 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Lein","email":"pjlein@ucdavis.edu","institution":"University of California, Davis","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055150","task":"2f682ce5e0614b9cbfadfe784392de14","id":"1997"}, {"dataset":"MSV000095686","datasetNum":"95686","title":"Anabolic Indices of Matrix Proteins Identify Regenerative Small RNA Intrinsic to Human Cartilage","user":"mfhsueh","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724445945000","created":"Aug. 23, 2024, 1:45 PM","description":"human articular cartilage from ankle, knee, and hip joints of osteoarthritis and non-osteoarthritis donors. 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Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c06dfd667d3b48f181482eef0df765c9","id":"1999"}, {"dataset":"MSV000095681","datasetNum":"95681","title":"Differential expression of proteins due to Cobalt(II) Chloride induced pseudohypoxia in Jurkat cells","user":"Ditipriya98","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724429760000","created":"Aug. 23, 2024, 9:16 AM","description":"To demonstrate the mechanisms underlying Cobalt(II) Chloride driven pseudohypoxia, proteomic dysregulations were studied in a human T-cell Lymphoma cell line (Jurkat). This proteomics data generated the abundance ratios of proteins in CoCl2 treated versus untreated Jurkat cells. Concisely, Jurkat cells were treated with CoCl2 (50uM) in complete RPMI media. Tryptic digested and desalted peptide samples were injected in Thermoscientific Q-Exactive Plus instruments through EasyNLC HPLC autosampler. The instruments were set to MS1 resolution of 70000 and MS2 resolution of 17500. The acquisition experiments were optimized to run on 2 hours gradients. The MS spectra were analyzed using the Thermoscientific mass informatics platform Proteome discoverer version 2.2. The common workflows for discovery proteomics were used with Mascot and SequestHT. This dataset assisted in identifying the pseudohypoxia-driven changes in lymphoma progression and revealed many druggable targets in the context of metastasis in T-cell malignanices. ","fileCount":"18","fileSizeKB":"11189896","spectra":"77241","psms":"38438","peptides":"16410","variants":"19681","proteins":"3220","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"Jurkat;Pseudohypoxia;Cobalt chloride","pi":[{"name":"Rahul Purwar","email":"purwarrahul@iitb.ac.in","institution":"IIT Bombay","country":"India"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD055142","task":"72bb896872cc4cbfb13add96f22a0520","id":"2000"}, {"dataset":"MSV000095680","datasetNum":"95680","title":"E. coli leverages growth arrest to remodel its proteome upon entry into starvation","user":"trendsetter","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724412082000","created":"Aug. 23, 2024, 4:21 AM","description":"It is widely believed that, owing to the limitation of nutrients in natural environments, bacteria spend most of their life in a non-growing state. However, despite its major clinical and ecological implications, very little is known about what determines the phenotype of starved bacteria, in particular what controls the concentration of different gene products inside the cells. Using microfluidics and quantitative fluorescence microscopy, we monitored growth and gene expression in many independent E. coli lineages as we switched them from exponential growth to starvation. We observed that all cells stopped growing immediately and that no cell death occurred for more than two days. At the same time, gene expression undergoes a dramatic remodeling upon entry into starvation in a promoter-dependent manner. Some promoters, including ribosomal protein promoters, arrest gene expression immediately, others show a slow exponential decay of expression on a 10 h time scale, while a third category exhibits a transient burst of activity before decaying exponentially. Remarkably, the time dynamics of these changes are highly homogeneous across single cells.\nIn addition, we demonstrated that the gene expression response does not qualitatively depend on the dynamics of starvation entry.\nCombining the observed time-dependent protein production and decay rates, we showed with mathematical modeling that a delay between growth arrest and shutdown of gene expression allows a massive increase in the concentration of certain proteins without requiring an upregulation of their expression. Moreover, protein concentrations deep in starvation appeared to be mainly determined by the expression dynamics during the first 10 h of starvation. Finally, we established that this expression program at the onset of starvation is critical for cell viability. In particular, by inhibiting gene expression during different periods of starvation, we were able to show that the tolerance to stress after 2 days is determined by gene expression occurring during the first 10 h, which thus constitutes a preventive response.\nThese results provide a starting point for quantitative studies of cell maintenance and the emergence of specific phenotypes when nutrients become scarce.","fileCount":"84","fileSizeKB":"90265923","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Exploris 480;Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Growth;ECOLI;Starvation","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055125","task":"0bf900251550432aa2dc2905121b201a","id":"2001"}, {"dataset":"MSV000095677","datasetNum":"95677","title":"GNPS - Gut microbiome extracts for study of bile acids","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724384710000","created":"Aug. 22, 2024, 8:45 PM","description":"microbial extracts analysed in positive and negative mode","fileCount":"37","fileSizeKB":"3391695","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gut microbiome;bile acids","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2aaabee44a6140809d3aab6072f00004","id":"2002"}, {"dataset":"MSV000095676","datasetNum":"95676","title":"Structural basis for Retriever-SNX17 assembly and endosomal sorting","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724360510000","created":"Aug. 22, 2024, 2:01 PM","description":"Plasma membrane proteomics by TMT:\n\n126: WT1\n127N: WT2\n127C: WT3\n128N: WT4\n128C: WT5\n129N: WT6\n129C: EV1\n130N: EV2\n130C: EV3\n131N: EV4\n131C: EV5\n132N: EV6\n132C: DM1\n133N: DM2\n133C: DM3\n134N: DM4\n134C: DM5\n135: DM6\n","fileCount":"3","fileSizeKB":"5395555","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Endosomal sorting;SNX17;Retriever","pi":[{"name":"Ezra Burstein","email":"ezra.burstein@utsouthwestern.edu","institution":"UT Southwestern Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5c1d74dcd63f4a4f8086687c8502058f","id":"2003"}, {"dataset":"MSV000095675","datasetNum":"95675","title":"Consistent Amyloid Fibril Structures Across Multiple Organs and Patients in ATTRv-T60A Amyloidosis Revealed by Cryo-EM","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724357698000","created":"Aug. 22, 2024, 1:14 PM","description":"Cardiac ATTRv-T60A amyloid fibrils from three different patients, and ATTRv-T60A fibrils from thyroid, explanted kidney, and explanted liver from one of the patients (tissues obtained from autopsy and transplant surgery).\n\nIdentification of tryptic and non-tryptic fragments in ATTRv-V30M). \nCardiac ATTR fibrils (patient 1):\nSample ID: 1176938\n\nCardiac ATTR fibrils (patient 2): \nSample ID: 1176937\n\nCardiac ATTR fibrils from (patient 3):\nSample ID: 1176932\n\nThyroid ATTR fibrils from (patient 3):\nSample ID: 1176934\n\nRenal ATTR fibrils from (patient 3):\nSample ID: 1176933\n\nHepatic ATTR fibrils from (patient 3):\nSample ID: 1176935\n","fileCount":"13","fileSizeKB":"5858584","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Transthyretin;Amyloidosis;ATTR","pi":[{"name":"Lorena Saelices Gomez","email":"lorena.saelicesgomez@utsouthwestern.edu","institution":"UT Southwestern Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"71aa1a0025354cbf88555e6eb1a87cf8","id":"2004"}, {"dataset":"MSV000095673","datasetNum":"95673","title":"mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation ","user":"RouhanifardLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724343772000","created":"Aug. 22, 2024, 9:22 AM","description":"Pseudouridine (psi) is one of the most abundant human mRNA modifications generated via psi synthases, including TRUB1 and PUS7. Nanopore direct RNA sequencing combined with our recent tool, Mod-p ID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and\/or conversion to cDNA. This method is sensitive for detecting changes in positional psi occupancies across cell types, which can inform our understanding of the impact on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, we find that conserved psi positions correspond to higher levels of protein expression than expected, suggesting translation regulation. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. Finally, we characterize sites with multiple psi modifications on the same transcript and found that these can be conserved or cell type specific, including examples of multiple psi modifications within the same k-mer. Our data support the hypothesis that psi modifications contribute to regulating translation and that cell type-specific trans-acting factors play a major role in driving pseudouridylation.","fileCount":"7","fileSizeKB":"8102085","spectra":"139926","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Proteomics ;RNA Modifications;Pseudouridine","pi":[{"name":"Sara Rouhanifard","email":"s.rouhanifard@northeastern.edu","institution":"Northeastern University ","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD055082","task":"bf7126f75a224893b38f303e08baaca6","id":"2005"}, {"dataset":"MSV000095671","datasetNum":"95671","title":"B.ovatus vs 4,4'-DDE in mouse model","user":"lichen_osu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724292108000","created":"Aug. 21, 2024, 7:01 PM","description":"raw data of lipidomics, metabolomics, bile acid, short-chain fatty acid analysis in vivo study","fileCount":"1129","fileSizeKB":"61007767","spectra":"1377731","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"mouse","instrument":"LC-MS, GC-MS","modification":"LOG10","keywords":"metabolomics, lipidomics, SCFAs, BAs, accumulation, pesticide, bacteria","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"42f05c0bf0a54a928ba5a85a994f8806","id":"2006"}, {"dataset":"MSV000095670","datasetNum":"95670","title":"GPC3-mediated metabolic rewiring of diabetic mesenchymal stromal cells enhances their cardioprotective functions via pyruvate kinase M2 activation","user":"darukeshwara","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724261145000","created":"Aug. 21, 2024, 10:25 AM","description":"Mesenchymal stromal cells (MSC) are promising stem cell therapy for treating cardiovascular and other degenerative diseases. Diabetes affects the functional capability of MSC and impedes cell-based therapy. Despite numerous studies, the impact of diabetes on MSC myocardial reparative activity, metabolic fingerprint, and the mechanism of dysfunction remains inadequately understood. We demonstrated that the transplantation of diabetic-MSC (db\/db-MSC) into the ischemic myocardium of mice does not confer cardiac benefit post-MI. Metabolomic studies identified defective energy metabolism in db\/db-MSC. Furthermore, we found that glypican-3 (GPC3), a heparan sulfate proteoglycan, is highly upregulated in db\/db-MSC and is involved in metabolic alterations in db\/db-MSC via pyruvate kinase M2 activation. GPC3-knockdown reprogrammed-db\/db-MSC restored their energy metabolic rates, immunomodulation, angiogenesis, and cardiac reparative activities. Together, these data indicate that GPC3-metabolic reprogramming in diabetic MSC may represent a strategy to enhance MSC-based therapeutics for myocardial repair in diabetic patients. ","fileCount":"10","fileSizeKB":"367816","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Q Exactive \\\/ Vanquish UPLC ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mesenchymal stromal cells","pi":[{"name":"Darukeshwara Joladarashi","email":"darukeshwara@gmail.com","institution":"Temple University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"16354a8f7f8f4a1fb537aeadf8a29630","id":"2007"}, {"dataset":"MSV000095666","datasetNum":"95666","title":"Volatilome of Theobroma grandiflorum at Different Stages of Maturation Analyzed by HS-SPME-GC-MS","user":"Monitpb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724206855000","created":"Aug. 20, 2024, 7:20 PM","description":"This dataset comprises the raw mass spectrometry files generated from the analysis of VOCs extracted from the pulp of Theobroma grandiflorum (Copoazu) at three distinct maturation stages (ripe, overripe, and medium). The study used HS-SPME-GC-MS. A Divinylbenzene\/carbon wide-range\/polydimethylsiloxane (DVB\/CWR\/PDMS) 80 um x 10 mm fiber was used in combination with a Gas Chromatograph HP 6890 Series equipped with an Agilent Mass Selective Detector 5973. The VOCs were separated on a capillary GC column of 5% Phenyl\/95% Dimethyl Polysiloxane (30 m x 0.25 mm x 0.25 um).","fileCount":"17","fileSizeKB":"589898","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Theobroma grandiflorum (NCBITaxon:108881)","instrument":"Gas Chromatograph HP 6890 Series equipped with an Agilent Mass Selective Detector 5973 ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Theobroma grandiflorum;VOCs;GC-MS;HS-SPME;Volatilomics","pi":[{"name":"Paula Galeano","email":"p.galeano@udla.edu.co","institution":"Universidad de la Amazonia","country":"Colombia"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"deda9e80a7a043a7baa1415477388be8","id":"2008"}, {"dataset":"MSV000095665","datasetNum":"95665","title":"GNPS - Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Rat Brain Tissue Section","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724205404000","created":"Aug. 20, 2024, 6:56 PM","description":"Proteomic data from rat brain. Replicate samples were analyzed via the microPOTS platform.","fileCount":"619","fileSizeKB":"184018957","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"timsTOF SCP","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"proteomics;multiomic","pi":[{"name":"Christopher Anderton","email":"christopher.anderton@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2b91cb1c79904c8eb680537b1c2a0f86","id":"2009"}, {"dataset":"MSV000095664","datasetNum":"95664","title":"GNPS - Inducible antimicrobial activity in Bacillus spp and 2-PBI confirmation","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724198263000","created":"Aug. 20, 2024, 4:57 PM","description":"Follow up confirmation of induced metabolites in bacterial cultures. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"78","fileSizeKB":"3410531","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis subsp. subtilis str. NCIB 3610 (NCBITaxon:535026);Bacillus cereus (NCBITaxon:1396)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"2-phenylbenzylimidazole;Bacillus subtilis","pi":[{"name":"Valeska Villegas","email":"vvilleg2@eafit.edu.co","institution":"Universidad EAFIT","country":"Colombia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c8ee3b80020a41c5a33ce3b7969aa558","id":"2010"}, {"dataset":"MSV000095663","datasetNum":"95663","title":"Enteropathogenic hemorrhagic bacteria limit ROCK-dependent epithelial cell extrusion to circumvent barrier immunity","user":"TKC008","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724186437000","created":"Aug. 20, 2024, 1:40 PM","description":"Diverse pathogen-encoded virulence factors disable apoptosis, pyroptosis, or ecroptosis, the host cell death programs that remove infected cells. In the intestine, the expulsion of infected cells into the lumen for elimination provides an additional layer of host defense, but no virulence mechanisms targeting this process are known. Here, we show that the Escherichia coli ubiquitin ligase NleL is an inhibitor of intestinal epithelial cell (IEC) expulsion that targets caspase-4, Rho-effector kinase 1 (ROCK1), and ROCK2 for proteasomal degradation. Genetic deletion of Rock1 and Rock2 from cultured IECs diminished inflammasome-induced IEC expulsion.\nMoreover, mice with Rock1- and Rock2-deficient IECs were less effective than wild-type (WT) mice at constraining Citrobacter rodentium replication in the colon. Importantly, NleL-deficient C. rodentium triggered more IEC expulsion than WT C. rodentium, resulting in diminished colon colonization in infected mice. This work highlights a host-pathogen arms race focused on dynamic regulation of the host epithelial barrier.","fileCount":"25","fileSizeKB":"10475600","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"bacterial ligase","pi":[{"name":"Christopher Rose","email":"rose.christopher@gene.com","institution":"Genentech","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0ce3f5df87cc427f9e06ab9869c98076","id":"2011"}, {"dataset":"MSV000095657","datasetNum":"95657","title":"GNPS - mice cecum infected with Salmonella","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724177692000","created":"Aug. 20, 2024, 11:14 AM","description":"Cecal content of mice infected with Salmonella run on Q-Exactive. 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Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"2b3ec5ca0a3d4e81845c389633119871","id":"2012"}, {"dataset":"MSV000095656","datasetNum":"95656","title":"GNPS - RiPP Metal Binding Assessment at High pH","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724175472000","created":"Aug. 20, 2024, 10:37 AM","description":"Does the RiPP compound bind Cu2+, Cu+, or Fe2+? Assessing to see whether this Novel RiPP compound binds or not since it possesses the properties of methanobactin","fileCount":"5","fileSizeKB":"305439","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"none","instrument":"QExactive Tandem Mass Spectrometry","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Copper, Fe metals","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d69bd77ea9914657aaca0e2dc170f2cb","id":"2013"}, {"dataset":"MSV000095654","datasetNum":"95654","title":"GNPS - 8202024_Dumitrescu_HILIC_orbitrap","user":"DanaMoradi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724165527000","created":"Aug. 20, 2024, 7:52 AM","description":"These data were collected by running different tissue samples from mice through a HILIC column with an Orbitrap.","fileCount":"444","fileSizeKB":"51212487","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Peromyscus maniculatus (NCBITaxon:10042)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HILIC_Orbitrap","pi":[{"name":"Alexander Aksenov","email":"aaaksenov@health.ucsd.edu","institution":"University of California San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"035ada3a3818415fb55d653d72d39d67","id":"2014"}, {"dataset":"MSV000095648","datasetNum":"95648","title":"GNPS - in vitro culture of human-associated gut microbes ","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724109625000","created":"Aug. 19, 2024, 4:20 PM","description":"In vitro culture of gut microbes run on Q-Exactive. Reversed-phase, ESI positive, polar C18 column (2.6 um particle size, 2.1 mm x 100 mm Phenomenex, Kinetex). The mPYG medium contains GABA, putrescine, cadaverine, cysteine, and taurine conjugated bile acids. ","fileCount":"458","fileSizeKB":"26310439","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Gut microbes, culture, LC-MS\/MS, in vitro, metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"a2b196ed4b0a4236ba7b0fdddbd0ebc7","id":"2015"}, {"dataset":"MSV000095646","datasetNum":"95646","title":"Proteomic Analysis of Hepatic Fbp1 Deficiency in Mouse Models","user":"gonzolabucsd","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724100201000","created":"Aug. 19, 2024, 1:43 PM","description":"Data from study comparing liver tissue of mice deficient of hepatic Fbp1. Lack of Fbp1 reveals Fbp1 and NRF2 as important protein regulations in metabolic dysfunction-associated steatohepatitis (MASH). 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VM-42, secondary metabolites","pi":[{"name":"Kristina Haslinger","email":"k.haslinger@rug.nl","institution":"Groningen Research Institute of Pharmacy, University of Groningen","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9352e95101614e3e88863a5250b96937","id":"2017"}, {"dataset":"MSV000095642","datasetNum":"95642","title":"Molecular basis for thiocarboxylation and release of Urm1 by its E1-activating enzyme Uba4","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724077332000","created":"Aug. 19, 2024, 7:22 AM","description":"Ubiquitin related modifier 1 (Urm1) is a highly conserved member of the Ubiquitin-like (UBL) family of proteins. Urm1 is a key component of the eukaryotic thiolation cascade, which is responsible for introducing sulfur at U34 in several eukaryotic tRNAs. Like other UBLs, Urm1 is also able to conjugate to target proteins under mild oxidative stress. In both cases, the C-terminus of Urm1 needs to be thiocarboxylated (Urm1-SH) by Ubiquitin-like protein activator 4 (Uba4). Uba4 first adenylates, and then thiocarboxylates the C-terminus of Urm1 using its AD and RHD domains. However, the detailed mechanisms of Uba4, the interplay between the two domains, and the release of Urm1 remain elusive. Here, we report a cryo-EM-based structural model of the Uba4\/Urm1 complex and a detailed biochemical analysis of its reaction cycle. Our results show how the chemical fate of Urm1s C-terminus depends on conserved cysteine residues of Uba4, how the complex avoids off-target reactions by the appearing volatile intermediates, and how the Urm1-SH product is released. Finally, we show that Urm1 only interacts with Ncs6, but not with Ncs2, of the downstream thioltransferase complex and Tum1 can functionally complement the RHD domain of Uba4.","fileCount":"15","fileSizeKB":"37648","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932);Chaetomium thermophilum (NCBITaxon:209285)","instrument":"micrOTOF-Q II","modification":"MOD:01778 - \\\"A protein modification that effectively converts a C-terminal glycine residue to N-(glycyl)-L-cysteine by forming a peptide bond with a free L-cysteine.\\\";UNIMOD:405 - \\\"AMP binding site.\\\"","keywords":"Urm1;thiocarboxylation","pi":[{"name":"Sebastian Glatt","email":"sebastian.glatt@uj.edu.pl","institution":"Malopolska Centre of Biotechnology (MCB), Jagiellonian University","country":"Poland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3f82a765ecc148d1abcc31cf1b8898e8","id":"2018"}, {"dataset":"MSV000095641","datasetNum":"95641","title":"Proteogenomics Analysis of X-Organ\/Sinus Gland Tissue in Callinectes sapidus from Brazilian Estuaries ","user":"jthalles","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724072657000","created":"Aug. 19, 2024, 6:04 AM","description":"We employed a proteogenomic approach with a transcriptome-based protein database from C. sapidus, followed by multi-round database searches on the XO\/SG tissue of specimens subjected to regular temperature (control, 24C), cold (19C), and heat (29C)","fileCount":"35","fileSizeKB":"12411093","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Callinectes sapidus (NCBITaxon:6763)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Blue crab;XO\/SG Tissue;Molting Cycle;Temperature;Proteogenomics","pi":[{"name":"Ana Maria L Castrucci","email":"amdlcast@ib.usp.br","institution":"University of Sao Paulo","country":"Brazil"},{"name":"Jose Thalles Lacerda","email":"thalles_lacerda2@hotmail.com","institution":"University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD054999","task":"8144bb9f901b4181b3d811a1ccf69969","id":"2019"}, {"dataset":"MSV000095639","datasetNum":"95639","title":"GNPS - The metabolomic and lipidomic mass spectrometry raw data about biofilms","user":"Yuzhen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724051870000","created":"Aug. 19, 2024, 12:17 AM","description":"The metabolomic and lipidomic mass spectrometry raw data about biofilms","fileCount":"36","fileSizeKB":"7008559","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli str. K-12 substr. MG1655 (NCBITaxon:511145)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Biofilms","pi":[{"name":"Yuzhen Zhang","email":"zhangyzh@tib.cas.cn","institution":"Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1c40bf3aa776451bba1def3c5f9d7d4c","id":"2020"}, {"dataset":"MSV000095638","datasetNum":"95638","title":"Proteomic changes with increasing biofilm size","user":"Yuzhen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724048603000","created":"Aug. 18, 2024, 11:23 PM","description":"The raw spectrum files about proteomics with increasing biofilm size","fileCount":"178","fileSizeKB":"30557414","spectra":"770154","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli str. K-12 substr. MG1655 (NCBITaxon:511145)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Biofilms","pi":[{"name":"Yuzhen Zhang","email":"zhangyzh@tib.cas.cn","institution":"Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054980","task":"c0c35aeb5f3f4955a6208ec6a62df798","id":"2021"}, {"dataset":"MSV000095637","datasetNum":"95637","title":"Extracellular proximity labeling_TIMP2 Interactome","user":"dpeeney","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1724016772000","created":"Aug. 18, 2024, 2:32 PM","description":"Assessment of the TIMP2 interactome in HT1080 and HS-5 cells using proximity labeling (TurboID and BioID2). File designations included in the excel spreadsheet.\r\n\r\nMetadata - file will be added when upload bugs are fixed. Comma separated metadata below:\r\n\r\nFile Name Prefix,Cell Line,Biotin Ligase,Treatment,Label,x Identity \/ Notes,\r\nP1301-x-EXP_1,HT1080,TurboID,Untreated,N\/A,1 = Control; 2 = TurboID; 3 = TIMP2-TurboID; 4 = TurboID-TIMP2,\r\nP1301-x-EXP_2,HT1080,TurboID,Untreated,N\/A,5 = Control; 6 = TurboID; 7 = TIMP2-TurboID; 8 = TurboID-TIMP2,\r\nP1314-x-EXP_5,HT1080,TurboID,Concanavalin A treated,N\/A,1 = Control; 2 = TurboID; 3 = TIMP2-TurboID; 4 = TurboID-TIMP2,\r\nP1314-x-EXP_6,HT1080,TurboID,Concanavalin A treated,N\/A,5 = Control; 6 = TurboID; 7 = TIMP2-TurboID; 8 = TurboID-TIMP2,\r\nP1314-x-EXP_7,HT1080,BioID2,Untreated,N\/A,9 = Control; 10 = BioID2; 11 = BioID2-TIMP2; 12 = TIMP2-BioID2,\r\nP1314-x-EXP_8,HT1080,BioID2,Untreated,N\/A,13 = Control; 14 = BioID2; 15 = BioID2-TIMP2; 16 = TIMP2-BioID2,\r\nP1333-EXP_9-x,HT1080,TurboID,3D culture (spheroid),N\/A,1 = Control; 2 = TurboID; 3 = TIMP2-TurboID; 4 = TurboID-TIMP2,\r\nP1407-x-EXP_21,HT1080,TurboID,3D culture (spheroid),N\/A,1 = TurboID; 2 = TIMP2-TurboID; 3 = TurboID-TIMP2,\r\nP1333-EXP_10-x,HT1080,TurboID,PMA treated,N\/A,1 = Control; 2 = TurboID; 3 = TIMP2-TurboID; 4 = TurboID-TIMP2,\r\nP1352-EX13-x,HT1080,TurboID,PMA treated,N\/A,1 = Control; 2 = TurboID; 3 = TIMP2-TurboID; 4 = TurboID-TIMP2,\r\nP1358-1_126-129C,HS-5,TurboID,Untreated,TMT,126 = Control; 127C = TurboID; 128C = TIMP2-TurboID; 129C = TurboID-TIMP2,\r\nP1358-2_127N-130N,HS-5,TurboID,Untreated,TMT,127N = Control; 128N = TurboID; 129N = TIMP2-TurboID; 130N = TurboID-TIMP2\r\n","fileCount":"163","fileSizeKB":"43315345","spectra":"0","psms":"227488","peptides":"13253","variants":"21502","proteins":"2380","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Scientific Orbitrap Exploris 240","modification":"na","keywords":"TIMP2;Proximity Labeling;Interactomics","pi":[{"name":"David Peeney","email":"david.peeney@nih.gov","institution":"National Cancer Institute","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054977","task":"fd4d3e4bdff74d8e8c7ce4340685a9e8","id":"2022"}, {"dataset":"MSV000095635","datasetNum":"95635","title":"Biofunctionalized dissolvable hydrogel microbeads enable efficient characterization of native protein complexes","user":"xyshao","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723975414000","created":"Aug. 18, 2024, 3:03 AM","description":"Evaluation of the target recovery rate and purification specificity for protein purification using various affinity beads or baits.","fileCount":"407","fileSizeKB":"45638154","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli","instrument":"Orbitrap Eclipse;timsTOF Pro","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\"","keywords":"protein purification","pi":[{"name":"Guanbo Wang","email":"guanbo.wang@pku.edu.cn","institution":"Peking University","country":"China"},{"name":"Jianbin Wang","email":"jianbinwang@tsinghua.edu.cn","institution":"Tsinghua University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054976","task":"cb9fab0082074fa5bc0b7b761772f97c","id":"2023"}, {"dataset":"MSV000095634","datasetNum":"95634","title":"GNPS - Direct Analysis in Real Time Mass Spectrometry (DART-MS) for Rapid Screening of Carpaine in Carica papaya Leaf Products","user":"PiyawadiK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723950098000","created":"Aug. 17, 2024, 8:01 PM","description":"DART-MS can rapidly detect carpaine in various forms of papaya leaf products.\r\nNo sample preparation is needed for DART-MS, enhancing efficiency.\r\nAnalysis with DART-MS takes less than a minute per sample, ideal for rapid screening.\r\nValidated DART-MS method demonstrated robust identification with low LOD.\r\n","fileCount":"5983","fileSizeKB":"69841292","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Carica papaya ","instrument":"DART-TOF-MS and LC-ESI-QTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"carpaine, Carica papaya leaf, DART-MS, identification, screening","pi":[{"name":"Rossarin Tansawat","email":"rossarin.t@pharm.chula.ac.th","institution":"Faculty of Pharmaceutical Sciences, Chulalongkorn University","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d9e3dfa8b4cf41369caf7f8d1c98cf91","id":"2024"}, {"dataset":"MSV000095633","datasetNum":"95633","title":"Lessons learned in label free single cell proteomics on a TIMSTOF SCP system","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723920384000","created":"Aug. 17, 2024, 11:46 AM","description":"This repository is an amalgamation of different single cells analyzed using label free approaches (both DDA\/PASEF and DIAPASEF) on a TIMSTOF SCP system. Cells analyzed including multiple immoratalized cancer cell lines and primary human hepatocytes isolated from a single donor","fileCount":"3843","fileSizeKB":"305364098","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Single cell proteomics;Single human hepatocytes;Polynucleated cancer cells;PC-3 cells;SW620 cells;H358 Cells;PASEF;diaPASEF","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7f37d8cdb3c54b9ea970a195b088772f","id":"2025"}, {"dataset":"MSV000095629","datasetNum":"95629","title":"Offset mass carrier proteome improves quantification of multiplexed single cell proteomics","user":"CMRose5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723840498000","created":"Aug. 16, 2024, 1:34 PM","description":"Multiplexed single cell proteomics by mass spectrometry (scpMS) approaches currently offer the highest throughput as measured by cells analyzed per day. These methods employ isobaric labels and typically a carrier proteome - a sample added at 20-500x the single cell level that improves peptide sampling and identification. Peptides from the carrier and single cell proteomes exist within the same precursor isotopic cluster and are co-isolated for identification and quantification. This represents a challenge as high levels of carrier proteome limit the sampling of peptide ions from single cell samples and can potentially lead to decreased accuracy of quantitative measurements. Here, we address this limitation by introducing a triggered by offset mass acquisition method for scpMS (toma-scpMS) that utilizes a carrier proteome labeled with non-isobaric tags that have the same chemical composition but different mass as the labels used for quantitative multiplexing. Within toma-scpMS the carrier proteome and single cell proteome are separated at the precursor level, enabling separate isolation, fragmentation, and quantitation of the single cell samples. To enable this workflow we implemented a custom data acquisition scheme within inSeqAPI, an instrument application programming interface program, that performed real-time identification of carrier proteome peptides and subsequent triggering of offset single cell quantification scans. We demonstrate that toma-scpMS is more robust to high-levels of carrier proteome and offers superior quantitative accuracy as compared to traditional multiplexed scpMS approaches when similar carrier proteome levels are employed. 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We flash-froze stomachs and intestines from each fish for metabolomics. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1633","fileSizeKB":"72125349","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gasterosteus aculeatus (NCBITaxon:69293)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory","pi":[{"name":"Daniel Bolnick","email":"daniel.bolnick@uconn.edu","institution":"University of Connecticut","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"57b902226c27416a8df5d4c4e07b59b9","id":"2031"}, {"dataset":"MSV000095616","datasetNum":"95616","title":"GNPS Too Much Botrytis Co-culture","user":"smata","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723736850000","created":"Aug. 15, 2024, 8:47 AM","description":"First try at GNPS. Bacillus mycoides is being investigated as a potential biological control agent against Botrytis cinerea, and we wish to elucidate what compounds are causing the inhibition of Botrytis cinerea growth. Bacillus mycoides was cultured in NB, Botrytis cinerea was cultured in NB, then B. cinerea and B. mycoides were cultured in NB together. 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The lock mass option was enabled using the 371.101236m\/z polysiloxane peak as an internal calibrant.\n\nPeaks Studio Xpro (Bioinformatics Solutions) was used to analyze the data against the 9\/30\/2021 version of the P. gingivalis strain ATCC 33277 protein sequences from the UniProtKB (proteome identifier UP000008842) considering semi specific Trypsin (maximum two missed cleavages) with fragment tolerance (0.5 Da) from the ITMS and parent tolerance (15 ppm) from the FTMS. FDR estimation was enabled in the algorithms. A proteins.csv file was exported for curation in Microsoft Excel. Proteins and peptides were accepted at the 1% FDR threshold.\n","fileCount":"46","fileSizeKB":"5396682","spectra":"20881","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Porphyromonas gingivalis (NCBITaxon:837)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"affinity purification;Bacterial PTK1 client proteins;One carbon metabolism","pi":[{"name":"Michael L. 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Each biological replicate contains five technical replicates per modified CpG dyad, resulting in a total of 15 replicates for C\/C, mC\/mC and hmC\/mC, and 10 replicates for hmC\/C and hmC\/hmC.","fileCount":"70","fileSizeKB":"194239886","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cytosine modifications, nuclear binding proteins, binding to VEGFA promoter, interaction proteomics, bottom-up proteomics","pi":[{"name":"Petra Janning","email":"petra.janning@mpi-dortmund.mpg.de","institution":"MPI of Molecular Physiology","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD054913","task":"f1dedda1c8fa4e6ca33a4c9d39c46d08","id":"2035"}, {"dataset":"MSV000095608","datasetNum":"95608","title":"GNPS-diaorao-test-dendrobne endophyte44","user":"diaorao","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723706941000","created":"Aug. 15, 2024, 12:29 AM","description":"plant dendrobine endophyteplant dendrobine endophyteplant dendrobine endophyteplant dendrobine endophyteplant dendrobine endophyteplant dendrobine endophyteplant dendrobine endophyteplant dendrobine endophyte","fileCount":"99","fileSizeKB":"5604165","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"bacteria ;dendrobine ","instrument":"Q excutive orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"endophyte bacteria ","pi":[{"name":"diaorao","email":"diaodiao19971126@sina.com","institution":"CAAS","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b9c0c2ce7c5a4bb48428aa376c567040","id":"2036"}, {"dataset":"MSV000095606","datasetNum":"95606","title":"GNPS - 20240814 HNRC drug microbial culture co-migration","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723681022000","created":"Aug. 14, 2024, 5:17 PM","description":"Co-migration \/ spiking experiment to confirm the retention time of drug analogs detected in HNRC fecal samples with those in microbial cultures","fileCount":"66","fileSizeKB":"4056907","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Q Exactive","modification":"NA","keywords":"NA","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ff134e1302354ff7a02a69483e6886d4","id":"2037"}, {"dataset":"MSV000095605","datasetNum":"95605","title":"GNPS_toxoplasma_mouse_11(organs,contents)_positive","user":"cmiddleton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723672346000","created":"Aug. 14, 2024, 2:52 PM","description":"Metabolites (aqueous & organic) were extracted from mouse tissues and tissues' contents (SI duodenum, SI jejunum, SI ileum, cecum, large intestine, small intestine, contents, cecum contents, large intestine contents, heart, liver, and quad) and were run by LC-MS, C8 in positive mode. ","fileCount":"1578","fileSizeKB":"102423407","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Toxoplasma gondii (NCBITaxon:5811)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Toxoplasma gondii, mouse, SI duodenum, SI jejunum, SI ileum, cecum, large intestine, small intestine, contents, cecum contents, large intestine contents, heart, liver, quad, microbiome ","pi":[{"name":"Laura-Isobel McCall","email":"lmccall@sdsu.edu","institution":"San Diego State University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"350f289fa67e4d2da7ca3b5fbaec1f5d","id":"2038"}, {"dataset":"MSV000095604","datasetNum":"95604","title":"Enhanced sample multiplexing-based targeted proteomics with intelligent data acquisition","user":"qingyu0126","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723669379000","created":"Aug. 14, 2024, 2:02 PM","description":"Targeted proteomics has been playing an increasingly important role in hypothesis-driven protein research and clinical bi-omarker discovery. We have previously created a workflow, Tomahto, to enable real-time targeted pathway proteomics assays using two-dimensional multiplexing technology. Coupled with the TMT 11-plex reagent, hundreds of proteins of in-terest from up to 11 samples can be targeted and accurately quantified in a single-shot experiment with remarkable sensi-tive. However, room remains to further improve sensitivity, accuracy, and throughput, especially for targeted studies de-manding a high peptide-level success rate. Here, bearing in mind the goal to improve peptide-level targeting, we introduce several new functionalities in Tomahto, featuring integration of gas-phase fractionation using the FAIMS device, an ac-companying software program (TomahtoPrimer) to customize fragmentation for each peptide target, and support for higher multiplexing capacity with the latest TMTpro18-plex reagent. 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Human embryonic stem cells (hESCs) serve as a valuable in vitro model for studying early human developmental processes due to their ability to differentiate into all three germ layers. Here, we present a comprehensive multi-omics dataset generated by differentiating hESCs into cardiomyocytes via the mesodermal lineage, collecting samples at 10 distinct time points. We measured mRNA levels by mRNA sequencing (mRNA-seq), translation levels by ribosome profiling (Ribo-seq), and protein levels by quantitative mass spectrometry. Technical validation confirmed high quality and reproducibility across all datasets, with strong correlations between replicates. This extensive dataset provides critical insights into the complex regulatory mechanisms of cardiomyocyte differentiation and serves as a valuable resource for the research community, aiding in the exploration of mammalian development and gene regulation.","fileCount":"24","fileSizeKB":"51488313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hESC differentiation, DIA, Gene expression","pi":[{"name":"Marko Jovanovic","email":"mj2794@columbia.edu","institution":"Columbia University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"48228e238f2c4024a8613d982b902c81","id":"2044"}, {"dataset":"MSV000095594","datasetNum":"95594","title":"LC-MS data of trypsin-digested human serum albumin with and without ester substrates (2-naphthyl acetate and p-nitrophenyl acetate) for different incubation times (45 minutes and 24 hours).","user":"deepakk1812","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723616544000","created":"Aug. 13, 2024, 11:22 PM","description":"Project description\nTo confirm the interaction or acetylation pattern of the human serum albumin (HSA) with ester substrates (2 naphthyl acetate and p nitrophenyl acetate), the LCMS study was carried out. 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When successful, the ICB response can be potent; however, half of patients fail to respond. ICB responsiveness is impacted by the harsh solid tumor microenvironment (TME), which is characterized by metabolic stress. The TME impacts tumor antigenicity, with ICB-responsive melanomas exhibiting increased major histocompatibility complex class I (MHC-I) expression. Further investigation of tumor immunogenicity in the context of the TME may improve cellular therapies. Here, we define and characterize an epigenetic mechanism regulating melanoma antigen presentation driven by prolonged metabolic stress. Murine and human melanoma cell lines were cultured under prolonged metabolic stress, forcing cells to adapt to the absence of glucose. Melanoma cells adapted to the absence of glucose have IFN-gamma-independent increases in MHC-I and an increased sensitivity to T cell-mediated killing. Proteomic analysis revealed dysregulation of histone epigenetic modifiers under prolonged metabolic stress, specifically loss of histone methyltransferase EZH2 (Enhancer of Zeste Homolog 2). EZH2 directly silences gene transcription via catalyzing H3K27me3. Following metabolic adaptation, ChIP-sequencing and ChIP-PCR revealed H3K27me3 loss at genes specific to MHC-I antigen presentation. Prolonged metabolic stress in melanoma cells blunt EZH2 levels and H3K27me3 levels at promoters of genes regulating MHC-I presentation, resulting in elevated MHC-I antigenicity and increased CD8+ T cell killing. This demonstrates potential for EZH2 abundance and mutational status as a prognostic indicators of ICB-responsiveness in metastatic melanoma and supports EZH2 inhibition as adjuvant for immunotherapies","fileCount":"44","fileSizeKB":"19286849","spectra":"0","psms":"128726","peptides":"65335","variants":"86805","proteins":"10385","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"melanoma;metabolic stress;EZH2;immune checkpoint","pi":[{"name":"Brian Koss","email":"BSKoss@uams.edu","institution":"University of Arkansas for Medical Sciences","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD054843","task":"90f6b07a5d12469d86b280208bc005a0","id":"2048"}, {"dataset":"MSV000095588","datasetNum":"95588","title":"GNPS - Dilution series experiment of native and 13C-labelled Remus wheat ear extracts","user":"chrmaisl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723540006000","created":"Aug. 13, 2024, 2:06 AM","description":"Data for Publication \"Accuracy and linearity of relative and comparative quantification in untargeted metabolomics\" of Christina Maisl, Rainer Schuhmacher and Christoph Bueschl","fileCount":"337","fileSizeKB":"13882409","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Wheat Cultivar Remus","instrument":"Orbitrap Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"wheat;plant metabolomics;dilution series","pi":[{"name":"Rainer Schuhmacher","email":"rainer.schuhmacher@boku.ac.at","institution":"University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cc86779c6eb74736acb91024627fcffc","id":"2049"}, {"dataset":"MSV000095587","datasetNum":"95587","title":"An Automated High-throughput Affinity Capture-Mass Spectrometry Platform with Data-Independent Acquisition","user":"huijing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723517619000","created":"Aug. 12, 2024, 7:53 PM","description":"Affinity capture (AC) combined with mass spectrometry (MS)-based proteomics is highly utilized throughout the drug discovery pipeline to determine small molecule target selectivity and engagement. However, the tedious sample preparation steps and time-consuming MS acquisition process has limited its use in high-throughput format. Here, we report an automated workflow employing biotinylated probes and streptavidin magnetic beads for small molecule target enrichment in 96-well plate format, ending with direct sampling from EvoSep Solid Phase Extraction tips for liquid chromatography (LC)-tandem mass spectrometry (MS\/MS) analysis. The streamlined process significantly reduced both overall and hands-on time needed for sample preparation. Additionally, we developed a data-independent acquisition-mass spectrometry (DIA-MS) method to establish an efficient label-free quantitative chemical proteomic kinome profiling workflow. DIA-MS yielded coverage of ~380 kinases, a >60% increase compared to using a data-dependent acquisition (DDA)-MS method and provided reproducible target profiling of the kinase inhibitor dasatinib. We further showcased the applicability of this AC-MS workflow for assessing the selectivity of two clinical-stage CDK9 inhibitors against ~250 probe-enriched kinases. Our study here provides a roadmap for efficient target engagement and selectivity profiling in native cell or tissue lysates using AC-MS. 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Here, for the first time, we present an on-filter in-cell (OFIC) processing approach, which can digest C. elegans proteins directly in the cells of the organism after methanol fixation. With OFIC processing and single-shot LCMS analysis, we identified over 9,400 proteins from a sample of only 200 worms, the largest C. elegans proteome reported to date that did not require fractionation or enrichment. We systematically evaluated the performance of the OFIC approach by comparing it with conventional lysis-based methods. Our data suggest equivalent and unbiased performance of OFIC processing for C. elegans proteome identification and quantitation. We further evaluated the OFIC approach with even lower input samples, then used this method to determine how the proteome is impacted by loss of superoxide dismutase sod-1, the ortholog of human SOD-1, a gene associated with amyotrophic lateral sclerosis (ALS). Analysis of 8,800 proteins from only 50 worms as the initial input showed that loss of sod-1 affects the abundance of proteins required for stress response, ribosome biogenesis, and metabolism. In conclusion, our streamlined OFIC approach, which can be broadly applied to other systems, minimizes sample loss while offering the simplest workflow reported to date for C. elegans proteomics analysis.","fileCount":"25","fileSizeKB":"44034346","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Quantitative proteomics;On-filter in-cell (OFIC) digestion;E4technology;Caenorhabditis elegans;SOD1;superoxide dismutase type 1","pi":[{"name":"Yanbao Yu","email":"yybyu@udel.edu","institution":"Department of Chemistry and Biochemistry, University of Delaware, Newark, DE","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bbdb8a0f13eb47139711f32dab88d562","id":"2051"}, {"dataset":"MSV000095583","datasetNum":"95583","title":"Conformational variants of I-Ak MHC class II molecules carry distinct immunopeptidomes","user":"padmananaware","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723500495000","created":"Aug. 12, 2024, 3:08 PM","description":"The immunnopeptidomes of M1-paired vs. total I-Ak class II molecules isolated from murine B cells","fileCount":"26","fileSizeKB":"3140962","spectra":"0","psms":"19609","peptides":"3044","variants":"3951","proteins":"1090","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"I-Ak immunopeptidome","pi":[{"name":"Lawrence J. 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We observed elevated ATF6 transcriptional activity in several cancers including colorectal carcinoma (CRC). Genetic silencing or small molecule inhibition of ATF6 blocked cell cycle progression and reduced viability of several human CRC cell lines in vitro and disrupted tumor progression in vivo. Unexpectedly, ATF6 interference also disabled Myc and Wnt signaling and reduced stemness. ATF6 inhibition attenuated growth of organoids derived from malignant but not normal human intestinal tissue, reducing Wnt-pathway activity and driving cellular differentiation. Wnt-surrogate agonism rescued the growth inhibitory phenotype of ATF6 interference. Our findings identify ATF6 as an unexpected facilitator of oncogenic Wnt signaling in CRC.","fileCount":"31","fileSizeKB":"10349173","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"Fixed Mod: C (+57.0215), K (+304.2071), peptide N-term (+304.2071);Varibale Mod: M (+15.994), Y (+304.2071)","keywords":"ATF6, IRE1, unfolded protein response, Wnt signaling pathway","pi":[{"name":"Avi Ashkenazi","email":"aa@gene.com","institution":"Genentech, Inc.","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7234bdeaf654444caa72a6a23c9c5d67","id":"2053"}, {"dataset":"MSV000095580","datasetNum":"95580","title":"mutant p53-interacting proteins analyzed by LC-MS\/MS","user":"haiyanzheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723490580000","created":"Aug. 12, 2024, 12:23 PM","description":"p53-\/- HCT116 cells transduced with the control empty vector or vectors expressing wtp53 or R175H mutp53 were employed for co-IP followed by LC-MS\/MS analysis. The potential wtp53 or R175H mutp53-interacting proteins are listed.","fileCount":"4","fileSizeKB":"3617133","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"p53;mutant p53","pi":[{"name":"Zhaohui Feng","email":"fengzh@cinj.rutgers.edu","institution":"Rutgers Cancer Institute of New Jersey","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c8ca7b4ba93648c3abef80e1a369a4b9","id":"2054"}, {"dataset":"MSV000095579","datasetNum":"95579","title":"In Vitro Exposures of A549, J774A.1 Cells to SiO2, TiO2 Nanoforms and Related Cellular and Molecular Level Effects: Application of Proteomics","user":"srphanse","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723489054000","created":"Aug. 12, 2024, 11:57 AM","description":"There is emerging interest in using proteomic data for environmental health-risk assessments. Meanwhile, due to attractive physicochemical properties, production and use of engineered nanomaterials (ENMs) are expanding with potential for exposure, thus necessitating toxicity information on these materials for human health risk analysis, where proteomic data can be informative. Here, cells (A549 human lung epithelial, J774 mouse monocyte\/macrophage) were exposed to ENMs (nanoforms of SiO2, TiO2) of different sizes, surface chemistries (dose:0-100 ug\/cm2, 24 h) for in vitro toxicity data. Cellular cytotoxicity (CTB, ATP, LDH), oxidative stress and proteomic analysis (MS-, antibody-based) were conducted post-nanoparticle (NP) exposures to determine cytotoxic potencies and identify molecular-level effects. Dose-, nanoform-, cell type-specific cytotoxicity changes were seen with both nanoSiO2 and nanoTiO2 exposures. Size, agglomeration, surface groups and metal impurities appeared to be cytotoxicity determinants. Proteomic data identified some common enriched mechanistic pathways relevant to phagocytosis, cell-shape changes, apoptosis, and inflammatory processes for nanoSiO2, nanoTiO2 exposed J774 cells. A549 cells exhibited pathway changes relevant to cell metabolism, endocytosis and inflammatory processes post-NP exposures. Concordance was seen between, cytotoxicity responses, notably cellular ATP, critical for cell viability, cellular oxidative stress and affected cellular pathways. These findings demonstrate the utility of proteomics in toxicology, warranting further exploration. ","fileCount":"251","fileSizeKB":"32023432","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"LTQ Orbitrap","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"NanoSiO2, NanoTiO2, In vitro toxicity, Nanoforms, Oxidative Stress, Proteomics, Cellular pathways","pi":[{"name":"Dr. Premkumari Kumarathasan","email":"premkumari.kumarathasan@hc-sc.gc.ca","institution":"Environmental Health Science and Research Bureau, HECSB, Health Canada, Ottawa, ON","country":"Canada"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"852edc262f924c649a332bfaa5d94e66","id":"2055"}, {"dataset":"MSV000095578","datasetNum":"95578","title":"Development and qualification of a dendritic cell internalization assay contributing to the immunogenicity risk evaluation of biotherapeutics","user":"ducreta","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723488704000","created":"Aug. 12, 2024, 11:51 AM","description":"The appended raw files, csv files and other documents were deposited into the public domain in support for the publication \"Development and characterization of a dendritic cell internalization assay contributing to the immunogenicity risk evaluation of biotherapeutics\" by Michel Siegel, Aman Padamsey, Anna-Lena Bolender, Patrick Hargreaves, Axel Ducret, Johannes Fraidling, Katharina Hartmann, Cary M. Looney, Olivier Rohr, Tim Hickling, Thomas Kraft, Celine Marban-Doran.\nThe abstract reads as follows: Assessing immunogenicity risks during the development of biotherapeutics is crucial. Given the complexity of immunogenicity - influenced by myriad biological, immunological, and patient-specific factors - Individual risk assessments are poorly predictive, necessitating a holistic approach to immunogenicity risk assessment. Anti-drug antibody production starts with the internalization of drugs by antigen presenting cells such as dendritic cells, which present drug-derived peptides to CD4+ T cells as peptide-MHC-II complexes. Assessing dendritic cell function is common in preclinical immunogenicity risk assessments, including presentation of potential T cell epitopes using the MAPPs assay. However, other aspects of dendritic cell biology are often overlooked. To better understand the dendritic cell contribution to immunogenicity, we developed two flow cytometry-based assays: the dendritic cell internalization assay and the dendritic cell activation assay. Our assay addresses two issues with existing methods for measuring internalization into antigen presenting cells; lack of specificity for the cellular compartment of internalization or the recycling of internalized antibodies, and the increased risk of aggregation, when using a large payload for the detection of antibodies, that would lead to activation of irrelevant scavenger receptors in the context of dendritic cell internalization. We also developed a DC activation assay, improving on various aspects of its relevance for immunogenicity risk assessment compared to previously published protocols. Additionally, we identified DC-SIGN (CD209) and CD80 as crucial for understanding dendritic cell activation mechanisms leading to immunogenicity. To evaluate the performance of these two assays, we used a set of marketed therapeutic antibodies. The dendritic cell internalization assay revealed differences in internalization rates for marketed therapeutic antibodies, even those targeting the same antigen (e.g. PCSK9-targeting antibodies: bococizumab, evolocumab and alirocumab or TNF-targeting antibodies: adalimumab and infliximab), potentially accounting for differential immunogenicity liabilities. The DC activation assay also showed different patterns of DC activation between bococizumab, which rapidly accumulates within the lysosomes, and the other PCSK9-targeting antibodies (evolocumab and alirocumab), giving new insights into specific immunogenicity profiles. Overall, this study provides valuable information for future risk assessments of therapeutic antibodies in development. doi: 10.3389\/fimmu.2024.1406804\nThe data deposited here were used to generate the supplementary figure 3.","fileCount":"86","fileSizeKB":"56479554","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"dendritic cell;CD internalization assay;MAPPs;immunogenicity;ATR-107;Ixekizumab;Bevacizumab;Adalimumab;Bococizumab;Briakinumab","pi":[{"name":"Axel Ducret","email":"axel.ducret@roche.com","institution":"Roche Innovation Center Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054823","task":"2f27fd2808ae4f07bda4c4c600f7f28a","id":"2056"}, {"dataset":"MSV000095576","datasetNum":"95576","title":"Raphe and Ventrolateral Medulla Proteomics in Sudden Unexplained Death in Childhood with Febrile Seizure History","user":"KanshinED1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723488667000","created":"Aug. 12, 2024, 11:51 AM","description":"Sudden unexplained death in childhood (SUDC) is death of a child 12 months old that is unexplained after autopsy and detailed analyses. Among SUDC cases, 28.8% have febrile seizure (FS) history, versus 2-5% in the general population. SUDC cases share features with sudden unexpected death in epilepsy (SUDEP) and sudden infant death syndrome (SIDS), in which brainstem autonomic dysfunction is implicated. To understand whether brainstem protein changes are associated with FS history in SUDC, we performed label-free quantitative mass spectrometry on microdissected midbrain dorsal raphe, medullary raphe, and the ventrolateral medulla (n=8 SUDC-noFS, n=11 SUDC-FS). Differential expression analysis at p<0.05 identified 178 altered proteins in dorsal raphe, 344 in medullary raphe, and 100 in the ventrolateral medulla. These proteins were most significantly associated with increased eukaryotic translation initiation (p=3.09x10-7, z=1.00), eukaryotic translation elongation (p=6.31x10-49, z=6.01), and coagulation system (p=1.32x10-5, z=1.00), respectively. The medullary raphe had the strongest enrichment for altered signaling pathways, including with comparisons to three other brain regions previously analyzed (frontal cortex, hippocampal dentate gyrus, cornu ammonus). Histological analyses of serotonin receptors identified 2.1-fold increased 5HT2A in the medullary raphe of SUDC-FS (p= 0.025). Weighted gene correlation network analysis (WGCNA) of case history indicated that longer FS history duration significantly correlated with protein levels in the medullary raphe and ventrolateral medulla; the most significant gene ontology biological processes were decreased cellular respiration (p=9.8x10-5, corr=-0.80) in medullary raphe and synaptic vesicle cycle (p=1.60x10-7, corr=-0.90) in the ventrolateral medulla. Overall, FS in SUDC was associated with more protein differences in the medullary raphe and was related to increased translation-related signaling pathways. Our study informs on SUDC pathogenesis and the potential development of prognostic biomarkers and preventive therapeutic strategies.","fileCount":"65","fileSizeKB":"270157509","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:736 - \\\"Dithiothreitol (DTT) on Cys.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\"","keywords":"febrile seizures;SUDC;Proteomics;FFPE;LCM","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyumc.org","institution":"NYU School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"bb885f59b75d49e7a49e661903642160","id":"2057"}, {"dataset":"MSV000095575","datasetNum":"95575","title":"Prenylation in Th1 cells assessed by click chemistry","user":"JanaKoch","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723488662000","created":"Aug. 12, 2024, 11:51 AM","description":"T helper cell activation is highly regulated to ensure proper immune responses while avoiding autoimmune reactions. Cell functions are determined by regulation of various levels of gene expression including posttranslational modifications of proteins. Protein prenylation is a posttranslational modification, which can be influenced by statin treatment and was shown to play a role in the differentiation and activation of various T cell populations, including Th1 cells. However, it is largely unknown which proteins are prenylated in Th1 cells and what the effect of statin treatment on protein prenylation is in this context. Here, using mass spectrometry, we show the comprehensive identification of prenylated proteins in human Th1 cells including changes during their activation, before analyzing the effect of statin treatment on this process. This approach additionally uncovered the prenylation of proteins, not yet known to be prenylated, including so far unknown motifs. These data provide valuable insights into novel aspects of protein prenylation in Th1 cell activation and deepen our understanding of the intended or unintended effects of statin treatment on the human immune system.","fileCount":"198","fileSizeKB":"335069790","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Th1 cells;Prenylation;Geranylgeranylation;Farnesylation;Click-iT Enrichment;Statin","pi":[{"name":"Katja Baerenfaller","email":"katja.baerenfaller@siaf.uzh.ch","institution":"Swiss Institute of Allergy and Asthma Research","country":"Switzerland"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ceb8150379a446e68dcecd851dadb374","id":"2058"}, {"dataset":"MSV000095572","datasetNum":"95572","title":"Inhibition of Cbl-b restores effector functions of human intratumoral NK cells","user":"katarzynabuczak","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723488636000","created":"Aug. 12, 2024, 11:50 AM","description":"Background: T cell-based immunotherapies including immune checkpoint blockade (ICB) and chimeric antigen receptor (CAR) T cells can induce durable responses in cancer patients. However, clinical efficacy is limited due to the ability of cancer cells to evade immune surveillance. While T cells have been the primary focus of immunotherapy, recent research has highlighted the importance of Natural Killer (NK) cells in directly recognizing and eliminating tumor cells and playing a key role in the set-up of an effective adaptive immune response. The remarkable potential of NK cells for cancer immunotherapy is demonstrated by their ability to broadly identify stressed cells, irrespective of the presence of neoantigens, and their ability to fight tumors that have lost their Major Histocompatibility Complex class I (MHC I) expression due to acquired resistance mechanisms.\nHowever, like T cells, NK cells can become dysfunctional within the tumor microenvironment. Strategies to enhance and reinvigorate NK cell activity hold potential for bolstering cancer immunotherapy. \nMethod: In this study, we conducted a high-throughput screen to identify molecules that could enhance primary human NK cell function. After compound validation, we investigated the effect of the top performing compound on dysfunctional NK cells that were generated by a newly developed in vitro platform. Functional activity of NK cells was investigated utilizing compounds alone and in combination with checkpoint inhibitor blockade. The findings were validated on patient-derived intratumoral dysfunctional NK cells from different cancer types.\nResults: The screening approach led to the identification of a Cbl-b inhibitor enhancing the activity of primary human NK cells. Furthermore, the Cbl-b inhibitor was able to reinvigorate the activity of in vitro generated and patient-derived dysfunctional NK cells. Finally, Cbl-b inhibition combined with TIGIT blockade further increased the cytotoxic potential and reinvigoration of both in vitro generated and patient-derived intratumoral dysfunctional NK cells.\nConclusion: These findings underscore the relevance of Cbl-b inhibition in overcoming NK cells dysfunctionality with the potential to complement existing immunotherapies and improve outcomes for cancer patients.\n","fileCount":"28","fileSizeKB":"33072461","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"qExactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"NK dysfunction;cancer immunotherapy;Cbl-b inhibitor;MHC I loss","pi":[{"name":"Alfred Zippelius","email":"alfred.zippelius@unibas.ch","institution":"University of Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD054820","task":"66eed5effff445aebe9cb7190e32cfdf","id":"2059"}, {"dataset":"MSV000095571","datasetNum":"95571","title":"Proteomic dataset of secretome derived from Placental mesenchymal stem cells","user":"kaka_HUANG","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723292798000","created":"Aug. 10, 2024, 5:26 AM","description":"The use of perinatal MSCs remains largely unexplored. Consequently, there is a significant gap in knowledge regarding the optimal selection of perinatal MSCs and their appropriate administration to maximize the benefits for DFU treatment. Moreover, there is a lack of direct comparison among different types of perinatal MSCs. In this study, we aimed to address these gaps by comparing the secretome profiles of MSCs derived from human umbilical cord (UC), chorionic villi (CV), and decidua basalis (DC) of the human placenta. We utilized mass spectrometry to analyze the protein components in the secretome derived from hUCMSCs, hCVMSCs, and hDCMSCs. Over 1000 secreted proteins were quantified by mass spectroscopy in secretome of MSCs, with 435 being commonly expressed.\n","fileCount":"21","fileSizeKB":"10197653","spectra":"199287","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mesenchymal stromal cells; Secretome; Placenta; Proteomics ","pi":[{"name":"Xiaohua Jiang, School of Biomedical Sciences, Faculty of Medicine","email":"xjiang@cuhk.edu.hk","institution":"The Chinese University of Hong Kong","country":"Hong Kong"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054775","task":"df292f00ce544e12ad8c3515a15908bc","id":"2060"}, {"dataset":"MSV000095570","datasetNum":"95570","title":"Integrated proteomics and machine learning approach reveals PYCR1 as a novel biomarker to predict prognosis of sinonasal squamous cell carcinoma","user":"watcharapong2024","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723265255000","created":"Aug. 9, 2024, 9:47 PM","description":"The LC-MS\/MS raw data (.mzxml) of nasal polyps and sinonasal squamous cell carcinoma patients.The study utilized 90 datasets from 30 individual nasal tissue samples across three independent experiments (Nasal polyps (NP): 48 datasets, SNSCC: 42 datasets).","fileCount":"91","fileSizeKB":"7691467","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Bruker Daltonics instrument model","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Sinonasal squamous cell carcinoma;Nasal polyps","pi":[{"name":"Watcharapong panthong","email":"watchara.p@kkumail.com","institution":"Department of Microbiology, Faculty of Medicine, Khon Kaen University","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4fa792294e594749ab1624b2652a91db","id":"2061"}, {"dataset":"MSV000095568","datasetNum":"95568","title":"Scnn1b transgenic mice: BALF exosome proteomics","user":"maomaobio_316","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723247136000","created":"Aug. 9, 2024, 4:45 PM","description":"We detected BALF exosome-derived proteins from adult Scnn1b transgenic (Scnn1b-Tg+) and wild type (WT) mice. A total of 3144 and 3119 proteins were identified in BALF exosomes from Scnn1b-Tg+ and WT mice, respectively. ","fileCount":"19","fileSizeKB":"1624210","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"no","keywords":"Exosome, Proteomics, Airspace, Scnn1b-Tg+ mice, Lung","pi":[{"name":"Yogesh Saini","email":"ysaini@ncsu.edu","institution":"North Carolina State University (NCSU)","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD054769","task":"5977ebc94a9840bb8e52dda63b8685cf","id":"2062"}, {"dataset":"MSV000095567","datasetNum":"95567","title":"GNPS - Plasma CHARTER Biopsychosocial Phenotypes (BPSP) R01 ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723227234000","created":"Aug. 9, 2024, 11:13 AM","description":"600 Samples of plasma from HNRC for CHARTER Biopsychosocial Phenotypes (BPSP) R01 project. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA). [doi:10.25345\/C5N29PJ4W] [dataset license: CC0 1.0 Universal (CC0 1.0)]","fileCount":"1663","fileSizeKB":"151591263","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plasma;BSPS","pi":[{"name":"Robert K. Heaton","email":"rheaton@ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"35dce80b28c64b88a822c15c779d2336","id":"2063"}, {"dataset":"MSV000095564","datasetNum":"95564","title":"Endophytic fungi of Calea pinnatifida","user":"BiaBarna","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723206464000","created":"Aug. 9, 2024, 5:27 AM","description":"Crude extract of endophytic fungal isolates from Calea pinnatifida","fileCount":"8","fileSizeKB":"3207112","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Colletotrichum karsti (NCBITaxon:1095194);Colletotrichum siamense (NCBITaxon:690259);Hypomontagnella barbarensis (NCBITaxon:2487001);Neopestalotiopsis clavispora (NCBITaxon:289240);Nigrospora sacchari-officinarum;Annulohypoxylon moriforme (NCBITaxon:326622)","instrument":"Q-ToF Maxis 3G","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Calea pinnatifida;Endophytic fungi;Secondary metabolism","pi":[{"name":"Bianca Barna Fernandes","email":"bianca.barna@unifesp.br","institution":"UNIFESP","country":"Diadema - SP"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"529e5671628746fe9a11baa5b4ecc53b","id":"2064"}, {"dataset":"MSV000095561","datasetNum":"95561","title":"Proteomic Characterization of NEDD4 in Gastric Cancer","user":"dlfzh1co","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723185569000","created":"Aug. 8, 2024, 11:39 PM","description":"Identification of Downstream Proteins of NEDD4 and Mechanistic Study through Proteomics Analysis in Gastric Cancer","fileCount":"25","fileSizeKB":"237544090","spectra":"1191467","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"NEDD4;gastric cancer","pi":[{"name":"Jae-Young Kim","email":"jaeyoungkim@cnu.ac.kr","institution":"Chungnam National University, GRAST","country":"Republic of korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"880e2efa57f1424682c11d344a916733","id":"2065"}, {"dataset":"MSV000095560","datasetNum":"95560","title":"Lipid Supplements Protect Dilated Cardiomyopathy","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723179760000","created":"Aug. 8, 2024, 10:02 PM","description":"Lipid (Plasmalogen) levels can be modulated via a dietary supplement called alkylglycerols (AG) which has demonstrated benefits in some disease settings. However, its therapeutic potential in cardiomyopathy remains unknown. This study explored an optimized AG supplement in restoring plasmalogen levels and attenuate cardiac dysfunction\/pathology. Here, we placed a cardiac-specific transgenic cardiomyopathy mouse model, with cardiac function and molecular landscape assessed. AG supplementation increased total plasmalogens in DCM hearts and attenuated lung congestion of both sexes, but only prevented cardiac dysfunction in males. This was associated with cardiac and renal enlargement, a more favorable pro-cardiac gene expression profile, and a trend for lower cardiac fibrosis. By lipidomics, specific d18:1 ceramide species associated with cardiac pathology were lower in the DCM hearts from mice on the AG diet, and tetra-linoleoyl cardiolipin, a lipid crucial for mitochondria function was restored with AG supplementation. Proteomic analysis of hearts from male DCM mice receiving AG supplementation revealed enrichment in mitochondrial protein network, as well as upregulation of extracellular matrix binding proteins associated with cardiac regeneration. Here we highlight that AG supplementation restored plasmalogens in DCM hearts, but showed greater therapeutic potential in males than females","fileCount":"132","fileSizeKB":"114606395","spectra":"4821782","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"heart","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"be73406454924134a62d5bf36a883672","id":"2066"}, {"dataset":"MSV000095559","datasetNum":"95559","title":"Label-free global proteome profiling of European American and African American bladder tumor patients.","user":"syjung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723161610000","created":"Aug. 8, 2024, 5:00 PM","description":"Bladder cancer (BLCA) mortality is higher in African American (AA) patients compared to their European American (EA) counterparts, but the molecular mechanism underlying differences are unknown. . Thus, we performed proteomics analysis of AA and EA BLCA and identified higher mitochondrial OXPHOS specifically through complex I activation in AA BLCA.","fileCount":"75","fileSizeKB":"44313510","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"bladder cancer","pi":[{"name":"Sung Yun Jung","email":"syjung@bcm.edu","institution":"Baylor College of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054731","task":"c5b4599d5ed14c6f93dfaedb2d066287","id":"2067"}, {"dataset":"MSV000095558","datasetNum":"95558","title":"In vivo and in vitro analysis of the role of the Prc protease in inducing mucoidy in Pseudomonas aeruginosa","user":"Trixi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723145179000","created":"Aug. 8, 2024, 12:26 PM","description":"In Pseudomonas aeruginosa,alginate biosynthesis gene expression is inhibited by the transmembrane anti-sigma factor MucA, which sequesters the AlgU sigma factor. Cell envelope stress initiates cleavage of the MucA periplasmic domain by site-1 protease AlgW, followed by further MucA degradation to release AlgU. However, after colonizing the lungs of people with cystic fibrosis,P. aeruginosa converts to a mucoid form that produces alginate constitutively. Mucoid isolates often have mucA mutations, with the most common being mucA22, which truncates the periplasmic domain. MucA22 is degraded constitutively, and genetic studies suggested that the Prc protease is responsible. Some studies also suggested that Prc contributes to induction in strains with wild type MucA, whereas others suggested the opposite. However, missing from all previous studies is a demonstration that Prc cleaves any protein directly, which leaves open the possibility that the effect of a prc null mutation is indirect. To address the ambiguities and shortfalls, we reevaluated the roles of AlgW and Prc as MucA and MucA22 site-1 proteases. In vivo analyses using three different assays, and two different inducing conditions, all suggested that AlgW is the only site-1 protease for wild type MucA in any condition. In contrast, genetics suggested that AlgW or Prc act as MucA22 site-1 proteases in inducing conditions, whereas Prc is the only MucA22 site-1 protease in non-inducing conditions. For the first time, we also show that Prc is unable to degrade the periplasmic domain of wild type MucA, but does degrade the mutated periplasmic domain of MucA22 directly. The mass spectrometric data in support of some of these findings are included here. 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Here we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification, using a Thumpd1 knockout mouse model. We find that loss of Thumpd1-dependent tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling, and activation of eIF2-alpha phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Remarkably, concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality, revealing a critical genetic interaction. Our findings demonstrate that a modification restricted to a single position within type II cytosolic tRNAs can regulate ribosome-mediated signaling in mammalian organisms. Insights into how tRNA modifications shape phenotype and signaling in response to stress provide a foundation for novel strategies for therapeutic intervention and translational control.","fileCount":"12","fileSizeKB":"8508331","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Thumpd1, tRNA, N4-acetylcytidine ","pi":[{"name":"Jordan Meier","email":"jordan.meier@nih.gov","institution":"National Cancer Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ee9bba5885ba4ef4b8e54bbd8ad4d04a","id":"2069"}, {"dataset":"MSV000095554","datasetNum":"95554","title":"Fenbendazole Met ID_in vitro_cross-species_FBMN","user":"jyoungheun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723106742000","created":"Aug. 8, 2024, 1:45 AM","description":"Fenbendazole Met ID by an integrative approach using feature-based molecular networking of cross-species in vitro liver microsomal and hepatocellular incubation.","fileCount":"18","fileSizeKB":"319044","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Macaca fascicularis (NCBITaxon:9541);Canis lupus familiaris (NCBITaxon:9615);CD1 mouse","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fenbendazole;comparative metabolism;liver microsomes;hepatocytes;feature-based molecular networking","pi":[{"name":"Ju-Hyun Kim","email":"jhkim@yu.ac.kr","institution":"College of Pharmacy, Yeungnam University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f421e3301e554a5a8c24242c77277213","id":"2070"}, {"dataset":"MSV000095551","datasetNum":"95551","title":"GNPS - MetaPhenotype: A transferable meta learning model for single-cell mass spectrometry-based cell phenotype prediction using limited number of cells","user":"greentea2411","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723082983000","created":"Aug. 7, 2024, 7:09 PM","description":"MetaPhenotype: A transferable meta learning model for single-cell mass spectrometry-based cell phenotype prediction using limited number of cells","fileCount":"95","fileSizeKB":"11140278","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap XL","modification":"NA","keywords":"primary melanoma;metastatic melanoma;untargeted metabolomics;single cell;machine learning","pi":[{"name":"Yihan Shao","email":"yihan.shao@ou.edu","institution":"University of Oklahoma","country":"USA"},{"name":"Zhibo Yang","email":"zhibo.yang@ou.edu","institution":"University of Oklahoma","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cfa324c17a664693b0cc253ddf782599","id":"2071"}, {"dataset":"MSV000095550","datasetNum":"95550","title":"GNPS - 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Protease inhibitors were added to the samples and the protein concentration was defined with Bradford Assay. Concentrated samples were processed with the filter aided sample preparation (FASP) method with minor modifications. Briefly, sample volume corresponding to 200 ug of total protein content was mixed with lysis buffer (0.1 M Tris HCl pH 7.6, supplemented with 4% SDS and 0.1 M DTE) and buffer exchange was performed in Amicon Ultra Centrifugal filter devices (0.5 mL, 30 kDa MWCO; Merck Millipore) at 14,000 rcf for 15 min at RT. Each sample was diluted with urea buffer (8 M urea in 0.1 M Tris HCl pH 8.5) and centrifuged.The concentrate was diluted again with urea buffer and centrifugation was repeated. Alkylation of proteins was performed with 0.05 M iodoacetamide in urea buffer for 20 min in the dark, RT, followed by a centrifugation at 14,000 rcf for 10 min at RT. Additional series of washes were conducted with urea buffer (2 times) and ammonium bicarbonate buffer (50 mM NH4 HCO3 pH 8.5, 2 times). Tryptic digestion was performed overnight at RT in the dark, using a trypsin to protein ratio of 1:100. Peptides were eluted by centrifugation at 14,000 rcf for 10 min, lyophilized and stored at -80C until further use.\r\n\r\nLC-MS\/MS analysis:\r\n\r\nSamples were resuspended in 200 uL mobile phase A (0.1% Formic acid ). A 5 uL volume was injected into a Dionex Ultimate 3000 RSLS nano flow system (Dionex, Camberly, UK) configured with a Dionex 0.1 x 20 mm, 5 um, 100 A C18 nano trap column with a flow rate of 5 uL \/ min. The analytical column was an Acclaim PepMap C18 nano column 75 um x 50 cm, 2 um 100 A with a flow rate of 300 nL \/ min. The trap and analytical column were maintained at 35C. Mobile phase B was 100% Acetonitrile:0.1% Formic acid. The column was washed and re- equilibrated prior to each sample injection. The eluent was ionized using a Proxeon nano spray ESI source operating in positive ion mode. For mass spectrometry analysis, a Q Exactive Orbitrap (Thermo Finnigan, Bremen, Germany) was operated in MS\/MS mode. The peptides were eluted under a 120 min gradient from 2% (B) to 80% (B). Gaseous phase transition of the separated peptides was achieved with positive ion electrospray ionization applying a voltage of 2.5 kV. For every MS survey scan, the top 10 most abundant multiply charged precursor ions between m\/z ratio 300 and 2200 and intensity threshold 500 counts were selected with FT mass resolution of 70,000 and subjected to HCD fragmentation. Tandem mass spectra were acquired with FT resolution of 35,000. Normalized collision energy was set to 33 and already targeted precursors were dynamically excluded for further isolation and activation for 15 sec with 5 ppm mass tolerance.\r\n\r\nMS data processing:\r\n\r\nRaw files were analyzed with Proteome Discoverer 1.4 software package (Thermo Finnigan), using the Sequest search engine and the Uniprot mouse (Mus musculus) reviewed database, downloaded on November 22, 2017, including 16,935 entries. The search was performed using carbamidomethylation of cysteine as static and oxidation of methionine as dynamic modifications. Two missed cleavage sites, a precursor mass tolerance of 10 ppm and fragment mass tolerance of 0.05 Da were allowed. False discovery rate (FDR) validation was based on q value: target FDR (strict): 0.01, target FDR (relaxed): 0.05. Normalized serum protein concentrations were imported into R for statistical and quantification analysis. Proteins were considered differentially abundant at a cutoff of |FC| > 1.5, and significant at P < 0.05, as determined by unpaired two-tailed Students t-test. \r\n\r\naPDL1 raw files correspond to the treated animals.\r\nPBS raw files correspond to the respective control animals.","fileCount":"42","fileSizeKB":"18055683","spectra":"399524","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"QExactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PD-L1;immunotherapy;cancer;proteomics;bone marrow;inflammation","pi":[{"name":"Panayotis Verginis","email":"pverginis@bioacademy.gr","institution":"Laboratory of Immune Regulation and Tolerance, Division of Basic Sciences, Medical School, University of Crete, Heraklion","country":"Greece"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054676","task":"a07b1f6af94c4b5a80c945a40362d7b4","id":"2077"}, {"dataset":"MSV000095540","datasetNum":"95540","title":"GNPS - Bolnick Alaska Experimental Evolution (2024) - PRJ7","user":"marwa38","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723042866000","created":"Aug. 7, 2024, 8:01 AM","description":"Livers preserved in Ethanol from threespine stickleback (Gasterosteus aculeatus). Thirty per lake from 15 lakes in Alaska. Seven of the lakes are native populations, and eight of the lakes are experimentally introduced populations founded in 2019. Samples were collected by Dan Bolnick and colleagues in 2024. We are tracking evolution of stickleback as the newly founded populations adapt to their lake environments. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1218","fileSizeKB":"94376759","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gasterosteus aculeatus (NCBITaxon:69293)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MSCollaboratory;Alaska;lakes;Evolution","pi":[{"name":"Daniel Bolnick","email":"daniel.bolnick@uconn.edu","institution":"University of Connecticut","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fd3392aaf72949fe8a6334c6cc1a5c10","id":"2078"}, {"dataset":"MSV000095539","datasetNum":"95539","title":"lipidomics analysis for gut bacteria after pesticide exposure","user":"lichen_osu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723039724000","created":"Aug. 7, 2024, 7:08 AM","description":"raw data for lipidomics analysis in gut bacteria after pesticide exposure.","fileCount":"8569","fileSizeKB":"983049423","spectra":"16999342","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"huaman gut bacteria","instrument":"UPLC QE Orbitrap MS","modification":"LOG10","keywords":"lipidomics, pesticide, gut bacteria","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2d721bae5ad544a6aa7ee80cd5097025","id":"2079"}, {"dataset":"MSV000095538","datasetNum":"95538","title":"GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 12C\/13C dataset ","user":"JRapp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723035179000","created":"Aug. 7, 2024, 5:52 AM","description":"In this study, we developed a workflow to systematically and selectively induce increases in metabolites by knocking down enzymes with CRISPR interference (CRISPRi). Therefore, we created a sorted CRISPRi library targeting all 1,515 metabolic genes in the most recent genome-scale metabolic model of E. coli (iML15159). In a first step, we screened the metabolome of the CRISPRi library with a fast flow-injection mass spectrometry, which revealed strong and specific accumulation of 36% of the predicted metabolites in the iML1515 model. The accumulating metabolites were unique to certain knockdowns, especially those metabolites associated with the CRISPRi targeted-pathway. Therefore, we followed-up on accumulating metabolites that were directly associated to the CRISPRi target-gene (i.e. all reactants of the respective enzyme) and measured their fragmentation spectra and chromatographic retention times with LC-MS2. This resulted in experimental fragmentation spectra and chromatographic retention times of 111 metabolites. Three of these fragmentation spectra were verified by 13C labelling experiments.","fileCount":"22","fileSizeKB":"20374411","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"6546 Q-TOF LC\\\/MS (Agilent instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"E. coli;CRISPRi;LC-MS2 spectra;isotope labelling","pi":[{"name":"Prof. Hannes Link","email":"hannes.link@uni-tuebingen.de","institution":"University Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"77654b5651344403a3cc4bf71a305fa1","id":"2080"}, {"dataset":"MSV000095536","datasetNum":"95536","title":"GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 dataset ","user":"JRapp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1723030245000","created":"Aug. 7, 2024, 4:30 AM","description":"In this study, we developed a workflow to systematically and selectively induce increases in metabolites by knocking down enzymes with CRISPR interference (CRISPRi). 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The sample was separated using ultra high-performance liquid chromatography, performed on a Dionex Ultimate 3000 UPLC system (Thermo Fisher Scientific, Waltham, MA) using a 150 by 2.1 mm Kinetex C18 column with 1.7-mm particle size (Phenomenex, Aschaffenburg, Germany) column with a flow rate of 300 ml\/min. Gradient elution with water with 0.1% (vol\/vol) formic acid as eluent A and acetonitrile with 0.1% (vol\/vol) formic acid as eluent B was run as follows: 1% B for t = 0 min to t = 2 min, linear gradient from 1% B to 100% B from t = 2 min to t = 20 min, hold 100% B until t = 25 min, and linear gradient from 100% B to 1% B from t = 25 min to t = 30 min. 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Both incubation mode and the presence of antioxidants impact sugars and aromatic catabolism, as well as lipid composition of the fungal mycelia, and the analyses reveal biosynthetic pathways for the production of extracellular fatty acids and phenylpropanoids by these fungi.","fileCount":"246","fileSizeKB":"86599825","spectra":"0","psms":"2063484","peptides":"720860","variants":"846993","proteins":"50503","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gelatoporia subvermispora (NCBITaxon:42742);Trametes versicolor (NCBITaxon:5325)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"lignin;aromatic compounds;4-hydroxybenzoate;hydroxyquinol;multi-omics;systems biology","pi":[{"name":"Davinia Salvachua","email":"davinia.salvachua@nrel.gov","institution":"National Renewable Energy Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054613","task":"feaf0bfbf966466684bfe23c7d0c886f","id":"2091"}, {"dataset":"MSV000095515","datasetNum":"95515","title":"NAR-00644-Z-2024 RNA analysis by direct infusion","user":"yufeixiang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722697142000","created":"Aug. 3, 2024, 7:59 AM","description":"Structural insights into RNA cleavage by a novel family of bacterial RNases","fileCount":"5","fileSizeKB":"89607","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RNA;Cleavage;RNases","pi":[{"name":"Yi Shi","email":"wally.yis@gmail.com","institution":"Icahn School of Medicine at Mount Sinai","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5cf4177027354f97a623822332613e29","id":"2092"}, {"dataset":"MSV000095512","datasetNum":"95512","title":"GNPS - Sugarloaf Hill Fire Containment Soil Experiment","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722631553000","created":"Aug. 2, 2024, 1:45 PM","description":"Untargeted metabolomics data of organic extracts of soil recovered from Sugarloaf Hill in Riverside, CA, after a fire event that was contained through use of air-dropped flame retardant.","fileCount":"81","fileSizeKB":"9349575","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"unidentified soil organisms (NCBITaxon:44770)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Soil;Fire;Flame retardant","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8efb336de68446c8aa3c93e94bc00624","id":"2093"}, {"dataset":"MSV000095508","datasetNum":"95508","title":"Northern elephant seal juvenile plasma proteome response to repeated ACTH administration ","user":"mirounga","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722617595000","created":"Aug. 2, 2024, 9:53 AM","description":"Plasma proteome response to repeated ACTH administration in juvenile northern elephant seals. Five ul of EDTA plasma were denatured with 200 ul of 5 percent w\/v SDC and 5 mM TCEP in 50 mM AmBiC at 60C for 1 hour, followed by alkylation with 20 mM CAA for 30 minutes in the dark at room temp. Samples were diluted to 0.5 percent SDC and proteins were digested using trypsin at a 1 to 50 ug enzyme to protein ratio for 16 hours at 37C. TFA was added to a final concentration of 1.0 percent to precipitate SDC, which was removed by centrifugation and extraction of the supernatant. Digested peptides were lyophilized, resuspended in 0.1 percent TFA, and desalted using Pierce Peptide Desalting Spin Columns. Eluted peptides were lyophilized and resuspended in 0.1 percent FA in LC-MS grade water. \n\nThree injections were used for each sample. For each run, 5 uL of the sample (1 ug total) was loop injected onto a reversed-phase trap column (Acclaim PepMap 100 C18 LC column; 75 um i.d. x 2 cm, 3 um particle size, 100 A pore size, Thermo Fisher Scientific, USA) by a Dionex Ultimate 3000 autosampler. Peptides were eluted onto a reversed-phase analytical column set at 35C for HPLC (EASY-SprayTM C18 LC column; 75 um i.d. x 15 cm, 100 A, Thermo Fisher Scientific, USA). Solvent A was water and B was acetonitrile (ACN), respectively (both with 0.1 percent formic acid). During each chromatographic run, which lasted 140 min, flow rates were held at 300 nl\/min. 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","fileCount":"86","fileSizeKB":"159846585","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mirounga angustirostris (NCBITaxon:9716)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"plasma;stress;seal","pi":[{"name":"Jane Khudyakov","email":"jkhudyakov@pacific.edu","institution":"University of the Pacific","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054543","task":"d98aa7ee62a24909af3ae028c8fc623a","id":"2094"}, {"dataset":"MSV000095503","datasetNum":"95503","title":"The Glycolytic Metabolite Methylglyoxal Covalently Inactivates the NLRP3 Inflammasome.","user":"carrose73","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722551699000","created":"Aug. 1, 2024, 3:34 PM","description":"Mass Spectrometry data showing MICA crosslinking of NLRP3 Pyrin cysteines and arginines induced by methylglyoxal (MGO)","fileCount":"7","fileSizeKB":"4884887","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Fisher Q Exactive Plus Hybrid Quadrupole-Orbitrap","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Methylglyoxal, MICA, NLRP3, PYN","pi":[{"name":"Michael Bollong","email":"mbollong@scripps.edu","institution":"The Scripps Research Institute- California","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"43e1210a7e784e5f96c998e5d157eaec","id":"2095"}, {"dataset":"MSV000095500","datasetNum":"95500","title":"GNPS - MassLite: An Integrated Python Platform for Single Cell Mass Spectrometry Metabolomics Data Pretreatment with Graphical User Interface and Advanced Peak Alignment Method ","user":"Zongkai_111","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722458809000","created":"Jul. 31, 2024, 1:46 PM","description":"Sample data for MassLite and result file. 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After treatment, queens were sampled to obtain proteomics data for hemolymph and mature oocytes (dissected from the ovaries), and workers were sampled to obtain pooled samples of antennae, hypopharangeal glands, and hemolymph. Data from worker antennae and hypopharangeal gland samples were acquired from a single plate, data from worker and queen hemolymph samples were acquired from a second plate, and oocyte data were acquired at a later date from a third plate. All samples were randomized within plates. The hemolymph, antennae, and hypopharangeal gland data were searched together (report_JF-all-tissues file) and the oocyte data were searched separately (report_JF-oocytes file). Data were all searched library-free using DIA-NN with default parameters except \"unrelated runs\" and \"MBR\" were selected, the neural network classifier was set to \"double-pass mode\", and protein inference was set to \"protein names from FASTA\".","fileCount":"8","fileSizeKB":"300381982","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"timsTOF Pro 2","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\"","keywords":"Pyriproxyfen;queens;workers;honeybees;honey bees;IGR","pi":[{"name":"Leonard Foster","email":"foster@msl.ubc.ca","institution":"The University of British Columbia (UBC)","country":"Canada"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4e0ffa1ac2504982912fe5d4211f87fa","id":"2097"}, {"dataset":"MSV000095497","datasetNum":"95497","title":"Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm","user":"metodi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722447824000","created":"Jul. 31, 2024, 10:43 AM","description":"Post-translational modification of proteins plays an important role in cancer cell biology. Protein encoded by oncogenes may be activated by phosphorylation, products of tumour suppressors might be inactivated by phosphorylation or ubiquitination, which marks them for degradation; Chromatin binding proteins are often methylated and\/or acetylated. These are just a few of the many hundreds of post-translational modifications discovered by years of painstaking experimentation and chemical analysis of purified proteins. In recent years, mass spectrometry-based proteomics emerged as the principal technique for identifying such modifications in samples from cultured cells and tumour tissue. Here we used a recently developed combinatorial search algorithm implemented in the MGVB toolset to identify novel modifications in samples from breast cancer cell lines. Our results provide a rich resource of coupled protein abundance and post-translational modification data seen in the context of an important biological function - the response of cells to interferon gamma treatment - which can serve as a starting point for future investigations to validate promising modifications and explore the utility of the underlying molecular mechanisms as potential diagnostic or therapeutic targets. ","fileCount":"62","fileSizeKB":"30488573","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens","instrument":"LTQ\\\/Orbitrap Velos","modification":"phosphorylation, methylation, acetylation;UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"breast cancer;interferon gamma;PTM;methylation","pi":[{"name":"Metoodi V. Metodiev","email":"mmetod@essex.ac.uk","institution":"University of Essex","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054457","task":"e602168d3e6b41b0a6668a3396d1c094","id":"2098"}, {"dataset":"MSV000095496","datasetNum":"95496","title":"Quantitative proteomics reveals extensive lysine ubiquitination in Arabidopsis thaliana","user":"jwalley","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722441980000","created":"Jul. 31, 2024, 9:06 AM","description":"In this study, we describe an antibody-based approach to enrich ubiquitinated peptides from vegetative tissues for detection via peptide mass spectrometry. This enrichment method can be coupled with isobaric labeling to enable quantification from up to 18-multiplexed samples. This approach identified 19,740 ubiquitinated lysine sites arising from 5,936 proteins in Arabidopsis primary roots, seedlings and rosette leaves. Gene Ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. Proteins with altered abundance and ubiquitination state in roots upon bortezomib treatment included transporters, adaptors, and transcription factors.","fileCount":"96","fileSizeKB":"97999009","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Exploris 480;Q Exactive Plus","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"di-glycine;ubiquitin;Arabidopsis","pi":[{"name":"Justin Walley","email":"jwalley@iastate.edu","institution":"Iowa State University","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054448","task":"b3c843d0d0bd4a768463effb5b96237c","id":"2099"}, {"dataset":"MSV000095495","datasetNum":"95495","title":"Alkylation reageant comparaison","user":"jwalley","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722441518000","created":"Jul. 31, 2024, 8:58 AM","description":"Comparison of off target alkylation using chloroacetamide (CAA) and iodoacetamide (IAA). The peptide preparation was performed side by side, following identical methods except the alkylation treatment with either IAA or CAA. None of the comparison of off-targets on between IAA and CAA showed a significant difference. The overall off-target level for both reagents was relatively low (< 0.1%) and the off-target rate on lysine residues was even lower (0.045% for IAA and 0.051% for CAA).","fileCount":"8","fileSizeKB":"6697453","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Exploris 480","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"iodoacetamide;chloroacetamide","pi":[{"name":"Justin Walley","email":"jwalley@iastate.edu","institution":"Iowa State University","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054447","task":"0f081396c65b4a84b7012ac53a7cb1b0","id":"2100"}, {"dataset":"MSV000095493","datasetNum":"95493","title":"Diurnal rhythms in durum wheat triggered by Rhopalosuphum padi (bird cherry-oat aphid)","user":"goldyosh","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722439458000","created":"Jul. 31, 2024, 8:24 AM","description":"Metabolomics datasets for:\nDiurnal rhythms in durum wheat triggered by Rhopalosuphum padi (bird cherry-oat aphid)","fileCount":"366","fileSizeKB":"56142451","spectra":"30586","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum turgidum subsp. durum (NCBITaxon:4567)","instrument":"Thermo Q-Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Rhopalosuphum padi;wheat","pi":[{"name":"Prof. Vered Tzin","email":"vtzin@bgu.ac.il","institution":"Ben Gurion University","country":"Israel"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"698ff8ea9a2a44b99667646233c46220","id":"2101"}, {"dataset":"MSV000095492","datasetNum":"95492","title":"The C. elegans PTPN22 ortholog functions in diverse developmental processes","user":"sbyrum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722435545000","created":"Jul. 31, 2024, 7:19 AM","description":"Non-receptor type protein tyrosine phosphatases (PTPNs) have been studied extensively in the context of the adaptive immune system, however, their roles beyond immunoregulation are less unexplored. Here we identify novel functions for the conserved C. elegans phosphatase, PTPN-22, establishing new links to worm molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppresses molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases, NEKL-2 (human NEK8\/9) and NEKL-3 (human NEK6\/7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22 we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22 and showed that loss of DNBP-1 also suppresses nekl-associated molting defects and partially co-localizes with PTPN-22 in the epidermis. Genetics analysis, co-localization studies, and proximity labeling also revealed roles for PTPN-22 in several epidermal adhesion complexes including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, our studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.","fileCount":"31","fileSizeKB":"12094129","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"C. elegans;Tyrosine Phosphatase;TurboID;proximity-dependent protein labeling","pi":[{"name":"David S. Fay","email":"DavidFay@uwyo.edu","institution":"University of Wyoming","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD054444","task":"121d79147e584f629e892d70e073112f","id":"2102"}, {"dataset":"MSV000095491","datasetNum":"95491","title":"Identification of Prx binding partners from Streptococcus pyogenes lysates","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722433335000","created":"Jul. 31, 2024, 6:42 AM","description":"The small prophage protein paratox (Prx) from Streptococcus pyogenes strain MGAS315 was used as bait in pull-down assays with bacterial lysates to discover potential binding partners. Bacterial lysates analyzed included MGAS315 stimulated with the quorum sensing pheromone XIP-- that induces natural competence, and MGAS315 stimulated with mitomycin C which induces bacteriophage protein expression. ","fileCount":"7","fileSizeKB":"4981975","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptococcus pyogenes MGAS315 (NCBITaxon:198466)","instrument":"Orbitrap Exploris 480","modification":"C+57.021","keywords":"bacteriophages;pathogenic conversion;binding partners","pi":[{"name":"Gerd Prehna","email":"Gerd.Prehna@umanitoba.ca","institution":"University of Manitoba","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"92444df5508849759b5a779591470717","id":"2103"}, {"dataset":"MSV000095490","datasetNum":"95490","title":" Size Exclusion Chromatography Based Proteomic and Degradomic Profiling of Inflammasome-Activated, Murine Bone Marrow-Derived Dendritic Cells ","user":"Daniel_Vogele","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722425576000","created":"Jul. 31, 2024, 4:32 AM","description":"This proteomic dataset explores the formation of protein complexes during inflammasome activation in bone marrow-derived dendritic cells (BMDCs) from gasdermin D-deficient mice. The study employs size exclusion chromatography (SEC) linked with mass spectrometry-based proteomics to provide a global overview of protein complexes and their dynamics, with a particular focus on proteolytic enzymes and truncated proteins in higher molecular weight complexes.\n\nBMDCs were cultured and differentiated using GM-CSF, then primed with LPS and treated with either nigericin or Val-boroPro (Talabostat). Proteins were separated by SEC, and fractions were labelled with tandem mass tags (TMT). The labelled fractions were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS\/MS). Raw mass spectrometry data were processed using the FragPipe pipeline (v20.0) with semi-specific tryptic cleavage specificity allowing one missed cleavage. Fixed modifications included carbamidomethylation at cysteines and a TMT mass delta of 229.16293 at lysines, while N-terminal acetylation and N-terminal TMT mass delta were set as variable modifications. Normalization across SEC fractions was performed using the reference channel in R (v4.1.0) within Rstudio, followed by further analysis of the processed data.","fileCount":"297","fileSizeKB":"117153114","spectra":"3021618","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"Protein Complex Dynamics;Size Exclusion Chromatography;Degradomic Profiling;Bone Marrow-Derived Dendritic Cells","pi":[{"name":"Prof. Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"Institute for Surgical Pathology, University Medical Center Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054430","task":"f50b905de5c940ce9ee25d9f747655f2","id":"2104"}, {"dataset":"MSV000095489","datasetNum":"95489","title":"Pilot Study on Differential Urine Proteomic Profile of Subjects with Community Acquired Acute Kidney Injury Who Recover Versus Those Who Do Not Recover Completely at 4 months after Hospital Discharge","user":"mails2sahok","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722425292000","created":"Jul. 31, 2024, 4:28 AM","description":"Community acquired acute kidney injury (CAAKI) is a sudden structural damage and loss of kidney function in otherwise healthy individuals outside of hospital settings having high morbidity and mortality rates worldwide. Long-term sequelae of AKI involve an associated risk of progression to chronic kidney disease (CKD). Serum creatinine (SCr) the currently used clinical parameter for diagnosing AKI varies greatly with age, gender, diet and muscle mass. In the present study, we investigated the difference in urinary proteomic profile of subjects that recovered (R) and incompletely recovered (IR) from CAAKI, 4 months after hospital discharge. This study helped in identifying potential proteins and associated pathways that are either upregulated or downregulated at the time of hospital discharge in incompletely recovered CAAKI patients that can be further investigated to check for their exact role in the disease progression or repair.","fileCount":"58","fileSizeKB":"98211970","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Community acquired acute kidney injury, proteomic, renal outcome, LCMS","pi":[{"name":"Dr. Ashok Kumar Yadav","email":"mails2ashok@gmail.com","institution":"Postgraduate Institute of Medical Education and Research (PGIMER) Chandigarh","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2d989f68580e499e9b335314bc42f076","id":"2105"}, {"dataset":"MSV000095486","datasetNum":"95486","title":"GNPS - LC-MS compound 4BL laboratorio 147 USP","user":"Gomes","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722393749000","created":"Jul. 30, 2024, 7:42 PM","description":"UDD laboratory chemical investigation of antimalarial.","fileCount":"2","fileSizeKB":"90947","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Byrsonima sp. C152 (NCBITaxon:1481449)","instrument":"micrOTOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plant","pi":[{"name":"giovane","email":"giovanni_gomes@icb.usp.br","institution":"USP","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"22e0ae206c5748ab9d5bfd63b9e020c0","id":"2106"}, {"dataset":"MSV000095484","datasetNum":"95484","title":"GNPS - TiO2 Nanoparticle for Siderophore Extraction","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722355974000","created":"Jul. 30, 2024, 9:12 AM","description":"Novel and more efficient technique for selectively enriching siderophore from complex microbiome","fileCount":"25","fileSizeKB":"862277","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas","instrument":"QExactive Orbitrap Tandem Mass Spectrometer","modification":"None","keywords":"Siderophore;Nanoparticle","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1ee0bd4d52064279a69b4a11569cd342","id":"2107"}, {"dataset":"MSV000095481","datasetNum":"95481","title":"Cleavage of oxidized phospholipids by circulating PLA2 enzymes","user":"Jokesch","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722334790000","created":"Jul. 30, 2024, 3:19 AM","description":"In this study, we have compared relative activities of different PLA2 enzymes by analyzing cleavage of OxPAPC and OxPAPE by diluted plasma in the presence of enzyme inhibitors.","fileCount":"334","fileSizeKB":"100438923","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"phospholipid cleavage;glycerophospholipid;lipidomic;epilipidom;mass spectrometry","pi":[{"name":"Bernd Gesslbauer","email":"bernd.gesslbauer@uni-graz.at","institution":"University of Graz","country":"Austria"},{"name":"Valery Bochkov","email":"valery.bochkov@uni-graz.at","institution":"University of Graz","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da8bb8a681d84d42a88b200d4b0444db","id":"2108"}, {"dataset":"MSV000095480","datasetNum":"95480","title":"3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes","user":"Wszymanski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722330830000","created":"Jul. 30, 2024, 2:13 AM","description":"Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its role for transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions yieldingcell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are enriched at promoters and related to increased gene expression, both. A role for G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has, however, remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we find that nuclear miR-9 is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis.","fileCount":"727","fileSizeKB":"37278280","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Ultra","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"TimsTof, sp3, mouse, interactome","pi":[{"name":"Guillermo Barreto","email":"Guillermo.Barreto@univ-lorraine.fr","institution":"Universite de Lorraine, CNRS, Laboratoire IMoPA, Nancy","country":"France"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD054375","task":"4c6bda25ae88449094792602c1470cd5","id":"2109"}, {"dataset":"MSV000095479","datasetNum":"95479","title":"Apolipoprotein A-II Increases Cholesterol Efflux Capacity of Mature High-Density Lipoproteins Via the Apolipoprotein A-I C-terminus","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722297372000","created":"Jul. 29, 2024, 4:56 PM","description":"Samples were processed using Global and Limited Proteolysis (LiP). Peptides and proteins were identified using MaxQuant (v1.6.17.0), then summarized using R package RomicsProcessor.","fileCount":"219","fileSizeKB":"74155929","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X;Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"apolipoproteins;ABCA1;cholesterol efflux;lipoprotein metabolism;lipoproteins;structure","pi":[{"name":"John T. 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Small (mg) pieces of tissue were solubilized with RapiGest (Waters), reduced, alkylated, and digested with trypsin. The resultant peptides were separated by HPLC and analyzed in data dependent MS mode using a Q Exactive mass spectrometer. The .raw LCMS files have been deposited.","fileCount":"16","fileSizeKB":"26356326","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus (NCBITaxon:10114)","instrument":"Q Exactive","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"E14; E16; E18; E20; adult; hindlimb bud; transversus abdominis muscle","pi":[{"name":"Michael Previs","email":"michael.previs@med.uvm.edu","institution":"University of Vermont","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c27136866bdf40309f321c0b53944526","id":"2112"}, {"dataset":"MSV000095476","datasetNum":"95476","title":"EcoFAB 2.0 Root Microbiome Ring Trial","user":"vnovak","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722276681000","created":"Jul. 29, 2024, 11:11 AM","description":"The experiment aimed to demonstrate the reproducibility of microbiome formation, metabolite production, and plant growth across multiple laboratories using the EcoFAB 2.0 system. To achieve this, five laboratories (A-E) conducted the identical experiment. In each laboratory, Brachypodium distachyon Bd21-3 was grown in the EcoFAB 2.0 system and subjected to the following treatments: an axenic (mock-inoculated) plant control, two synthetic communities SynCom16 or SynCom17 (+\/-Burkholderia sp. OAS925, a strong root colonizer), or a plant-free medium control. Each treatment was replicated seven times (n=7). After 22 days, the spent hydroponic growth medium was collected and analyzed using polar HILIC metabolomics to determine the exometabolite composition.","fileCount":"325","fileSizeKB":"31788644","spectra":"1527363","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brachypodium distachyon (NCBITaxon:15368)","instrument":"Orbitrap Exploris 120","modification":"NA","keywords":"Ring trial;Brachypodium;SynCom;microbiome;reproducibility;exudates","pi":[{"name":"Trent Northen ","email":"trnorthen@lbl.gov","institution":"Lawrence Berkeley National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"17114361d3a442dd8fe8871cfdf4630b","id":"2113"}, {"dataset":"MSV000095473","datasetNum":"95473","title":"The promiscuous biotin ligase TurboID reveals the proxisome of the T3SS chaperone IpgC in the cytoplasm of Shigella flexneri","user":"HMI_LAB","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722266153000","created":"Jul. 29, 2024, 8:15 AM","description":"Using TurboID to study the proxisome of Shigella flexneri's Type 3 Secretion System (T3SS) chaperone IpgC, and transcriptional activator MxiE. 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This system provides >200-Hz MS\/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. This instrument allows a narrow-window data-independent (nDIA) strategy, improving sensitivity and reproducibility even when using very short LC gradients. Although this represents a new technical milestone in peptide-centric proteomics, this new system has not yet been evaluated for the analyses of very complex and clinically important proteomes, such as represented by the plasma glycoproteome. Here, we evaluated the Orbitrap Astral mass spectrometer for the analysis of the plasma glycoproteome, and pioneer a dedicated nDIA workflow, themed nGlycoDIA. With substantially adjusted parameters and varying collision energies, nGlycoDIA has clear benefits for plasma glycoproteomics. We tested our method both in glycopeptide enriched and crude plasma, leading to the identification of more than 3000 unique glycoPSMs from 181 glycoproteins, covering a dynamic range of 7 orders of magnitude in the enriched plasma sample in just 40 minutes. In addition, we detect for the first time several glycosylated cytokines that have a reported plasma concentration in the ng\/L range. Furthermore, shortening the gradient to 10 min still allows the detection of almost 2500 unique glycoPSMs from enriched plasma, indicating that high-throughput in-depth clinical plasma glycoproteomics may be within reach.","fileCount":"5084","fileSizeKB":"3219261967","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"N-glycosylation","keywords":"glycosylation;astral;data-independent acquisition ","pi":[{"name":"Albert J.R. Heck ","email":"a.j.r.heck@uu.nl","institution":"Utrecht University","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054333","task":"628297fa791f4a27bce5d1a7885fe347","id":"2116"}, {"dataset":"MSV000095469","datasetNum":"95469","title":"A Chemoselective Enrichment Strategy for In-Depth Coverage of the Methyllysine Proteome","user":"Lufeng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722222482000","created":"Jul. 28, 2024, 8:08 PM","description":"There are the raw data of Kme1 peptides identification in the paper titled \"A Chemoselective Enrichment Strategy for In-Depth Coverage of the Methyllysine Proteome\".","fileCount":"285","fileSizeKB":"113003686","spectra":"2208747","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480;timsTOF Pro 2","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:199 - \\\"DiMethyl-CHD2.\\\";UNIMOD:298 - \\\"Deuterated methyl ester.\\\"","keywords":"Lysine monomethylation","pi":[{"name":"Mingxuan Wu","email":"wumingxuan@westlake.edu.cn","institution":"Westlake University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"505db72242cb4c21a30c638566f59347","id":"2117"}, {"dataset":"MSV000095466","datasetNum":"95466","title":"GNPS - Metabolomics of human urine and stool samples from the PRIMA study","user":"nicolaproch","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722159420000","created":"Jul. 28, 2024, 2:37 AM","description":"MS\/MS data of global pools of human urine and faeces from the PRIMA study NCT04804319, targeting features associated with gut environment","fileCount":"25","fileSizeKB":"28786749","spectra":"699","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Vion IMS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics","pi":[{"name":"Henrik Roager","email":"hero@nexs.ku.dk","institution":"University of Copenhagen","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"55dc017152b94452ba73402c9d6ef769","id":"2118"}, {"dataset":"MSV000095464","datasetNum":"95464","title":"Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control","user":"PatrickTreffon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722102272000","created":"Jul. 27, 2024, 10:44 AM","description":"Site-specific S-nitrosoproteome of hot5-2 inflorescences.","fileCount":"14","fileSizeKB":"12386110","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion","modification":"MOD:00460 - \\\"A protein modification that effectively trioxygenates an L-cysteine residue to L-cysteine sulfonic acid.\\\"","keywords":"gsnor\/hot5_2 site specific S-nitrosoproteome, AT5G43940","pi":[{"name":"Elizabeth Vierling","email":"vierling@umass.edu","institution":"University of Massachusetts Amherst","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f163eeeffa0e409ba40ec1afa323a39d","id":"2119"}, {"dataset":"MSV000095463","datasetNum":"95463","title":"GNPS - Livia Soman research group - fungi metabolites","user":"liviasoman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722040706000","created":"Jul. 26, 2024, 5:38 PM","description":"Livia Soman research group - fungi metabolites - Penicillium","fileCount":"34","fileSizeKB":"136589","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Penicillium sp. (NCBITaxon:5081)","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"penicillium","pi":[{"name":"Livia Soman","email":"livia.soman@unifesp.br","institution":"UNIFESP","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"539c95972c414923a53467cb741becc3","id":"2120"}, {"dataset":"MSV000095462","datasetNum":"95462","title":"20240726_EPAD_MICU_fecaltargetedpanels","user":"jess_cleary","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722035284000","created":"Jul. 26, 2024, 4:08 PM","description":"Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality risk. Targeted metabolomics panels for Bile Acids, Tryptophan pathway, and SCFAs, see methods document for full description.","fileCount":"4152","fileSizeKB":"210621986","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6470A Triple Quadrupole LC\\\/MS;6546 Q-TOF LC\\\/MS (Agilent instrument model);Agilent 7890A GC system, Agilent 5975C MS detector","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbiome;metabolomics","pi":[{"name":"Eric Pamer","email":"egpamer@uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"24a010b7e6a34ac88cd45b3848c88cc0","id":"2121"}, {"dataset":"MSV000095461","datasetNum":"95461","title":"GNPS - Understanding the biosynthesis, metabolic regulation, and anti-phytopathogen activity of 3,7-dihydroxytropolone in Pseudomonas spp.","user":"andtrum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722034197000","created":"Jul. 26, 2024, 3:49 PM","description":"LC-MS data associated with the discovery and biosynthesis of 3,7-dihydroxytropolone in Pseudomonas sp. 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After 4 days, the 8-well chamber was detached from the glass slide, and omental tissue was removed with a razor blade prior to desiccation. Agarose cocultures were desiccated on the ITO-glass slide in an incubator at 30C on a home-built spinning apparatus for 4 hours. (Lusk JASMS 2022)\n\nMALDI matrices alpha-cyano-4-hydroxycinnamic acid (CHCA (98%), C2020, Sigma-Adlrich) and 2,5-dihydroxybenzoic acid (DHB (98%), 149357, Sigma-Aldrich) were recrystallized in-house as previously described. The MALDI matrix used for MSI was a 50:50 mixture of CHCA:DHB at 10 mg\/mL dissolved in 90:10 ACN:H2O with 0.1% TFA applied using a TM sprayer (HTX Imaging).\n\nBefore MSI analysis, slides were scanned using Tissue Scout (Bruker Daltonics) for the initial screen and Epson Perfection V850 Pro for subsequent experiments. Scanned images were used to guide irradiation. MSI data was acquired using timsControl v2.0.51.0_9669_1571 and flexImaging 5.1 software for the initial screen, fleximaging 7.4 for subsequent experiments at 100 micron spatial resolution on a timsTOF fleX mass spectrometer (Bruker Daltonics). Data were collected using a mass range of 50-1500 Da in positive ion mode with the laser width set to 100 micron imaging and the laser power set to 90%. At each raster point, 1,000 laser shots were delivered at a frequency of 1,000 Hz. The instrument was calibrated manually using phosphorus red prior to imaging. MSI data was analyzed, and statistical analysis was performed using SCiLS Lab version 2023c core (Bruker Daltonics). All spectra were normalized to the root mean square (RMS). ","fileCount":"14","fileSizeKB":"7879290","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;mass spectrometry imaging;3D cell culture;ovarian cancer","pi":[{"name":"Laura Sanchez","email":"lmsanche@ucsc.edu","institution":"University of California Santa Cruz","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da354312aae04cc6a920daea4581341a","id":"2124"}, {"dataset":"MSV000095457","datasetNum":"95457","title":"Polyomavirus ALTOs, but not MTs, downregulate viral early gene expression by activating the NF-KB pathway","user":"FHproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722028774000","created":"Jul. 26, 2024, 2:19 PM","description":"Polyomaviruses are small, circular dsDNA viruses that can cause cancer. Alternative splicing of polyomavirus early transcripts generates large and small tumor antigens (LT, ST) that play essential roles in viral replication and tumorigenesis. Some polyomaviruses also express middle tumor antigens (MTs) or alternate LT open reading frames (ALTOs), which are evolutionarily related but have distinct gene structures. MTs are a splice variant of the early transcript whereas ALTOs are overprinted on the second exon of the LT transcript in an alternate reading frame and are translated via an alternative start codon. Merkel cell polyomavirus (MCPyV), the only human polyomavirus that causes cancer, encodes an ALTO but its role in the viral lifecycle and tumorigenesis has remained elusive. In this MassIVE entry, we provide mass spectrometry data and result files associated with a TurboID experiment to identify human and viral proteins that bind to ALTO.","fileCount":"33","fileSizeKB":"77507212","spectra":"0","psms":"282234","peptides":"58852","variants":"70216","proteins":"6776","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Merkel cell polyomavirus (NCBITaxon:493803)","instrument":"Orbitrap eclipse w\\\/FAIMS","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"label free quantification, LFQ, Merkel cell carcinoma, ALTO","pi":[{"name":"Denise Galloway","email":"dgallowa@fredhutch.org","institution":"Fred Hutchinson Cancer Center","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"ee32d593ee2d49468d4aa4ec5b021808","id":"2125"}, {"dataset":"MSV000095456","datasetNum":"95456","title":"Advanced multimodal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722023997000","created":"Jul. 26, 2024, 12:59 PM","description":"We advanced our previously developed Metabolome Informed Proteome Imaging (MIPI) workflow and demonstrated its application in bio-medical science to elucidate molecular processes at microscale resolution. To prove MIPI's ability to functionally reduce the heterogeneity and complexity of human tissue, we utilized a full-term placenta from an obese person. Lipidomic and metabolomic imaging by MALDI-MSI visualized molecular composition and dynamic activities across the tissue sections, mapping placental villous regions with enriched metabolic activity related to sterol lipids and fatty acid processing. Our complementary proteome profiling of mapped regions allowed us to capture region-specific enzymes. Integration of the data from our multimodal MS-based approaches reconstructed underlying biological pathways relevant to placental function across histologically distinct villi regions.","fileCount":"210","fileSizeKB":"123956297","spectra":"1881167","psms":"1937232","peptides":"1096112","variants":"1195925","proteins":"40534","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"MIPI;placenta","pi":[{"name":"Kristin Burnum-Johnson","email":"Kristin.Burnum-Johnson@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054289","task":"97c0561a84b34584a3fc39768dd75979","id":"2126"}, {"dataset":"MSV000095455","datasetNum":"95455","title":"Lusk_2024_aTRAQ_AA_quant_OvC_Secondary_Metastasis","user":"hlusk0529","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722020141000","created":"Jul. 26, 2024, 11:55 AM","description":"Amino acids quantified in OvC\/omentum coculture extracts using aTRAQ kit from SCIEX","fileCount":"2288","fileSizeKB":"87601759","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mammalian cells, Ovarian cancer, Omentum, Metastasis","pi":[{"name":"Laura Sanchez","email":"lmsanche@ucsc.edu","institution":"University of California Santa Cruz","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b824a783b9424099b39e962eb13cf3ca","id":"2127"}, {"dataset":"MSV000095454","datasetNum":"95454","title":"P. fluorescens in Succinate Minimal Media, Iron Infusion","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722014635000","created":"Jul. 26, 2024, 10:23 AM","description":"Pseudomonas fluorescens FW300-N2C3 was cultured in succinate minimal media (SMM) and analyzed for metabolites on LCMS with iron infusions of either 2 mM or 500 micromolar iron.","fileCount":"37","fileSizeKB":"1826497","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"pseudomonas;fluorescens;succinate minimal;iron","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fe86d5e042304b3d855d967493fb34b8","id":"2128"}, {"dataset":"MSV000095452","datasetNum":"95452","title":"E. meliloti Strains USDA 1021 and USDA 1157, Succinate Minimal Media with\/without Iron","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722013560000","created":"Jul. 26, 2024, 10:06 AM","description":"Ensifer meliloti strains USDA 1021 and USDA 1157 were cultured in succinate minimal media (SMM) with and without 10 micromolar FeCl3. 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(NCBITaxon:10095)","instrument":"6540 Q-TOF LC\\\/MS","modification":"yes","keywords":"sildenafil","pi":[{"name":"kwak","email":"smart1301@naver.com","institution":"kra","country":"korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2148d4a1b01b4cb7b4756bcc8d08420c","id":"2133"}, {"dataset":"MSV000095445","datasetNum":"95445","title":"GNPS - Cardiomyocyte-specific NAMPT Knockout Mice: Metabolomics of Heart Ventricle Tissues at 2-weeks Post-Deletion","user":"Khanh_UPenn_Baur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1722000933000","created":"Jul. 26, 2024, 6:35 AM","description":"Metabolomics from heart ventricular tissues of wild-type (WT) and cardiomyocyte-specific conditional NAMPT knockout (cNKO) mice untreated or treated with nicotinamide riboside (cNKO-NR), harvested at 2-weeks post-NAMPT deletion (post-tamoxifen). For untargeted metabolomic running, mass spectrometer was operated in both negative (NEG, 70 to 1000 m\/z) and positive (POS, 50 to 117.9 m\/z) ion mode with the HILIC 25-minute method for the detection of metabolites. For targeted metabolomic running, mass spectrometer was operated in two positive-mode scans (SCAN1 at 118.5 to 800 m\/z and SCAN2 at 70 to 117.5 m\/z) with the HILIC 20-minute method for the detection of NAD derivatives.","fileCount":"41","fileSizeKB":"1345709","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"Heart, NAMPT, Cardiomyocyte, Metabolomics, NAD","pi":[{"name":"Joseph A. 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Experiment Set C compared lysosomal compositions between germ-free and conventional microbiome states. Experiment Set G compared ad libitum and 24h fasted conditions within stem cells. In each case, these RAWs represent the inputs to lyso-IP, not the lysosomally-enriched samples that are produced from lyso-IP. Sample preparation was performed using the S-TRAP method, with MMTS (methyl methanethiosulfonate) alkalyting free Cys side chains and trypsin digesting C-terminal to lysines and arginines. DDA experiments collected spectra for all 120 minutes of a two hour run, while DIA experiments using the high resolution MS1 (HRMS1) technique collected scans at two different FAIMS compensation voltages for 75 minutes during each 105 minute run, with scan events ending when the B solvent of the gradient reached 45%.","fileCount":"577","fileSizeKB":"322836791","spectra":"0","psms":"4998029","peptides":"829009","variants":"1042868","proteins":"121000","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MOD:00110 - \\\"A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Lyso-IP;HRMS1","pi":[{"name":"John P. 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They are made up of an external capsule surrounding 3-5 intrafusal muscle fibers and a nuclear bag complex. Dysfunction of muscle spindles leads to abnormal muscle tone, poor limb coordination and abnormal proprioceptor function. The latter has been linked to aberrant bone and cartilage development, scoliosis, kyphosis and joint contractures. Congenital myopathies are often accompanied by skeletal alterations and joint contractures but so far the link between genetic mutations and altered muscle spindle function has not been explored. In the present study we investigated whether mutations in RyR1, the calcium release channel of the sarcoplasmic reticulum and the most common cause of human congenital myopathies, cause alterations of muscle spindles. To this end we investigated dHT mice an animal model we created carrying recessive Ryr1 mutations isogenic to those present in a severely affected child. Here we show that (i) the RyR1 protein is expressed at the polar regions of intrafusal fibers and exhibits a doubled row distribution pattern, typical for junctional sarcoplasmic reticulum proteins, and (ii) its content in intrafusal muscle fibers from dHT mice is reduced by 64%. Such a massive reduction of mutant RyR1 leads to severe scoliosis, altered expression of proteins in intrafusal muscle fibers and is paralleled by a decreased balance and inter limb coordination. These results support the hypothesis that RYR1 mutations not only affect the function of extrafusal muscles, but might also affect that of intrafusal muscles. The latter may be one of the underlying causes of skeletal abnormalities seen in patients affected by recessive RYR1 mutations.","fileCount":"47","fileSizeKB":"35107872","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Ryanodine receptor 1;congenital myopathies;muscle spindles;intrafusal muscle fibers","pi":[{"name":"Susan Treves","email":"susan.treves@unibas.ch","institution":"University of Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD054222","task":"09ff33af463e430f8e40ce18bf5cf1d2","id":"2139"}, {"dataset":"MSV000095431","datasetNum":"95431","title":"GNPS - Microbial Metabolomics of Methanotrophes from Gradient Syringe","user":"JarmoK","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721841960000","created":"Jul. 24, 2024, 10:26 AM","description":"Non-targeted metabolomics of organic extracts from methanotropes cultured on agarose in gradient syringe (ambient air vs methane)","fileCount":"136","fileSizeKB":"12960666","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Methylosinus (NCBITaxon:425);Methylocystis (NCBITaxon:133);Methylomonas (NCBITaxon:416);Methylopila (NCBITaxon:61653);Methylobacter (NCBITaxon:429)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bacterial methanotrophes UCR","pi":[{"name":"Aaron Puri","email":"awpuri@uw.edu","institution":"University of Washington","country":"USA"},{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b5b0f2be5332415bbe02d1113836f966","id":"2140"}, {"dataset":"MSV000095428","datasetNum":"95428","title":"Autophagic stress activates two distinct compensatory secretory pathways in neurons","user":"fazeliniah","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721830313000","created":"Jul. 24, 2024, 7:11 AM","description":"Neurons are reliant on autophagy to constitutively degrade damaged proteins and organelles in order to maintain cellular homeostasis. Autophagic dysfunction is associated with neurodegenerative diseases including Parkinson Disease. Mutations in the kinase LRRK2 are one of the most common causes of familial Parkinson disease; neurons expressing pathogenic LRRK2 mutations exhibit impaired autophagosome maturation. Here, we use biochemical, live cell imaging and unbiased proteomic approaches to demonstrate that LRRK2 mutant neurons engage two distinct secretory autophagy pathways as compensatory quality control mechanisms. First, we find that LRRK2 mutant neurons upregulate secretory autophagy, releasing cargos usually degraded by basal autophagy such as synaptic proteins and mitochondria. Second, we find that LRRK2 mutant neurons exhibit increased release of MVB-derived exosomes. We propose that these two secretory pathways act in tandem to dispose of cellular waste and to induce transcellular communication, respectively. We demonstrate that both pathways are upregulated in a knockin mouse model expressing pathogenic LRRK2 and that exosomal release prevents the apoptosis-mediated cell death of neurons from this mouse. These findings identify compensatory pathways that are upregulated by expression of pathogenic mutations disrupting neuronal autophagy. These pathways contribute to the maintenance of cellular homeostasis and thus may delay neurodegenerative disease progression over the short term, but have the potential to exacerbate degeneration over the longer term through the release of proinflammatory components such as mitochondrial DNA.","fileCount":"27","fileSizeKB":"85711428","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Neuron;Homeostasis;Neurodegenerative diseases;LRRK2;Mitochondria","pi":[{"name":"Erika Holzbaur, Ph.D.","email":"holzbaur@pennmedicine.upenn.edu","institution":"University of Pennsylvania","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD054181","task":"4ac3f6d0322a4abeac424dca3c4bedf8","id":"2141"}, {"dataset":"MSV000095427","datasetNum":"95427","title":"LINE-1 ORF1p co-immunoprecipitations analyzed by DDA and two DIA methods","user":"dtabb73","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721813971000","created":"Jul. 24, 2024, 2:39 AM","description":"Using an anti-ORF1 monoclonal (clone 4H1; Milipore), four co-immunoprecipitations to enrich for LINE-1 ORF1p and its interactors as described in Di Stefano, L.H. et al. (https:\/\/doi.org\/10.1007\/978-1-0716-2883-6_12), from either HEK-293TLD (cells transfected with pMT646- containing a L1 sequence) or N2102Ep (embryonal carcinoma cells with endogenous expression of LINE-1) lysates were then analyzed in DDA, HRMS1, and Variable Window modes. Mouse polyclonal IgG were used as mock IPs as nonspecific binding controls. MMTS alkylated the cysteines. DDA and Variable Window experiments collected spectra for 60 minutes of the one hour run time. The HRMS1 experiments collected spectra for 90 minutes of a two hour run time. The UP000005640 reference proteome for Homo sapiens, including unreviewed sequences and reviewed isoforms was used as a search space (104,558 sequences)","fileCount":"207","fileSizeKB":"61121759","spectra":"0","psms":"185599","peptides":"54643","variants":"60768","proteins":"88747","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00110 - \\\"A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"co-immunoprecipitation;data-independent acquisition;LINE-1","pi":[{"name":"John P. 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The organization of the file list into cohorts is described in readme.tsv in Metadata.","fileCount":"152","fileSizeKB":"238588141","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"dia-PASEF;dda-PASEF","pi":[{"name":"Benedikt Kessler","email":"benedikt.kessler@ndm.ox.ac.uk","institution":"TDI-NDM (University of Oxford)","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f8a89b8d351e40fe880e7f9471718dfc","id":"2143"}, {"dataset":"MSV000095425","datasetNum":"95425","title":"GNPS - Enviornmental Metabolomics of CCE2024 HT Incubations","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721785117000","created":"Jul. 23, 2024, 6:38 PM","description":"Non-targeted metabolomics of DOM samples from the CCE2024 cruise analyzed in positive mode","fileCount":"132","fileSizeKB":"19764045","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DOM;Marine","pi":[{"name":"Andrew Allen","email":"aallen@ucsd.edu","institution":"University of California San Diego","country":"USA"},{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5233ff67202a412fb673132e99044dfc","id":"2144"}, {"dataset":"MSV000095424","datasetNum":"95424","title":"GNPS - Environmental Metabolomics of CCE2024 Marine Heatwave ","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721785069000","created":"Jul. 23, 2024, 6:37 PM","description":"Non-targeted Metabolomics from CCE2024 Dissolved Organic Matter (DOM) samples analyzed in positive mode ","fileCount":"440","fileSizeKB":"73790155","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DOM;Marine","pi":[{"name":"Andrew Allen","email":"aallen@ucsd.edu","institution":"University of California San Diego","country":"USA"},{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0e4c1fa8ca9346099900d4caad4444c1","id":"2145"}, {"dataset":"MSV000095423","datasetNum":"95423","title":"GNPS - Retention time matching - N-acyl lipids","user":"helenamrusso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721780482000","created":"Jul. 23, 2024, 5:21 PM","description":"Runs used for retention time matching between N-acyl lipids (combinatorial synthesis) and biological samples (HNRC - stool; Salmonella infection - cecum; Dead bodies - skin swab; Microbial monocultures - extracts). Two gradients were used (LC1 - total 11 min; LC2 - total 14 min) and a Kinetex 1.6 um polar C18 column (100 x 2.1 mm) was employed . Two spiking levels were used for coinjection (high - 1:3 sample:reaction pool; low - 3:1 sample:reaction pool).","fileCount":"647","fileSizeKB":"25815682","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"N-acyl lipids;infection;skin;stool;monoculture","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a44cfa0c342e4c3fa33fa77b1bac5412","id":"2146"}, {"dataset":"MSV000095419","datasetNum":"95419","title":"GNPS - PCOS mouse fecal samples metabolomics ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721769120000","created":"Jul. 23, 2024, 2:12 PM","description":"Metabolomics for Erica Maissy PCOS mouse model sampleset. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size Polar C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA)","fileCount":"464","fileSizeKB":"33504000","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fecal;mouse fecal;PCOS","pi":[{"name":"Amir Zarrinpar","email":"azarrinpar@ucsd.edu","institution":"University of California San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fc2126930adb43019bdfecc0a8b10c2d","id":"2147"}, {"dataset":"MSV000095418","datasetNum":"95418","title":"GNPS - ADRC Fecal Main Study Set one","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721768846000","created":"Jul. 23, 2024, 2:07 PM","description":"Corrected U19 ADRC Dataset Main study human fecal samples (set one). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). ","fileCount":"719","fileSizeKB":"30297867","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fecal;stool;U19;Alzheimer's Disease","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"58f56e5db4ae4c8ba56d05ee865a2629","id":"2148"}, {"dataset":"MSV000095417","datasetNum":"95417","title":"Identification of Disease-relevant, Sex-based Proteomic Differences in iPSC-derived Vascular Smooth Muscle","user":"nariyasi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721754233000","created":"Jul. 23, 2024, 10:03 AM","description":"The prevalence of cardiovascular disease varies with sex, and the impact of intrinsic sex-based differences on vasculature is not well understood. Animal models can provide important insight into some aspects of human biology, however not all discoveries in animal systems translate well to humans. To explore the impact of chromosomal sex on proteomic phenotypes, we used iPSC-derived vascular smooth muscle cells from healthy donors of both sexes to identify sex-based proteomic differences and their possible effects on cardiovascular pathophysiology. Our analysis confirmed that differentiated cells have a proteomic profile more similar to healthy primary aortic smooth muscle than iPSCs. We also identified sex-based differences in iPSC-derived vascular smooth muscle in pathways related to ATP binding, glycogen metabolic process, and cadherin binding as well as multiple proteins relevant to cardiovascular pathophysiology and disease. Additionally, we explored the role of autosomal and sex chromosomes in protein regulation, identifying that proteins on autosomal chromosomes also show sex-based regulation that may affect the protein expression of proteins from autosomal chromosomes. This work supports the biological relevance of iPSC-derived vascular smooth muscle cells as a model for disease, and further exploration of the pathways identified here can lead to the discovery of sex-specific pharmacological targets for cardiovascular disease. ","fileCount":"126","fileSizeKB":"55330625","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Scientific Orbitrap Fusion Lumos Tribrid","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Vascular Smooth Muscle, Sex Differences, Proteomics, iPSCs, Disease Model","pi":[{"name":"Sarah J Parker","email":"sarah.parker@cshs.org","institution":"Cedars-Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054151","task":"84610998c80a4c769d96d4bf2b3fe724","id":"2149"}, {"dataset":"MSV000095414","datasetNum":"95414","title":"Autophosphorylation of conserved yeast and human casein kinase 1 isozymes regulates Elongator dependent tRNA modifications","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721732554000","created":"Jul. 23, 2024, 4:02 AM","description":"Casein kinase 1 (CK1) family members are crucial for ER-Golgi trafficking, calcium signaling, DNA repair, tRNA modifications and circadian rhythmicity. Whether and how substrate interactions and kinase autophosphorylation contribute to these diverse cellular processes and CK1 plasticity remains largely unknown. Here, we undertake a comprehensive phylogenetic, cellular and molecular characterization of Hrr25 from budding yeast and identify isozyme CK1 epsilon as its human ortholog. We analyze the effect of Hrr25 depletion and catalytically inactive mutants in vivo and show that perturbations in CK1 activity lead to pleiotropic stress-induced growth defects, morphological abnormalities and loss of Elongator-dependent tRNA modification. We use purified Hrr25 protein to identify distinct autophosphorylation patterns and phospho-sites on several physiological substrates in vitro and find that only human isozyme CK1epsilon can replace yeast Hrr25 functions essential for tRNA modification and cell proliferation in vivo. Furthermore, we demonstrate that human and yeast CK1 orthologs share conserved autophosphorylation sites, which regulate their activities and mutually exclusive interactions with Sit4, a phosphatase antagonist of Hrr25, and Elongator subunit Elp1. Thus, autophosphorylation controls CK1 activity and regulates the tRNA modification pathway. Our data offer mechanistic insights into regulatory roles of CK1 that are conserved from yeast to human cells and reveal a complex phosphorylation network behind CK1 plasticity.","fileCount":"212","fileSizeKB":"42993453","spectra":"0","psms":"67433","peptides":"2946","variants":"5958","proteins":"419","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Q Exactive","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"yeast Hrr25;kinase 39 autophosphorylation;Elongator complex;Casein kinase 1 epsilon","pi":[{"name":"Raffael Schaffrath","email":"schaffrath@uni-kassel.de","institution":"Institute of Biology, Department of Microbiology, University of Kassel","country":"Germany"},{"name":"Sebastian Glatt","email":"sebastian.glatt@uj.edu.pl","institution":"Malopolska Centre of Biotechnology (MCB), Jagiellonian University","country":"Poland"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054138","task":"0d21894c3b884ec7a53f2d98e5d4e91d","id":"2150"}, {"dataset":"MSV000095413","datasetNum":"95413","title":"Untargeted metabolomics of SPF mouse cecum samples","user":"KarinMeier","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721718655000","created":"Jul. 23, 2024, 12:10 AM","description":"Cecum samples of mice from different SPF vivaria (samples from international labs).","fileCount":"258","fileSizeKB":"27724349","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gut microbiome;SPF mice;cecum","pi":[{"name":"Prof. Dr. Uwe Sauer","email":"sauer@imsb.biol.ethz.ch","institution":"ETH Zurich","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f2ae0fc4f95349ad87a96a1915b2e7e2","id":"2151"}, {"dataset":"MSV000095410","datasetNum":"95410","title":"Mpyrifera_fucoidan_digest_Wv323GH107_ LC-MSMS","user":"MPI_MarineMicro","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721708658000","created":"Jul. 22, 2024, 9:24 PM","description":"HILIC-MS and HILIC-MS\/MS data from Wv323 endo-fucoidanase digest of commercial Macrocystis pyrifera fucoidan. Oligosaccharides were desalted prior to analysis. The negative control contains heat-inactivated enzyme. ","fileCount":"7","fileSizeKB":"386466","spectra":"1046","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Macrocystis pyrifera (NCBITaxon:35122)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fucoidan;Glycan;Carbohydrate;Oligosaccharide;tSIM;tSIM-ddMS2","pi":[{"name":"Manuel Liebeke","email":"mliebeke@mpi-bremen.de","institution":"MPI Bremen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d6a957959c864e55ae47ee03d57a85ca","id":"2152"}, {"dataset":"MSV000095407","datasetNum":"95407","title":"Barbulescu_Fam72a_TripleTOF6600_P124","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721671536000","created":"Jul. 22, 2024, 11:05 AM","description":"This dataset consists of 12 raw MS files and associated peak lists and results files, acquired on an ABSciex TripleTOF6600 operated in Data Dependent Acquisition mode. \r\nSamples were generated and affinity purification was performed by Philip Barbulescu. Trypsin digestion was performed by Laura McGary. Mass spectrometry acquisition was performed by Laura McGary. Analysis was performed by Philip Barbulescu, Alberto Martin, and Laura McGary. \r\nThe files are associated with a manuscript submitted for publication by Philip Barbulescu et al. The main goal of this dataset was to validate CTLH and UNG2 as interactors of FAM72A. \r\nAlberto Martin (alberto.martin@utoronto.ca) is the corresponding authors of the manuscript; Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\r\n\r\nThis submission is associated with 3 Supplementary Files (in addition to this README file)\r\nTable 1 describes the composition of this dataset\r\nTable 2 lists all the peptide identification evidence\r\nTable 3 lists the SAINTexpress interactions\r\n","fileCount":"67","fileSizeKB":"25049174","spectra":"0","psms":"161276","peptides":"23343","variants":"27705","proteins":"51678","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"FAM72A;Affinity purification;UNG2;GID\/CLTH complex;Antibody maturation","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054121","task":"b73b243e4df64440936e7262e5573256","id":"2153"}, {"dataset":"MSV000095406","datasetNum":"95406","title":"GNPS - wild elk tissue extracts","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721670425000","created":"Jul. 22, 2024, 10:47 AM","description":"Extracts of tissue samples from elk experiencing mysterious mortalities in Nevada. Samples are from Nevada Department of Wildlife.","fileCount":"118","fileSizeKB":"9286194","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cervus canadensis nelsoni (NCBITaxon:9864)","instrument":"Q Exactive","modification":"NA","keywords":"elk;fecal;spleen;liver;heart","pi":[{"name":"Pieter C. 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Through proteomics, we aimed to compare the circulating protein profiles and identify differentially expressed proteins of 10 responsive (R-PE) and 10 nonresponsive (NR-PE) patients to 10 healthy pregnant controls (HP). 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We show that DNA O-MAP can be coupled with sample multiplexed quantitative proteomics and next-generation sequencing to quantify DNA-protein and DNA-DNA interactions at specific genomic loci.","fileCount":"30","fileSizeKB":"13354646","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Proteomics;OMAP","pi":[{"name":"Devin Schweppe","email":"dkschwep@uw.edu","institution":"University of Washington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054080","task":"6dbc55a7bba149a2ac8f2e2a61d30b71","id":"2161"}, {"dataset":"MSV000095392","datasetNum":"95392","title":"GNPS - Enviornmental Metabolomics ECOHAB 2024 DOM \/ POM ","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721433430000","created":"Jul. 19, 2024, 4:57 PM","description":"Non-targeted LC-MS\/MS analysis of DOM and POM samples form the Pacific Ocean (Californian off-shore) taken via PPL solid-phase extraction and GFF filtering. 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Here, we observed that Sirt2-\/- males, but not females, have decreased body fat, moderate hypoglycemia upon fasting, and perturbed glucose handling during exercise compared to wild type controls. Conversion of injected lactate, pyruvate, and glycerol boluses into glucose via gluconeogenesis was impaired, but only in males. Primary Sirt2-\/- male hepatocytes exhibited reduced glycolysis and reduced mitochondrial respiration. RNAseq and proteomics were used to interrogate mechanisms behind this liver phenotype. Loss of Sirt2 did not lead to transcriptional dysregulation, as very few genes were altered in the transcriptome. In keeping with this, there was also negligible changes to protein abundance. Site-specific quantification of the hepatic acetylome, however, showed that 13% of all detected acetylated peptides were significantly increased in Sirt2-\/- male liver versus wild type, representing putative Sirt2 target sites. Strikingly, none of these putative target sites were hyperacetylated in Sirt2-\/- female liver. The target sites in male liver were distributed across mitochondria (44%), cytoplasm (32%), nucleus (8%), and other compartments (16%). Despite the high number of putative mitochondrial Sirt2 targets, Sirt2 antigen was not detected in purified wild type liver mitochondria, suggesting that Sirt2 regulation of mitochondrial function occurs from outside the organelle. We conclude that Sirt2 regulates hepatic protein acetylation and metabolism in a sex-specific manner. 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Recently, we discovered a quinolone-binding hot spot in TDP1s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide valuable insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare several covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1-binding ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting. Adding this capability to the chemical biology toolbox of resources for studying TDP1 could have far reaching consequences.","fileCount":"14","fileSizeKB":"3499132","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Exactive Plus;Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"TDP1;SuFEx;Tyrosine","pi":[{"name":"Terrence Burke","email":"burkete@mail.nih.gov","institution":"National Cancer Institute","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5bdeb2d494ee4e3fa059c953a77eae2d","id":"2164"}, {"dataset":"MSV000095386","datasetNum":"95386","title":"Enhancing anti-EGFRvIII CAR T cell therapy against glioblastoma with a paracrine SIRPgamma-derived CD47 blocker","user":"katarzynabuczak","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721378182000","created":"Jul. 19, 2024, 1:36 AM","description":"A significant challenge for chimeric antigen receptor (CAR) T cell therapy against glioblastoma (GBM) is its immunosuppressive tumor microenvironment (TME), which is densely populated and supported by protumoral glioma-associated microglia and macrophages (GAMs). Targeting CD47, a don't-eat-me signal overexpressed by tumor cells, disrupts the CD47-SIRPalpha axis and induces GAM phagocytic function. However, antibody-mediated CD47 blockade monotherapy is associated with toxicity and low bioavailability in solid tumors. To overcome these limitations, we combined local CAR T cell therapy with paracrine GAM modulation to effectively eliminate GBM. To this end, we engineered a new CAR T cell against epidermal growth factor receptor variant III (EGFRvIII) that constitutively secretes a signal regulatory protein gamma (SIRPgamma)-related protein (SGRP) with high affinity to CD47. Anti-EGFRvIII-SGRP CAR T cells eliminated EGFRvIII+ GBM in a dose-dependent manner in vitro and eradicated orthotopically xenografted EGFRvIII-mosaic GBM by locoregional application in vivo. This resulted in significant tumor-free long-term survival, followed by partial tumor control upon tumor re-challenge. Combining anti-CD47 antibodies with anti-EGFRvIII CAR T cells failed to achieve a similar therapeutic effect, underscoring the importance of sustained paracrine GAM modulation. Multidimensional brain immunofluorescence microscopy and in-depth spectral flow cytometry on GBM-xenografted brains showed that anti-EGFRvIII-SGRP CAR T cells accelerated GBM clearance, increased CD68+ cell trafficking to tumor scar sites and promoted GAM-mediated tumor cell uptake. In a peripheral lymphoma mouse xenograft model, anti-CD19-SGRP CAR T cells had superior efficacy to conventional anti-CD19 CAR T cells. Validation on human GBM explants revealed that anti-EGFRvIII-SGRP CAR T cells had a similar tumor-killing capacity to anti-EGFRvIII CAR monotherapy but showed a slight improvement in the maintenance of tumor-infiltrated CD14+ cells. Thus, local anti-EGFRvIII-SGRP CAR T cell therapy combines the potent antitumor effect of engineered T cells with the modulation of the surrounding innate immune TME. This results in the additive elimination of bystander EGFRvIII- tumor cells in a manner that overcomes the main mechanisms of CAR T cell therapy resistance, including tumor innate immune suppression and antigen escape.","fileCount":"23","fileSizeKB":"9827016","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"glioblastoma;EGFRvIII;CAR T cell therapy;CD47;microglia modulation;SGRP","pi":[{"name":"Gregor Hutter","email":"g.hutter@unibas.ch","institution":"Department of Biomedicine, University of Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD054059","task":"a1b0183b582548eda092f2487ba065fb","id":"2165"}, {"dataset":"MSV000095385","datasetNum":"95385","title":"Understanding the maintenance and regulation of HSCs in spleen by niche cells","user":"shmehatre77","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721366985000","created":"Jul. 18, 2024, 10:29 PM","description":"Recent years have seen exploration into the hematopoietic stem cell (HSC) niche in adult bone marrow (BM). Due to their relatively rare occurrence, research on splenic HSCs and their role in hematopoiesis under steady-state conditions has been limited. However, studies have been taken up to understand extramedullary hematopoiesis (EMH) in spleen under stress and pathological conditions. Moreover, activation of EMH also has been linked to mobilized BM derived HSCs, and contribution from the splenic HSCs has not been clear. Our studies have identified a myofibroblastic niche in spleen that supports HSCs under homeostatic conditions. To assess the maintenance and regulation of HSCs in spleen tissue by niche cells, we performed label-free mass spectrometry (MS) based quantitative proteomic analysis. The splenic HSC niche cells including capsular and trabecular myofibroblasts (or CTMs\/TBs), Lin-CD45- stromal cell population (or STs) and HSPCs (Lin-CD45+c-kit+Sca-1+) were isolated by fluorescence-activated cell sorting (FACS). The sorted cells were then lysed in lysis buffer, sonicated, thermally denatured, reduced, alkylated and tryptic digests were processed, desalted and analyzed on nano-LC coupled with high resolution mass spectrometer. Using Proteome Discoverer program and computational analysis performed on the global protein expression we examined the protein-protein interactions, cell-cell interactions and molecular pathways enriched in each cell population. This study demonstrates the molecular components HSC niche and presents a model to uncover novel hematopoietic regulators crucial for improving the function of adult and pluripotent stem cell derived HSCs.","fileCount":"125","fileSizeKB":"43908413","spectra":"0","psms":"120447","peptides":"11702","variants":"14184","proteins":"2499","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HSC;Hematopoietic stem cell;Myofibroblast;Stromal cell;Spleen;Hematopoiesis","pi":[{"name":"Dr. Satish Khurana","email":"satishkhurana@iisertvm.ac.in","institution":"Indian Institute of Science Education and Research Thiruvananthapuram","country":"India"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD054056","task":"47cb8e9d4233462ca9a7ca65b4ea8c30","id":"2166"}, {"dataset":"MSV000095383","datasetNum":"95383","title":"GNPS - U19 Mars Wisconsin Serum Alzheimer's Disease","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721349476000","created":"Jul. 18, 2024, 5:37 PM","description":"Corrected U19 Wisconsin Serum dataset. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1052","fileSizeKB":"53195274","spectra":"439457","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"serum;U19;AD;Alzheimer's","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"672ce0cd8cf3460cbfaa187f916cb0b9","id":"2167"}, {"dataset":"MSV000095382","datasetNum":"95382","title":"GNPS - CMMC_3_keto_acyl_lipids_VD_68_69_71_72_73_74_78_84_88","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721345266000","created":"Jul. 18, 2024, 4:27 PM","description":"MS\/MS fragmentation data of N acyl lipids 2 acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"19","fileSizeKB":"836535","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"3-keto, acyl lipid, microbial","pi":[{"name":"Pieter C. 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Blood was drawn from the hepatic, portal, renal, splenic, and inferior mesenteric veins, the lateral auricular vein, the aorta, and the coronary sinus using a 23G butterfly needle attached to a 1 mL syringe. The external jugular vein and the left and right ventricles were sampled using a 27G needle connected to a 1 mL syringe. All organ blood samples were taken within 5-10 minutes of the initial sampling. 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We found that histidine levels increased by 8 days of blue light exposure, both in the treated subcutaneous adipose tissue and in circulation. Additionally, blue light-induced circulating histidine levels were not affected by the central blockade of histidine decarboxylase activity using FMH (Fluoromethylhistidine) in the hypothalamus. The details are described in the Summary Excel file.","fileCount":"149","fileSizeKB":"130301","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"GCMS_Agilent 7980B Gas Chromatograph and Pegasus HT TOF MS;RP_Shimadzu Nexera UPLC and Sciex TripleTOF 6600;TQ_Shimadzu Nexera UPLC and Sciex 5500 Triple Quadrupole MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomic profiles, Mouse, Adipose, Light exposure","pi":[{"name":"Yu-Hua Tseng","email":"yu-hua.tseng@joslin.harvard.edu","institution":"Joslin Diabetes Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054050","task":"bacba273e3164f909d3378d0f3ac9077","id":"2170"}, {"dataset":"MSV000095375","datasetNum":"95375","title":"Ahmed_LINC00324_timsTOFPro2_P124_VS18_VS19","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721331518000","created":"Jul. 18, 2024, 12:38 PM","description":"This dataset consists of 12 raw MS files and associated peak lists and results files, acquired on a timsTOF Pro 2 mass spectrometer. Six files were acquired in Data Dependent Acquisition mode and six were acquired in Data Independent Acquisition mode. \nSamples were generated by Sameen Ahmed. Sample clean-up, digestion, and mass spectrometry acquisition were performed by Cassandra Wong. Analysis was performed by Sameen Ahmed, Philipp Maass, and Cassandra Wong. \nThe files are associated with a manuscript submitted for publication by Sameen Ahmed et al. The main goal of this paper was to determine total protein levels in wildtype (WT) and deltaLINC00324 C-28\/I2 chondrocytes. Specifically, investigated how the loss of the tRNA-overlapping lncRNA locus LINC00324 locus affected codon usage at the protein level. \nPhilipp G. 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Searle","email":"bsearle@systemsbiology.org","institution":"Institute for Systems Biology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054037","task":"487a6c766a69431da884c1023b5bc819","id":"2173"}, {"dataset":"MSV000095370","datasetNum":"95370","title":"Proteomic profiling of acoustically isolated extracellular vesicles from blood plasma during murine bacterial sepsis","user":"AxelBroman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721299225000","created":"Jul. 18, 2024, 3:40 AM","description":"Extracellular vesicles were isolated from plasma in a murine sepsis model. The proteomes of both plasma and EVs were analyzed and compared for healthy and infected (S. pyogenes or E. coli) mice. 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Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 2.6 um 100 A pore size Polar C18 reversed phase UHPLC column 100 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"31","fileSizeKB":"995105","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ink;etoh;ethanol;MSCollaboratory","pi":[{"name":"Daniel Bolnick","email":"daniel.bolnick@uconn.edu","institution":"University of Connecticut","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4a15964f5fa943c2bc761eea34fa7396","id":"2175"}, {"dataset":"MSV000095362","datasetNum":"95362","title":"GNPS - 2024_SICRIT_ESI_Vibrio_fischeri_cholerae","user":"amcatamn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721244538000","created":"Jul. 17, 2024, 12:28 PM","description":"Microbial metabolomics data from both ESI and SICRIT sources on V. fischeri and V. cholerae extracts.","fileCount":"31","fileSizeKB":"5628464","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aliivibrio fischeri (NCBITaxon:668);Vibrio cholerae (NCBITaxon:666)","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbial;vibrio;metabolomics","pi":[{"name":"Laura Sanchez","email":"lmsanche@ucsc.edu","institution":"University of California, Santa Cruz","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"53aa680eec8c4a82ae0b141d94fe2167","id":"2176"}, {"dataset":"MSV000095360","datasetNum":"95360","title":"An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues","user":"nathanhendricks","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721228899000","created":"Jul. 17, 2024, 8:08 AM","description":"This technical note presents a comprehensive proteomics workflow for the new combination of Orbitrap and Astral mass analyzers across biofluids, cells, and tissues. Central to our workflow is the integration of Adaptive Focused Acoustics (AFA) technology for cells and tissue lysis, to ensure robust and reproducible sample preparation in a high-throughput manner. Furthermore, we automated the detergent-compatible single-pot, solid-phase-enhanced sample Preparation (SP3) method for protein digestion, a technique that streamlines the process by combining purification and digestion steps, thereby reducing sample loss and improving efficiency. The synergy of these advanced methodologies facilitates a robust and high-throughput approach for cells and tissue analysis, an important consideration in translational research. This work disseminates our platform workflow, analyzes the effectiveness, demonstrates reproducibility of the results, and highlights the potential of these technologies in biomarker discovery and disease pathology. For cells and tissues (heart, liver, lung, and intestine) proteomics analysis by data-independent acquisition mode, identifications exceeding 10,000 proteins can be achieved with a 24-minute active gradient. In 200ng injections of HeLa digest across multiple gradients, an average of more than 80% of proteins have a CV less than 20%, and a 45-minute run covers ~90% of the expressed proteome. In plasma samples including naive, depleted, perchloric acid precipitated, and Seer nanoparticle captured, all with a 24-minute gradient length, we identified 87, 108, 96 and 137 out of 216 FDA approved circulating protein biomarkers, respectively. This complete workflow allows for large swaths of the proteome to be identified and is compatible across diverse sample types.","fileCount":"552","fileSizeKB":"2517654456","spectra":"35551443","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"UNIMOD:5 - \\\"Carbamylation.\\\"","keywords":"Orbitrap Astral;High-Throughput;Plasma Proteomics;tissue proteomics;automation;biomarker;Missing proteins;PBMC","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"},{"name":"susan mockus","email":"susan.mockus@cshs.org","institution":"Precision Biomarker Laboratories, Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054015","task":"f0294c48645742e3b5cd786d5cea7a78","id":"2177"}, {"dataset":"MSV000095359","datasetNum":"95359","title":"GNPS - Metabolomic analysis of Streptomyces ansochromogenes ssp. pallens aqueous fraction","user":"Rolandoo1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721227134000","created":"Jul. 17, 2024, 7:38 AM","description":"All chemicals were from Fisher Scientific unless otherwise noted. All solvents for extraction were HPLC grade, all solvents for mass spectrometry analysis were LCMS (Thermo Optima) grade. Streptomyces ansochromogenes subspecies pallens NRRL B-12018 was obtained from the ARS Culture Collection of the United States Department of Agriculture. A 30 mL Streptomyces ansochromogenes subspecies pallens NRRL B-12018 was inoculated from an ISP2 agar culture and cultivated in liquid ISP2 medium (4 g yeast extract, 10 g malt extract, 4 g D-glucose in 1 L deionized water, pH 7.3) for 11 days at 30 celsius at 225 rpm. The medium was then centrifuged in 50 mL centrifuge tube at 3200 g for 30 min. The cell pellet and supernatant were separated subsequently, and the supernatant (30 mL) was extracted three times with 50 mL ethyl acetate to remove lipophilic components. Then the supernatant was dried by rotary evaporation at 40 celsius. Finally, the dried supernatant was resuspended in 3.5 mL deionized water, centrifuged for 5 min at 16000 g, filtered with a Cytiva syringeless filter (0.2 micron mesh size, Cytiva, US503NPEORG). The filtered supernatant was immediately analyzed by liquid-chromatography-tandem mass spectrometry on a Thermo QExactive orbitrap mass spectrometer with a H-ESI-II ion source coupled to a Vanquish HPLC system. The LC parameters were as follows: Phenomenex Kinetex 2.6 micrometer C18 reverse phase 100 Ang. 150 x 3 mm LC column, solvent A: 20mM ammonium formate (pH 3.2), solvent B: 90% acetonitrile and 10% 200 mM ammonium formate (pH 3.2), column compartment temperature 30 celsius, injection volume 5 microliter, flow rate 0.5 mL\/min, 0 min: 0% B, 5 min: 40% B, 4.5 min: 95% B, 5.5 min: 95% B, 6 min: 0% B, 10 min: 0% B. Electrospray ion source (Thermo H-ESI-II source) parameters were as follows: negative ion mode, sheath gas flow 35 psi, aux gas flow 3 psi, electrospray capillary temperature 320 celsius, electrospray capillary voltage 3.6 kV. MS parameters were as follows: full MS, resolution 70000, mass range 400-1200 m\/z, dd-MS2 (data-dependent MS\/MS), resolution 17500, AGC target 1x10^5, loop count 5, isolation width 1.0 m\/z, collision energy 25 eV and dynamic exclusion 0.5 s. LC-MS data were analyzed with QualBrowser in the Thermo Xcalibur software package (v.4.3.73.11, Thermo Scientific).","fileCount":"2","fileSizeKB":"139149","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces ansochromogenes subsp. pallens (NCBITaxon:2306568)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces ansochromogenes","pi":[{"name":"Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan, Ann Arbor","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1a39f0767fcb4901a8c8a9e79eb616e8","id":"2178"}, {"dataset":"MSV000095358","datasetNum":"95358","title":"Nuclear Proteomic comparison of lateral temporal cortex tissue from control and dementia with Lewy body cases","user":"NUPPA","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721223391000","created":"Jul. 17, 2024, 6:36 AM","description":"Data Dependent acquisition of 0.5-1ug nuclear extract generated from post-mortem frozen temporal cortex tissue (BA21\/22) obtained from control or Dementia with Lewy body case.","fileCount":"21","fileSizeKB":"24208806","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Dementia with Lewy bodies;Synucleiopathies;DNA damage;Nucleus;Brain;Cortex","pi":[{"name":"David J. 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This work investigates the degree to which autophagy participates in the remodeling by comparing corneocytes from the sole (foot pads) of wild type (WT, n=5, samples names NK70-74) to those from mice (EKO, n=6, samples names NK75-80) with epidermal keratinocyte-specific deletion of Autophagy-related gene 7 (Atg7). Sample NK81 is a blank. The cornified layer of the epidermis (stratum corneum) was sampled by tape-stripping from the soles of hind limbs and subjected to label-free proteomics as previously described (Karim et al. PLoS One 2023;18:e0283619). Among more than 170 proteins detected, 10 proteins were significantly increased in abundance when autophagy was suppressed. The autophagy-dependent alterations in the protein composition of corneocytes are less pronounced than those in hard cornified skin appendages. 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RSI indicates the raw intensity normalized to the molecular weight of the protein to prevent biases in the peptide counts due to protein size. \n\nThe files herein are as follows:\nHEK-GDE2-EV MS results: RSI values obtained for extracellular vesicles derived from HEK293T cells transfected with GDE2, H243A, or no transfection. \n\nWT and Gde2KO-EV MS results: RSI values obtained for extracellular vesicles derived from DIV14-17 WT or Gde2KO cortical neuronal cultures. \n\nGDE2-eFLAG MS results: RSI values obtained for extracellular vesicles derived from DIV14-17 WT (Control) or GDE2-eFLAG heterozygous cortical neuronal cultures. 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When methionine analogs are incorporated into a proteome, enrichment of the BA-labeled proteins allows the detection of newly synthesized proteins (NSP) by mass spectrometry. We previously reported that using our Direct Detection of Biotin-containing Tags (DidBIT) strategy, protein identifications and confidence are increased by enriching for BA-peptides instead of BA-proteins. We compared cleavable BA (DADPS) and uncleavable BA in the identification and TMT quantification of NSP. More than fifty percent more proteins were identified and quantified using DADPS than with uncleavable BA. Interrogation of the data revealed that multiple factors are responsible for the superior performance of DADPS.","fileCount":"71","fileSizeKB":"144079732","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse;Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"BONCAT;DidBIT;azidohomoalanine;azidonorleucine;DADPS","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053959","task":"2fd701f792b843079bf0bf133742a406","id":"2190"}, {"dataset":"MSV000095341","datasetNum":"95341","title":"A. muciniphila, B. longum, E. coli, headspace metabolites","user":"AmaliaBerna","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721076665000","created":"Jul. 15, 2024, 1:51 PM","description":"Culture headspaces of A. muciniphila, B. longum, E. coli, and sterile media controls using sorbent tubes and GCMS (Figure 4C)","fileCount":"17","fileSizeKB":"8263203","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Akkermansia muciniphila (NCBITaxon:239935);Bifidobacterium longum subsp. longum (NCBITaxon:1679);Escherichia coli (NCBITaxon:562);BHI-mucin","instrument":"Pegasus 4D","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"volatile organic compounds;culture;headspace","pi":[{"name":" Andrew L. 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","fileCount":"13","fileSizeKB":"21053680","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"endocytosis;clathrin;CCDC32;AP2;CFNDS","pi":[{"name":"Zhiming Chen","email":"chenzm095@gmail.com","institution":"University of South China","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3402282d122e41f5b688a2bf7be519a7","id":"2193"}, {"dataset":"MSV000095337","datasetNum":"95337","title":"GNPS - Klebsiella oxytoca facilitates microbiome recovery via antibiotic degradation and restores colonization resistance in a diet-dependent manner","user":"acv20","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721051932000","created":"Jul. 15, 2024, 6:58 AM","description":"Cecal samples (ca. 100 mg) were thawed on ice. 2-ml homogenizing tubes were pre-filled with 1 ml cold extraction solvent (0.1 microgram\/ml caffeine in 80% MeCN, stored at -20 degrees C) and an appropriate amount of zirconia beads (0.1 mm) was added. The thawed cecal samples were transferred to the prepared tubes and the samples homogenized by bead beating for two minutes. The samples were stored on ice for two minutes before bead beating was repeated. Post homogenization, the samples were centrifuged twice at 13,000 x g, 4 degrees C for ten minutes. From each sample, 900 microliter supernatant was removed in two 450 microliter portions, and each portion was added to separate 1.5-mL Eppendorf tubes. All samples were concentrated using a CentriVap fitted with a -80 degrees C cold trap (Labconco, Kansas, MO, USA). The dry extracts were stored at -80 degrees C until processed further for LC-MS\/MS analysis. The dried extracts were reconstituted in 100 microliter 80% MeCN containing 10 ng\/ml trimethoprim (TMP) as internal standard (IS) for normalization. To determine the ampicillin content, 1 microliter of the reconstituted extract was analyzed by using a 1290 Infinity II LC System (Agilent Technologies, Santa Clara, CA, USA) coupled to an AB SCIEX QTrap 6500 triple quadrupole mass spectrometer (AB SCIEX Germany GmbH, Darmstadt, Germany). The samples were separated on a Gemini 3-micrometer NX-C18 column (110 angstrom, 50 x 2 mm; Phenomenex, Torrance, CA, USA). Samples were analyzed in positive mode (electrospray ionization; ionization voltage: 4.5 kV; source temperature: 400 deg C) using solvent A (water supplemented with 0.1% formic acid) and solvent B (acetonitrile supplemented with 0.1% formic acid). The elution was run at a flow rate of 0.7 ml\/minute as follows: 5% B from 0 to 1 minutes followed by a linear gradient from 5% B to 95% B from 1 to 5 minutes, keeping this composition (95% B) for the final minute (5 to 6 minutes). Ampicillin, caffeine and trimethoprim were detected as [M+H]+ ions using a multiple reaction monitoring (MRM) The transitions used for ampicillin were 350.301 -> 106.1 (quantifier, collision energy 17 V), 350.301 -> 160 (qualifier, collision energy 15 V), 350.301 -> 114 (qualifier, collision energy 33 V) and 350.301 -> 79.1 (qualifier, collision energy 67 V). The transitions for caffeine were the following: 195.116 -> 138.1 (quantifier, collision energy 27 V), 195.116 -> 110.1 (qualifier, collision energy 50 V). The transitions for trimethoprim were the following: 291.112 -> 230.2 (quantifier, collision energy 31 V), 291.112 -> 261.2 (qualifier, collision energy 33 V) The retention time for ampicillin was 1.9 min, for caffeine 2.0 min and 1.8 min for trimethoprim. \r\nThe transition list and raw data were loaded into the Skyline software package (version 22.2.0527). The peaks were integrated, and the ampicillin peak areas normalized to the internal standard TMP. Data were plotted and statistical evaluation performed using GraphPad Prism v9.1.\r\n","fileCount":"59","fileSizeKB":"8708","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"QTRAP 6500","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ampicillin, mouse, caecum, Klebsiella oxytoca","pi":[{"name":"Prof. Dr. Till Strowig","email":"till.strowig@helmholtz-hzi.de","institution":"Helmholtz Centre for Infection Research","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3a7bb5c8717c45449ddf12a9509fc484","id":"2194"}, {"dataset":"MSV000095333","datasetNum":"95333","title":"Quantitative high sensitivity proteomics with the Orbitrap ASTRAL platform ","user":"Valdemaras","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721028782000","created":"Jul. 15, 2024, 12:33 AM","description":"The repository contains the data associated with the manuscript.","fileCount":"3460","fileSizeKB":"879142511","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral;Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Single-cell proteomics;Quantitative accuracy;Orbitrap Astral","pi":[{"name":"Erwin Marten Schoof","email":"erws@dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2945872aa8dd41e0bde9ba9110a6ffc5","id":"2195"}, {"dataset":"MSV000095331","datasetNum":"95331","title":"GNPS - Drug metabolism - Bacterial synthetic community ","user":"vlamoureux","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1721000828000","created":"Jul. 14, 2024, 4:47 PM","description":"Bacterial culture with drugs acquired on Q Exactive with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 150 x 2.1 mm). 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This study utilizes UPLC-ESI-QTOF untargeted metabolomics combined with biochemometrics to identify novel serum biomarkers for PD. Analyzing a Brazilian cohort of serum samples from 39 PD patients and 15 healthy controls, we identified fifteen metabolites significantly associated with PD","fileCount":"235","fileSizeKB":"78815052","spectra":"149519","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Xevo G2-S QTof","modification":"no","keywords":"Metabolomics;Parkinson's disease;Biomarkers;Caffeine metabolism;Multivariate analysis;Machine learning.","pi":[{"name":"Albert Katchborian Neto","email":"albert_katchborian@hotmail.com","institution":"Federal University of Alfenas","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"90c80c9e6dd54be99f3b7e566d6895a0","id":"2200"}, {"dataset":"MSV000095322","datasetNum":"95322","title":"Understanding the genetic and structural bases of hornworts' carbon-concentrating mechanism","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720825026000","created":"Jul. 12, 2024, 3:57 PM","description":"Proteomic measurements to identify putative Rubisco interacting proteins in hornworts compared to the green alga Chlamydomonas, the traditional model for studying pyrenoid-based CO2-concentrating mechanisms (pCCM). Using antibodies and immunoprecipitation against hornwort Rubisco large subunits to pull down Rubisco and any proteins that bind to it. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline against Anthoceros agrestis proteome.","fileCount":"44","fileSizeKB":"29540276","spectra":"0","psms":"1568681","peptides":"914337","variants":"1141400","proteins":"52359","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Anthoceros agrestis (NCBITaxon:41834)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"hornworts;CO2-concentrating mechanism;proteomics;LC-MS\/MS","pi":[{"name":"Fay-Wei Li","email":"fl329@cornell.edu","institution":"Boyce Thompson Institute for Plant Research, Cornell University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053926","task":"84cd54bf88174ba5a3d99535b3c32131","id":"2201"}, {"dataset":"MSV000095321","datasetNum":"95321","title":"The discovery and structural basis of two distinct state-dependent inhibitors of BamA Mass Spectrometry Data","user":"phungw","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720813464000","created":"Jul. 12, 2024, 12:44 PM","description":"Mass spec raw data files for \"The discovery and structural basis of two distinct state-dependent inhibitors of BamA\".","fileCount":"156","fileSizeKB":"2456719","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"BamA;beta-barrel outer membrane proteins;bacteria;antibacterials","pi":[{"name":"Steven Rutherford","email":"rutherford.steven@gene.com","institution":"Genentech","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"23e00e8c876941e5b430e3154b2d45df","id":"2202"}, {"dataset":"MSV000095320","datasetNum":"95320","title":"Therapeutic reduction of rad23a extends lifespan and mitigates pathology in TDP-43 mice. ","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720811630000","created":"Jul. 12, 2024, 12:13 PM","description":"Therapeutic reduction of rad23a extends lifespan and mitigates pathology in TDP-43 mice. \nXueshui Guo, Ravindra Prajapati, Jiyeon Chun, Insuk Byun, Kamil K Gebis, Yi-Zhi Wang, Karen Ling, Casey Dalton, Jeff Blair, Anahid Hamidianjahromi, Jeffrey N. Savas, Min Jae Lee, Jemeen Sreedharan, Robert Kalb","fileCount":"44","fileSizeKB":"83872153","spectra":"0","psms":"278512","peptides":"31940","variants":"31940","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"rad23a","pi":[{"name":"Jeffrey N. Savas, PhD","email":"jeffrey.savas@northwestern.edu","institution":"Department of Neurology Northwestern University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053922","task":"7f990daec30f4e33a3050b36807a948d","id":"2203"}, {"dataset":"MSV000095319","datasetNum":"95319","title":"GNPS_koolengroup_mircorganisms_B","user":"moyses","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720802002000","created":"Jul. 12, 2024, 9:33 AM","description":"LC-MS\/MS of fungi studied in the metabolomics and mass spectrometry research group (MMSRG) at the State University of Amazonas, Brazil.","fileCount":"92","fileSizeKB":"626119","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Penicillium (NCBITaxon:5073);Fusarium (NCBITaxon:5506)","instrument":"micrOTOF-Q","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fungi;Natural Product;microrganism","pi":[{"name":"Hector Koolen","email":"hectorkoolen@gmail.com","institution":"University of the State of Amazonas","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8afc1a72f0c94e59b7aecd1f8678095e","id":"2204"}, {"dataset":"MSV000095318","datasetNum":"95318","title":"GNPS_koolengroup_mircorganisms_A","user":"moyses","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720800381000","created":"Jul. 12, 2024, 9:06 AM","description":"LC-MS\/MS of fungi studied in the metabolomics and mass spectrometry research group (MMSRG) at the State University of Amazonas, Brazil.","fileCount":"261","fileSizeKB":"2532644","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Penicillium (NCBITaxon:5073);Talaromyces (NCBITaxon:5094);Trichoderma (NCBITaxon:5543);Pestalotiopsis (NCBITaxon:37840);Arcopilus sp. (NCBITaxon:2029755)","instrument":"micrOTOF-Q;6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fungi;Natural product;microrganism","pi":[{"name":"Hector Koolen","email":"hectorkoolen@gmail.com","institution":"University of the State of Amazonas","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4aaf1ac84d4841bf8edd2487a41318fe","id":"2205"}, {"dataset":"MSV000095315","datasetNum":"95315","title":"Identification of the Senescence Associated Secretory Phenotype from THP-1 Monocytes","user":"reemabanarjee","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720795599000","created":"Jul. 12, 2024, 7:46 AM","description":"Senescence was induced in THP-1 monocytes in culture and the senescence associated secretory phenotype (SASP) was measured for the complete conditioned medium by applying nanoparticle based Proteograph technology for enrichment followed by DIA mass spectrometry","fileCount":"67","fileSizeKB":"318465823","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Senescence;Secretome;Monocytes;Proteograph","pi":[{"name":"Dr. Nathan Basisty","email":"nathan.basisty@nih.gov","institution":"NIH-National Institute on Aging, Baltimore, MD","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"eb7742fb31cb49f7a410406942077aed","id":"2206"}, {"dataset":"MSV000095314","datasetNum":"95314","title":"GNPS - Secondary metabolites from bacteria isolated from Mangroves","user":"girishbeedessee","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720795382000","created":"Jul. 12, 2024, 7:43 AM","description":"Secondary metabolites from bacteria isolated from Mangroves","fileCount":"7","fileSizeKB":"1169734","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Shewanella ","instrument":"thermofischer","modification":"MS:1002864 - 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"drugs;microbial community;biotransformation","pi":[{"name":"Daniel Petras ","email":"danie.petras@uni-tuebingen.de","institution":"University of Tuebigen ","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c3c8c30c8d294d0087b7792eca9b10b3","id":"2209"}, {"dataset":"MSV000095310","datasetNum":"95310","title":"Engineering the Secretome of Aspergillus niger for Cellooligosaccharides Production from Plant Biomass","user":"Fabiano","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720770782000","created":"Jul. 12, 2024, 12:53 AM","description":"Fermentation of sugars derived from plant biomass feedstock is crucial in achieving sustainability. Hence, utilizing customized enzymatic cocktails to obtain oligosaccharides instead of monomers is an alternative fermentation strategy to produce prebiotics, cosmetics, and biofuels. This study developed an engineered strain of Aspergillus niger producing a tailored cellulolytic cocktail capable of partially degrading sugarcane straw to yield cellooligosaccharides. The A. niger prtT strain created resulted in a reduced extracellular protease production. The prtT background was then used to create strains by deleting exoenzymes encoding genes involved in mono- or disaccharide formation. Consequently, we successfully generated a tailored prtTbglA strain by eliminating a beta-glucosidase (bglA) gene and subsequently deleted two cellobiohydrolases and one beta-xylosidase encoding genes using a multiplex strategy, resulting in the Quintuple strain (prtT; bglA; cbhA; cbhB; xlnD). When applied for sugarcane biomass degradation, the tailored secretomes produced by A. niger resulted in a higher ratio of cellobiose and cellotriose compared with glucose relative to the reference strain. Mass spectrometry revealed that the Quintuple strain secreted alternative cellobiohydrolases and beta-glucosidases to compensate for the absence of major cellulases. Enzymes targeting minor polysaccharides in plant biomass were also upregulated in this tailored strain. Tailored secretome use increased COS\/glucose ratio during sugarcane biomass degradation showing that deleting some enzymatic components is an effective approach for producing customized enzymatic cocktails. Our findings highlight the plasticity of fungal genomes as enzymes that target minor components of plant cell walls, and alternative cellulases were produced by the mutant strain. Despite deletion of important secretome components, fungal growth was maintained in plant biomass.","fileCount":"23","fileSizeKB":"11994802","spectra":"251321","psms":"2705","peptides":"702","variants":"816","proteins":"184","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus niger (NCBITaxon:5061)","instrument":"Q-Exactive","modification":"Oxidation (M), GlcNac (N) and Acetyl on proteins N-termini, cysteine carbamidomethyl","keywords":"Aspergillus niger, CAZymes, cellooligosaccharides, fungal engineering, tailor-made enzymatic cocktail, sugarcane biomass","pi":[{"name":"Andre Damasio","email":"adamasio@g.unicamp.br","institution":"Universidade Estadual de Campinas (UNICAMP)","country":"Brazil"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"2a8c65a1eac3470ca84e5c95807cc125","id":"2210"}, {"dataset":"MSV000095309","datasetNum":"95309","title":"GNPS - 20240711_RiPP_Metal-binding_Native_MS","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720740798000","created":"Jul. 11, 2024, 4:33 PM","description":"Metal-infusion experiments were run on purified RiPP from Vinayak Agarwal's laboratory. ","fileCount":"6","fileSizeKB":"723149","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RiPP;metal;copper","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b25fb651e4d24b05baa6453e01cf3a79","id":"2211"}, {"dataset":"MSV000095306","datasetNum":"95306","title":"Effect of CIGB-300 on OCI and HL-60 Acute Myeloid Leukemia cell lines","user":"vbesada","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720719441000","created":"Jul. 11, 2024, 10:37 AM","description":"Relative quantification of phosphoproteome modulated by CK2 inhibitor CIGB-300 [40 uM] after 30 min treatment for two leukemia cell lines. Protein extracts were processed by FASP procedure. File names labeled with letters L and T for Lys-C and Trypsin derived digestions, respectively. Labeled P for enriched phosphopeptides via TiO2.","fileCount":"48","fileSizeKB":"75095699","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"CIGB-300;phosphoproteomic;leukemia","pi":[{"name":"Vladimir Besada","email":"vladimir.besada@cigb.edu.cu","institution":"Center for Genetic Engineering and Biotechnology","country":"Cuba"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"86ccc3eec65444f5b080c79be78086e2","id":"2212"}, {"dataset":"MSV000095305","datasetNum":"95305","title":"RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum (HyPR_Mito dataset)","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720716029000","created":"Jul. 11, 2024, 9:40 AM","description":"Mass spectrometry analysis of HyPR_Mito samples used for identifying mitochondrial rRNA-associated proteins.","fileCount":"215","fileSizeKB":"54988834","spectra":"0","psms":"485638","peptides":"25077","variants":"35306","proteins":"3552","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Plasmodium falciparum (NCBITaxon:5833)","instrument":"LTQ Orbitrap Elite","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"apicoplast;Plasmodium;noncoding RNA;PfRAP03;PfRAP08","pi":[{"name":"Laurence Florens","email":"laf@stowers.org","institution":"The Stowers Institute for Medical Research","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD053889","task":"fa395be7791642318ec221cf6e101b80","id":"2213"}, {"dataset":"MSV000095304","datasetNum":"95304","title":"RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum (IP-MS_RAP03_RAP08 dataset)","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720715582000","created":"Jul. 11, 2024, 9:33 AM","description":"Mass spectrometry analysis of IP-MS samples used for identifying RAP03 and RAP08 associated proteins.","fileCount":"320","fileSizeKB":"74543924","spectra":"0","psms":"106225","peptides":"9311","variants":"12045","proteins":"1386","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Plasmodium falciparum (NCBITaxon:5833)","instrument":"LTQ Orbitrap Elite","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"apicoplast;Plasmodium;noncoding RNA;PfRAP03;PfRAP08","pi":[{"name":"Laurence Florens","email":"laf@stowers.org","institution":"The Stowers Institute for Medical Research","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD053888","task":"45b82d950c884d24b63c0e59f4bd81b1","id":"2214"}, {"dataset":"MSV000095302","datasetNum":"95302","title":"Quantitative Proteomic Profiling Reveals Sexual Dimorphism in the Retina and RPE of C57BL6 mice.","user":"jackcrabb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720710988000","created":"Jul. 11, 2024, 8:16 AM","description":"Background: Sex as a biological variable is not a common consideration in molecular mechanistic or preclinical studies of retinal diseases. Understanding the sexual dimorphism of adult RPE and retina under physiological conditions is an important first step in improving our understanding of sex-based physio-pathological mechanisms.\n\nMethods: Isobaric tags for relative and absolute quantitation (iTRAQ) were used for quantitative proteomics of male and female mouse retina and RPE (10 mice of each sex for each tissue type). Differentially expressed proteins were subjected to Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA).\n\nResults: Differential expression analysis identified 21 differentially expressed proteins in the retina and 58 differentially expressed proteins in the RPE. Ingenuity pathway analysis identified the top canonical pathways differentially activated in the retina to be calcium transport I, nucleotide excision repair, molecular transport and cell death and survival. In the RPE, the top canonical pathways were calcium signaling, dilated cardiomyopathy signaling, actin cytoskeletal signaling and cellular assembly and organization.\n\nConclusions: These results provide insights into sex differences in the retina and RPE proteome of mice and begin to shed clues into the sexual dimorphism seen in retinal diseases.","fileCount":"57","fileSizeKB":"89590878","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:730 - \\\"Representative mass and accurate mass for 113, 114, 116 & 117.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Sexual Dimorphism;Retina;RPE;iTRAQ8Plex;mouse","pi":[{"name":"Bela Anand-Apte","email":"anandab@ccf.org","institution":"Cleveland Clinic","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"65e681553e6e492bb7d11bd1b541b1fe","id":"2215"}, {"dataset":"MSV000095301","datasetNum":"95301","title":"Towards a universal method for middle down analysis of antibodies via proton transfer charge reduction Orbitrap mass spectrometry","user":"Fornelli_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720709623000","created":"Jul. 11, 2024, 7:53 AM","description":"We report the development and benchmark of a middle down mass spectrometry strategy based on the combination of different ion fragmentation techniques with proton transfer charge reduction (PTCR) to simplify the gas phase sequencing of mAb subunits. Applied on the liquid chromatography time scale using an Orbitrap Tribrid mass spectrometer, PTCR produces easy to interpret mass spectra with limited ion signal overlap. 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They were then extracted using XAD7 and methanol. Two additional cultures, a 50 mL culture and a 250 mL culture, were extracted using ethyl acetate. The extractions were then analyzed using MS.","fileCount":"77","fileSizeKB":"373581","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Myxococcus xanthus (NCBITaxon:34)","instrument":"Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"M. Xanthus;Myxococcus xanthus;Metabolome;Metabolites","pi":[{"name":"Markus Nett","email":"markus.nett@tu-dortmund.de","institution":"TU Dortmund","country":"Germany"},{"name":"Till Steinmetz ","email":"till.steinmetz@tu-dortmund.de","institution":"TU Dortmund","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"63cd69c34c224a328b0d1e0ee9f7977c","id":"2232"}, {"dataset":"MSV000095265","datasetNum":"95265","title":"TAK285, GSK1838705A and Src inhibitor 3 Kinobeads selectivity profiling","user":"Polina_prokofeva_Kusterlab_1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720384971000","created":"Jul. 7, 2024, 1:42 PM","description":"This dataset contains the raw files, search results, and the analyzed data of the Kinobead selectivity profiling of TAK285, GSK1838705A, and Src inhibitor 3.","fileCount":"5559","fileSizeKB":"102512844","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Kinobeads, Selectivity profiling, target profiling, TAK285, GSK1838705A, Src inhibitor 3","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053729","task":"b797459b3d8f4d2a81ebe732ca5ecd29","id":"2233"}, {"dataset":"MSV000095264","datasetNum":"95264","title":"An Integrative SP3 Workflow for Multi-PTM Proteomics Profiling","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720324400000","created":"Jul. 6, 2024, 8:53 PM","description":"Global proteomic, redox proteomic, and phosphoproteomic data from mouse C10 epithelial cells and skeletal muscle tissue, no treatments used for method development experiments using these biological sytems. Global proteomic, redox proteomic, phosphoproteomic, and acetylomic data from mouse Beta-TC-6 pancreatic Beta-cells, untreated (mock) and cytokine-treated Beta-cells experimental details follow: Time points 4, 8, and 24 hours; 4 biological replicates. Samples were digested with trypsin and Lys-C, then analyzed by LC-MS\/MS. Data were searched with MS-GF+, MASIC, and MaxQuant using PNNL's DMS processing pipeline.","fileCount":"603","fileSizeKB":"274520883","spectra":"0","psms":"5397246","peptides":"2130225","variants":"3113983","proteins":"63826","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480;Q Exactive HF-X;Q Exactive Plus","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:108 - \\\"N-ethylmaleimide on cysteines.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"post-translational modifications;functional proteomics;SP3","pi":[{"name":"Tong Zhang","email":"tong.zhang@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"","task":"6409182308e7406197f37ea413ec268d","id":"2234"}, {"dataset":"MSV000095263","datasetNum":"95263","title":"RAW files for manuscript 'Profiling the antigen-ome of the cystic fibrosis pathogen Achromobacter xylosoxidans'","user":"csahl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720251342000","created":"Jul. 6, 2024, 12:35 AM","description":"RAW files for manuscript 'Profiling the antigen-ome of the cystic fibrosis pathogen Achromobacter xylosoxidans'","fileCount":"25","fileSizeKB":"15631211","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Achromobacter xylosoxidans (NCBITaxon:85698)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Achromobacter xylosoxidans;Cystic fibrosis;IgG antigent;Systems antigenomics","pi":[{"name":"Lisa Pahlman","email":"lisa.pahlman@med.lu.se","institution":"Lund University","country":"Sweden"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b16b4c087aba4dcc97292a9b80818cd8","id":"2235"}, {"dataset":"MSV000095262","datasetNum":"95262","title":"Proteomics Analysis of Round and Wrinkle Pea (Pisum sativum L.) 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Relatively more proteins were identified during early seed development compared to later stages, and the protein profiles were also drastically different between early and late stages. Statistical analysis identified 735 significantly different proteins between wrinkled and round seeds, regardless of the growth stage. These detected proteins were characterized into different functional classes including metabolic enzymes, proteins involved in protein biosynthesis and homeostasis, carbohydrate metabolism, vesicle trafficking, cell division, and cell wall organization. Cell division-related proteins were more abundant in the early stages of seed development, whereas storage proteins and proteins implicated in lipid metabolism were more abundant at the later stages. Wrinkled seeds had a significantly lower abundance of starch-branching enzyme than did round seeds. This enzyme is involved in the biosynthesis of the amylopectin component of starch. Seed storage proteins such as legumin and a form of albumin (PA2) accumulated more in round pea genotypes, whereas vicilin was more abundant in the wrinkled pea genotype. In summary, this study can enhance our understanding of pea seed development, highlighting key differences in protein profiles between round and wrinkled pea seeds.","fileCount":"45","fileSizeKB":"42271250","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pisum sativum (NCBITaxon:3888)","instrument":"Orbitrap Fusion Lumos","modification":"Oxidation [M]","keywords":"Label-free proteomics, differentially abundant proteins, protein functional classes, round and wrinkled peas","pi":[{"name":"Rebecca J. 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Reversed-phase, ESI positive, C18 column (1.7 um particle size, 2.1 mm x 50 mm Phenomenex, Kinetex)","fileCount":"221","fileSizeKB":"6675647","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"None","keywords":"Matrix Tube; Metabolomics","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"73aaff7f3d614fa8b423da9d53f502ad","id":"2237"}, {"dataset":"MSV000095254","datasetNum":"95254","title":"GNPS : Specialized metabolites in Medicago truncatula with or witout Aphid in NO3 nutrition","user":"stephINRAE","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720160992000","created":"Jul. 4, 2024, 11:29 PM","description":"Analysis of specialized metabolites of Medicago truncatula leaves under 4 conditions : 1. Symbiosis 2. Nitrate solution 3. Symbiosis + Aphid 4. 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","fileCount":"175","fileSizeKB":"10837447","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Monotropa uniflora (NCBITaxon:50148)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"monotropa;ghost pipe","pi":[{"name":"Josh J Kellogg","email":"jjk6146@psu.edu","institution":"Pennsylvania State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3281d099adb64e3183c8eee2a7aeb825","id":"2239"}, {"dataset":"MSV000095252","datasetNum":"95252","title":"Proteomic Investigation of Neurotrophic trans-Banglene Reveals Potential Link to Iron Homeostasis","user":"kyungmee","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720136188000","created":"Jul. 4, 2024, 4:36 PM","description":"Neurodegenerative diseases remain an area where the causative disease mechanisms, with few exceptions, are poorly understood and which are very resistant to modern therapeutic advances. Current FDA-approved medications result in modest improvements in quality of life measures and no increase in life expectancy. In this context, insight into cellular elements that dictate neuronal survival and growth versus degradation or death (the shared feature of all neurodegenerative disorders), is valuable. Molecular agents that modulate these responses can be uniquely beneficial in such inquiries because of their ease of administration, frequent robustness in biological media, and their potential for pharmacokinetic optimization or derivatization in the hands of a medicinal chemist. Further, investigation of the mechanism of action for small molecule natural products can lead to unexpected insights, such as the serendipitous discovery of the mTOR protein (mammalian target of rapamycin), a central controller of cell metabolism. We performed a global proteomic analysis of t-BG's effects in PC-12 cells and compared it to the impact of natural nerve growth factor (NGF), a neurotrophin protein which causes similar phenotypic changes in PC-12 cells. To our surprise, while we gained insight into classic pro-growth, pro-differentiation, and pro-survival pathways, we also observed changes in iron-binding proteins in the cell that were unanticipated. Since iron dyshomeostasis is an increasingly recognized element of neurodegenerative disease, particularly in early stages of Alzheimer\u2019s and Parkinson\u2019s disease,10 the potential connection between neurotrophic activity and altered iron homeostasis is quite notable.\r\n\r\nCell pellets were lysed in 4% SDS 100mM tris pH 6.8 and total protein concentration was estimated with BCA assay. Approximately 20 micrograms of total protein was reduced and alkylated with dithiothreitol and iodoacetamide (PMID12724530) and loaded onto 10% SDS-PAGE. Each sample's lane was separated into 5 fractionations and the proteins were digested out of the gels using MS-grade trypsin (PMID8779443). Resulting peptides were cleaned with C-18 STop And Go Extraction (STAGE) tips (PMID 12498253) using 40% (v\/v) acetonitrile in 0.1% (v\/v) formic acid as the elution buffer. Peptide concentration was estimated with NanoDrop One (Thermo Scientific) to load equal amounts of total peptides on Impact II Qtof (Bruker Daltonics) coupled to easy nLC 1200 (Thermo Scientific) using a in-house constructed column set up consisting a fritted 2-cm-long trap column made with 100-?m-inner diameter fused silica and 5 ?m Aqua C-18 beads (Phenomenex, cat 04A-4331) packing material, and a 30-50 cm-long analytical column with an integrated spray tip (6-8 ?m-diameter opening, pulled on a P-2000 laser puller from Sutter Instruments) made with 75-?m-inner diameter fused silica and 1.9 ?m-diameter Reprosil-Pur C-18-AQ beads (Dr. Maisch, cat r119.aq.0003) packing material. The column was heated to 50degC with another in-house constructed column heater, and was used for 60 min sample separation using the acquisition settings described in PMID 32539747. Four biological replicates of the treatment sets were processed and each sample was analyzed twice for duplicate technical replicates. The samples were randomized before injection.\r\nThe resulting data were searched on MaxQuant version 1.6.7.0 (PMID27809316) using Uniprot's rat proteome and common contaminants. Label-free quantitation, and match-between-run options were enabled using fixed modification of carbamidomethylation of cysteines, and variable modifications of oxidation of methionines and acetylation of protein N-termini. Specific proteolytic cleavages after arginine and lysine with up to 2 missed cleavages were set. The data were filtered for 1% false discovery at protein, peptide and PSM levels using revert decoy search mode.","fileCount":"124","fileSizeKB":"374817300","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"proteomics;LC-MSMS;Neurotrophic trans-Banglene;neurodegenerative diseases","pi":[{"name":"Leonard Foster","email":"foster@msl.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053648","task":"d0db1f5e99a74d1aadcff18ba0250dc2","id":"2240"}, {"dataset":"MSV000095251","datasetNum":"95251","title":"GNPS - Personal Care Product reference dataset negative ionization","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720134034000","created":"Jul. 4, 2024, 4:00 PM","description":"Personal Care Product extracted with 80:20 ACN\/H2O with sulfadimethoxine-d6 and cleaned up with EMR-Lipid SPE. Analyzed with 15 cm phenomenex polar C18 column, 15 minute HPLC gradient, orbitrap DDA method.","fileCount":"1041","fileSizeKB":"88684353","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"N\\\/A","instrument":"Q Exactive","modification":"N\\\/A","keywords":"Personal Care Products;Negative ionization","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"207b04107b0e4d72b81a48261bbcc661","id":"2241"}, {"dataset":"MSV000095250","datasetNum":"95250","title":"Molecular Basis of Spindle Morphology Changes at the Meiosis to Mitosis Transition","user":"Arminja","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720120415000","created":"Jul. 4, 2024, 12:13 PM","description":"The transition from meiotic divisions in the oocyte to mitotic divisions in the early embryo is a critical step in animal development. Despite negligible changes to cell size, shape, and content, following fertilization the small, barrel-shaped meiotic spindle is replaced by a large zygotic spindle that nucleates abundant astral microtubules at spindle poles. To identify underlying mechanisms, we applied a drug screening approach using eggs of the simple chordate Ciona robusta (sea squirt) and found that inhibition of Casein Kinase 2 (CK2) caused a shift from meiotic to mitotic-like spindle morphology with nucleation of robust astral microtubule arrays, an effect reproduced in Xenopus laevis (frog) egg extracts. In both species, a kinase assay revealed that CK2 activity decreases at fertilization. To identify substrates and downstream effectors, we assessed the global phosphoproteomic changes that accompany both the meiosis to mitosis transition and CK2 inhibition in Xenopus, which identified components of the Ran-GTP pathway as potential downstream targets. Inhibition of Ran-GTP-driven microtubule nucleation suppressed CK2-induced spindle morphology changes in both Xenopus and Ciona. These data support a model in which attenuation of CK2 activity at fertilization in chordates leads to activation of Ran-regulated spindle assembly factors that drive microtubule growth and the transition to mitotic spindle morphology.","fileCount":"386","fileSizeKB":"80787379","spectra":"0","psms":"2048478","peptides":"1186104","variants":"1513061","proteins":"45167","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xenopus laevis (NCBITaxon:8355)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Frog, mitosis, meiosis, embryo, cell cycle phases","pi":[{"name":"Arminja Nadine Kettenbach","email":"Arminja.N.Kettenbach@Dartmouth.edu","institution":"Dartmouth College","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053646","task":"1b156a1237084712a1c3ec9a46916a25","id":"2242"}, {"dataset":"MSV000095249","datasetNum":"95249","title":"Phenotypic screening against P. falciparum under physiologically relevant nutrients levels reveals novel chemical diversity and highlights the importance of the PSAC channel for parasite survival.","user":"jacobgeri","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720110898000","created":"Jul. 4, 2024, 9:34 AM","description":"Microenvironment mapping was used to identify the binding targets of two small molecules in Plasmodium Falciparum cells. In the method, small molecule - photocatalyst conjugates sensitize biotinylation of proteins binding the small molecules, which were reduced, alkylated with iodoacetamide, and immunoprecipitated using streptavidin beads. Labeling was subject to offcompete using a large excess of the free small molecule. On-bead tryptic digestion yielded peptides, which were subjected to DDA-PASEF MS measurement using a timsTOF Pro 2. CLAG3 was significantly enriched by labeling by both molecules. ","fileCount":"1884","fileSizeKB":"35292059","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Plasmodium falciparum (NCBITaxon:5833)","instrument":"timsTOF Pro 2","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Proteomics, microenvironment mapping, target identification, TIMSTOF","pi":[{"name":"Jacob Geri","email":"jag4016@med.cornell.edu","institution":"Weill Cornell Medicine","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD053644","task":"3a0ddee3f45c424fba3d40fa6e1d36eb","id":"2243"}, {"dataset":"MSV000095244","datasetNum":"95244","title":"GNPS Senna didymobotrya leaf methanolic extract","user":"Dr_Andima","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720088970000","created":"Jul. 4, 2024, 3:29 AM","description":"Powdered leaf samples were extracted with 70% methanol. ","fileCount":"2","fileSizeKB":"10033","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Senna didymobotrya (NCBITaxon:72401)","instrument":"Bruker max 4G ","modification":"Samples Extracted with methanol","keywords":"Senna didymotrya (Leaf extract)","pi":[{"name":"Dr. Andima Moses","email":"andima.moses@gmail.com","institution":"Busitema University","country":"Uganda"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a1ace3cdeda140ffa033f415138f2c7a","id":"2244"}, {"dataset":"MSV000095242","datasetNum":"95242","title":"Serum metabolomics in schizophrenia","user":"dianfengxin_XX1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720077231000","created":"Jul. 4, 2024, 12:13 AM","description":"Twenty-nine patients with schizophrenia and 30 healthy controls were enrolled.","fileCount":"62","fileSizeKB":"7875644","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"none","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Serum ;metabolomics ;schizophrenia","pi":[{"name":"DongDong Qi","email":"13314811012@163.com","institution":"Hulunbuir Third People's Hospital (Hulunbuir Mental Health Center)","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053635","task":"2c109630905641ac907cbd3d39ea7e68","id":"2245"}, {"dataset":"MSV000095241","datasetNum":"95241","title":"Serum proteomics in schizophrenia","user":"dianfengxin_XX1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720073623000","created":"Jul. 3, 2024, 11:13 PM","description":"Twenty-nine patients with schizophrenia and 30 healthy controls were enrolled.","fileCount":"661","fileSizeKB":"37213770","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"none","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Serum;schizophrenia;proteomics ","pi":[{"name":"DongDong Qi","email":"13314811012@163.com","institution":"Hulunbuir Third People's Hospital (Hulunbuir Mental Health Center)","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053629","task":"a5d6f8a2c1804cc0b3a0c929ab21a315","id":"2246"}, {"dataset":"MSV000095240","datasetNum":"95240","title":"Bacillus coagulans Capable of Utilizing Pentose and Hexose Sugars","user":"richjg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720056717000","created":"Jul. 3, 2024, 6:31 PM","description":"Expanded Genome and Proteome Reallocation in a Novel, Robust Bacillus coagulans Capable of Utilizing Pentose and Hexose Sugars","fileCount":"23","fileSizeKB":"18962615","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus coagulans (NCBITaxon:1398)","instrument":"Q Exactive Plus","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\"","keywords":"Bacillus coagulans;lactate overproducer;biomass hydrolysates;switchgrass;thermophile;overflow metabolism","pi":[{"name":"Cong Trinh","email":"ctrinh@utk.edu","institution":"University of Tennessee, Knoxville","country":"USA"},{"name":"Richard J. Giannone","email":"giannonerj@ornl.gov","institution":"Oak Ridge National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053622","task":"7c7ecdc4ccc74c65bdd1c62daa4fa3fd","id":"2247"}, {"dataset":"MSV000095239","datasetNum":"95239","title":"GNPS_CG_plantas_native_brazil_metabolomics","user":"karolinaruiz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720051122000","created":"Jul. 3, 2024, 4:58 PM","description":"Extraction protocols were adopted as described by Gachet et al. (2017), with specific modifications. The solvent dichloromethane (DCM) was replaced by ethanol (EtOH) for samples intended for analysis by low and high resolution Liquid Chromatography coupled to Mass Spectrometry (LC-MS). For samples obtained in the form of sachets for tea preparation, the procedure began with grinding the substrates, using a basic analytical grinder A 11 (IKA Moinhos). For materials obtained in natura, the procedure began with drying using liquid hydrogen and subsequent grinding of the substrates with the analytical grinder. The sample\/solvent ratio adopted was 1 g of sample for 10 ml of solvent in both types of materials. Then, ultrasound extraction was carried out with EtOH.","fileCount":"21","fileSizeKB":"459841","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Petiveria alliacea (NCBITaxon:46142);Eucalyptus globulus (NCBITaxon:34317);Syzygium aromaticum (NCBITaxon:219868);Dorstenia brasiliensis (NCBITaxon:984796);Anemopaegma arvense (NCBITaxon:2029556);Coutarea hexandra (NCBITaxon:85718);Ruta graveolens (NCBITaxon:37565);Allium sativum (NCBITaxon:4682)","instrument":"GCMS-QP2010SE","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"natural products;Oganic Chemistry","pi":[{"name":"Karolina Eduarda Ruiz Gomes","email":"karolina.ruiz@unesp.br","institution":"UNESP","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b31a564c58334e938072c5aefc6b4b6b","id":"2248"}, {"dataset":"MSV000095237","datasetNum":"95237","title":"Sirt5 regulates chondrocyte metabolism and osteoarthritis development through protein lysine malonylation","user":"JoannaBons","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720040451000","created":"Jul. 3, 2024, 2:00 PM","description":"Chondrocyte metabolic dysfunction plays an important role in osteoarthritis (OA) development during aging and obesity. However, it is unknown how metabolic dysfunction occurs during these two conditions. Proteins posttranslational modifications (PTMs) have recently emerged as an important regulator of cellular metabolism. We previously reported that one type of PTM, lysine malonylation (MaK) was increased in cartilage during obesity. Sirt5, the only known mammalian demalonylase, declines in cartilage during aging. To elucidate the interplay between Sirt5 deficiency and obesity in joint degeneration, we deploy systemic and cartilage specific conditional knockout mouse models. Our findings reveal that the combination of Sirt5 deficiency and obesity exacerbates joint degeneration in mice. Through comprehensive proteomics analysis, we delineate the malonylome in chondrocytes, pinpointing MaK's predominant impact on various metabolic pathways such as carbon metabolism and glycolysis. Further biochemical investigation focuses on glyceraldehyde 3 phosphate dehydrogenase (GAPDH), a target of MaK, confirming a reduction in its enzymatic activity and functionality by MaK. Lastly, we identified a rare coding mutation in SIRT5 that dominantly segregates in a family with hand OA. The mutation results in substitution of an evolutionally invariant phenylalanine (Phe F) to leucine (Leu L) (F101L), which is located in the catalytic domain. F101L mutant results in higher MaK level and decreased expression of cartilage ECM genes (e.g., Acan and Col2a1) and upregulation of inflammation associated genes (e.g., Il6 and Nos2). In conclusion, we found that Sirt5 mediated MaK is an important regulator of chondrocyte cellular metabolism and dysregulation of Sirt5-MaK could be an important mechanism underlying aging and obesity associated OA development. ","fileCount":"20","fileSizeKB":"30400614","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Data-independent acquisition (DIA);Sirtuin 5;Chondrocyte;Osteoarthritis ;Quantitative proteomics","pi":[{"name":"Birgit Schilling","email":"bschilling@buckinstitute.org","institution":"Buck Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053614","task":"698e43b08c354177bb5227ac7cc400f5","id":"2249"}, {"dataset":"MSV000095236","datasetNum":"95236","title":"Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms ","user":"haolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720033712000","created":"Jul. 3, 2024, 12:08 PM","description":"SILAC proteomics is a powerful metabolic labeling technique that limits experimental variation, while enabling accurate protein quantification. However, multiple isotopic versions (e.g. heavy and light) of the same proteins are generated, increasing spectral complexity and requiring sample deconvolution. Despite the widespread application of SILAC proteomics, various acquisition modes and software have not been comparatively evaluated. Here, we designed a comprehensive benchmarking workflow to systematically compare the performance of several software (e.g. FragPipe, MaxQuant, Proteome Discoverer, DIA-NN and Spectronaut) compatible with SILAC proteomics. ","fileCount":"35","fileSizeKB":"56863343","spectra":"0","psms":"143578","peptides":"42874","variants":"58081","proteins":"5721","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:259 - \\\"13C(6) 15N(2) Silac label.\\\";UNIMOD:267 - \\\"13C(6) 15N(4) Silac label.\\\"","keywords":"benchmarking;iPSC;SILAC;Heavy amino acid;Human ;Ratio","pi":[{"name":"Ling Hao","email":"linghao@gwu.edu","institution":"George Washington University","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD053612","task":"d7c7d663a22f4cc38ecd313842c48db3","id":"2250"}, {"dataset":"MSV000095235","datasetNum":"95235","title":"Isolation and characterization of two recently isolated Novosphingobium oxfordensis sp. nov. and Novosphingobium mississippiensis sp. nov. strains from soil, with LCMS and genome-based investigation of their glycosphingolipid productions ","user":"Tahirolemiss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720031807000","created":"Jul. 3, 2024, 11:36 AM","description":"Isolation and characterization of two recently isolated Novosphingobium oxfordensis sp. nov. and Novosphingobium mississippiensis sp. nov. strains from soil, with LCMS and genome-based investigation of their glycosphingolipid productions","fileCount":"5","fileSizeKB":"154799","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Novosphingobium oxfordensis sp. nov.;Novosphingobium mississippiensis sp. nov.","instrument":"6530C Q-TOF LC\\\/MS (Agilent instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Novosphingobium, Glycosphingolipids, Whole genome sequencing, Chemotaxonomic analysis, LCMS Lipidomics, Sequence Similarity Networking, LCMS\/MS.","pi":[{"name":"Paul Boudreau","email":"boudreau@olemiss.edu","institution":"University of Mississippi - School of Pharmacy","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f9bf5bb257314208ab3cb454aae42580","id":"2251"}, {"dataset":"MSV000095232","datasetNum":"95232","title":"GNPS - Community-wide interactions sustain life in geothermal spring habitats","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720015878000","created":"Jul. 3, 2024, 7:11 AM","description":"We investigated an alga-dominated geothermal spring community in Yellowstone National Park (YNP), USA to determine how the biota cope with abiotic stressors. Microbes showed a community level response to toxic metal resistance and energy cycling that spans the three domains of life. Arsenic detoxification is accomplished via complementary expression of genes by different lineages. Photosynthetic primary production is dominated by the obligate photoautotrophic alga Cyanidioschyzon, with the mixotroph, Galdieria, largely relegated to nighttime heterotrophy. Many key functions, including the cell cycle, are strongly regulated by diurnal fluctuations in light and nutrients. These results demonstrate that biotic interactions are highly structured and constrained in extreme habitats. We suggest this was also the case on the early Earth when geothermal springs were cradles of microbial life.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000481) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"2057","fileSizeKB":"236212189","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"geothermal spring microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"geothermal spring;arsenic detoxification;algae;Cyanidioschyzon;Galdieria","pi":[{"name":"Debashish Bhattacharya","email":"debash.bhattacharya@gmail.com","institution":"Rutgers University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7b95c3e1865444ebbc60d1316517d7f0","id":"2252"}, {"dataset":"MSV000095231","datasetNum":"95231","title":"Selective Gas Phase Enrichment of Modified Peptides for Activity-Based Protein Profiling","user":"peterbellotti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720015530000","created":"Jul. 3, 2024, 7:05 AM","description":"Gas phase enrichment separates ionized peptides by their physicochemical properties, offering both simplified sample processing and integration with existing MS technology. We leveraged differential ion mobility of labeled peptides to develop a gas phase enrichment approach for reactive amino acid profiling. A compact cysteine-reactive reagent dramatically increases the ion mobility of labeled peptides and enables their selective fragmentation and sequencing. ","fileCount":"17110","fileSizeKB":"737455965","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:1 - \\\"Acetylation.\\\";[C] [137.0840] S-(hex-5-yn-1-ylcarbamoyl)-L-cysteine;[C] [432.2962] S-((4-(1-(2-(4-(2-(4-methylpiperazin-1-yl)ethyl)piperazin-1-yl)-2-oxoethyl)-1H-1,2,3-triazol-4-yl)butyl)carbamoyl)cysteine;[C] [422.3118] S-(2-((4-(1-(2-(bis(2-(dimethylamino)ethyl)amino)-2-oxoethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)-2-oxoethyl)cysteine;[C] [366.2492] S-(2-((4-(1-(2-(bis(2-aminoethyl)amino)-2-oxoethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)-2-oxoethyl)cysteine;[C] [418.2805] S-(2-oxo-2-((4-(1-(2-oxo-2-(4-(2-(piperazin-1-yl)ethyl)piperazin-1-yl)ethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)ethyl)cysteine;[C] [392.2648] S-(2-((4-(1-(2-(1,4,7,10-tetraazacyclododecan-1-yl)-2-oxoethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)-2-oxoethyl)cysteine;[C] [530.3805] S-(2-oxo-2-((4-(1-(2-oxo-2-(4-(2-(4-(2-(piperazin-1-yl)ethyl)piperazin-1-yl)ethyl)piperazin-1-yl)ethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)ethyl)cysteine;[C] [573.4227] S-(2-((4-(1-(2-(4-(2-(bis(2-(piperazin-1-yl)ethyl)amino)ethyl)piperazin-1-yl)-2-oxoethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)-2-oxoethyl)cysteine;[C] [531.36454] S-(2-((4-(1-(2-(4-(2-(4-(2-morpholinoethyl)piperazin-1-yl)ethyl)piperazin-1-yl)-2-oxoethyl)-1H-1,2,3-triazol-4-yl)butyl)amino)-2-oxoethyl)cysteine;[C] [438.2845] 3-(6-(4-(4-(2-((2-amino-2-carboxyethyl)thio)acetamido)butyl)-1H-1,2,3-triazol-1-yl)hexyl)-1-(2-(3-methyl-1H-imidazol-3-ium-1-yl)ethyl)-1H-imidazol-3-ium;[C] [438.2845] 3-(6-(4-(4-(2-((2-amino-2-carboxyethyl)thio)acetamido)butyl)-1H-1,2,3-triazol-1-yl)hexyl)-1,1',3'-trimethyl-1H,1'H-[2,2'-biimidazole]-3,3'-diium;[C] [518.3220] 3-(2-(1H-imidazol-1-yl)ethyl)-1-(2-(3-(6-(4-(4-(2-((2-amino-2-carboxyethyl)thio)acetamido)butyl)-1H-1,2,3-triazol-1-yl)hexyl)-1H-imidazol-3-ium-1-yl)ethyl)-1H-imidazol-3-ium;[C] [532.3370] 3-(6-(4-(4-(2-((2-amino-2-carboxyethyl)thio)acetamido)butyl)-1H-1,2,3-triazol-1-yl)hexyl)-1-(2-(3-(2-(3-methyl-1H-imidazol-3-ium-1-yl)ethyl)-1H-imidazol-3-ium-1-yl)ethyl)-1H-imidazol-3-ium;[C] [391.2209] 3-(1-amino-1-carboxy-5-oxo-9,12,15-trioxa-3-thia-6-azaheptadecan-17-yl)-1,1',3'-trimethyl-1H,1'H-[2,2'-biimidazole]-3,3'-diium;[C] [297.1683] 3-(1-amino-1-carboxy-5-oxo-9,12,15-trioxa-3-thia-6-azaheptadecan-17-yl)-1-methyl-1H-imidazol-3-ium;[C] [283.1532] 17-amino-1-(1H-imidazol-1-yl)-13-oxo-3,6,9-trioxa-15-thia-12-azaoctadecan-18-oic acid;[C] [514.3005] 3-(2-(2-(2-(2-(4-(4-(2-((2-amino-2-carboxyethyl)thio)acetamido)butyl)-1H-1,2,3-triazol-1-yl)ethoxy)ethoxy)ethoxy)ethyl)-1,1',3'-trimethyl-1H,1'H-[2,2'-biimidazole]-3,3'-diium;[C] [296.1848] S-(2-((2-(6-((4R,5S)-5-methyl-2-oxoimidazolidin-4-yl)hexanamido)ethyl)amino)-2-oxoethyl)cysteine","keywords":"ion mobility;shift;activity-based protein profiling;reactive cysteines;enrichment","pi":[{"name":"Jacob B. Geri","email":"jag4016@med.cornell.edu","institution":"Weill Cornell Medicine","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0ca00eef3f7b4a7fb7a5234a4c3a226b","id":"2253"}, {"dataset":"MSV000095230","datasetNum":"95230","title":"Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis","user":"verizy27","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720014620000","created":"Jul. 3, 2024, 6:50 AM","description":"Deleterious mutations in the LRBA (Lipopolysaccharide Responsive Beige-like Anchor protein) gene cause severe childhood immune dysregulation. The clinical manifestations of LRBA deficiency syndrome are highly variable. Thus, the complexity of the symptoms involving multiple organs and the broad range of unpredictable clinical manifestations complicate the choice of therapeutic interventions. Although LRBA has been linked to Rab11-dependent trafficking of the immune checkpoint protein CTLA-4, its precise cellular role remains elusive. We show that LRBA, however, only slightly colocalize with Rab11. Instead, LRBA is recruited by members of the small GTPase Arf protein family to the TGN and to Rab4+ endosomes, where it controls intracellular traffic. In patient-derived fibroblasts, loss of LRBA led to defects in the endosomal pathway yielding the accumulation of enlarged endolysosomes and lysosome secretion. Thus, LRBA appears to regulate flow through the endosomal system on Rab4+ endosomes. Our data strongly suggest functions of LRBA beyond CTLA-4 trafficking and provide a conceptual framework to develop new therapies for LRBA deficiency.","fileCount":"44","fileSizeKB":"81022507","spectra":"198290","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;timsTOF Ultra","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LRBA (Lipopolysaccharide Responsive Beige-like Anchor protein), CTLA-4, Arf protein family, severe childhood immune dysregulation ","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053605","task":"2c42fe36134944c5b3d67913638df82a","id":"2254"}, {"dataset":"MSV000095229","datasetNum":"95229","title":"GNPS - Cardiomyocyte-specific NAMPT Knockout Mice: Targeted Metabolomics for NAD Derivatives from Heart Ventricle Tissues","user":"Khanh_UPenn_Baur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720011325000","created":"Jul. 3, 2024, 5:55 AM","description":"Targeted metabolomics for NAD-related metabolites from heart ventricular tissues of wild-type (WT) and cardiomyocyte-specific conditional NAMPT (cNKO) mice untreated or treated with nicotinamide riboside (cNKO-NR), harvested at 8-weeks post-NAMPT deletion. Mass spectrometer was operated in two positive-mode scans (SCAN1 at 118.5 to 800 m\/z and SCAN2 at 70 to 117.5 m\/z) with the HILIC 20-minute method for the detection of NAD derivatives.","fileCount":"33","fileSizeKB":"978988","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"Heart, NAMPT, Cardiomyocyte, Metabolomics, NAD","pi":[{"name":"Joseph A. Baur","email":"baur@pennmedicine.upenn.edu","institution":"University of Pennsylvania","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a20cfeb2ee4a401cb89070971d2feeb2","id":"2255"}, {"dataset":"MSV000095228","datasetNum":"95228","title":"Atypical contribution of caspase-3 to melanoma cancer cell motility by regulating coronin-1B activity","user":"fdelolme","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720009324000","created":"Jul. 3, 2024, 5:22 AM","description":"Recent studies have unveiled unexpected connections between cell death and cell motility involving caspases, key regulators of apoptosis. While traditionally recognized for their pro-apoptotic roles, caspases have emerged as regulators of physiological processes beyond cell death, including cellular differentiation and motility. In some particularly aggressive cancers like melanoma, caspase-3, a prominent executioner caspase, is unexpectedly and inexplicably highly expressed. Here, we describe a novel non-apoptotic role for caspase-3 in melanoma cell motility. Through comprehensive molecular and cellular analyses, we demonstrate that caspase-3 is constitutively associated with the cytoskeleton and crucially regulates melanoma cell migration and invasion in vitro and in vivo. Mechanistically, caspase-3 interacts with and modulates the activity of coronin1-B, a key regulator of actin polymerization, thereby promoting melanoma cell motility, independently of its apoptotic protease function. Furthermore, we identify specificity protein 1 (SP1) as a transcriptional regulator of CASP3 expression, and show that its inhibition reduces caspase-3 expression and impairs melanoma cell migration. Overall, this study provides insights into the multifaceted roles of caspase-3 in cancer progression, highlighting its relevance as a novel target for anti-metastatic therapies.","fileCount":"106","fileSizeKB":"31950449","spectra":"1422843","psms":"259594","peptides":"29996","variants":"37801","proteins":"4027","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Caspase-3, motility, Cytoskeleton, Coronin-1B, lamellipodia","pi":[{"name":"Gabriel ICHIM","email":"Gabriel.ichim@lyon.unicancer.fr","institution":"Center for Research on Cancer of Lyon (CRCL) University of Lyon 28, rue Laennec, 69008, Lyon","country":"FRANCE"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"6be1decae1fe40ad81d7eb58196d3b8c","id":"2256"}, {"dataset":"MSV000095227","datasetNum":"95227","title":"GNPS - Metabolomics-based LC-HRMS Analysis of Liquid Fermentation Co-culture of Penicillium sp. LBKURCC34, Trichoderma sp. LBKURCC1 and LBKURCC2 Antibacterial1234","user":"Niko160702","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720008656000","created":"Jul. 3, 2024, 5:10 AM","description":"Metaboanalysis targeted and untargeted from liquid fermentation co-culture fungi penicillium sp and trichoderma spp ","fileCount":"9","fileSizeKB":"1456887","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichoderma asperellum (NCBITaxon:101201);Trichoderma asperelloides (NCBITaxon:702382);Penicillium citrinum (NCBITaxon:5077)","instrument":"UHPLC Vanquish Tandem Q Exactive Plus Orbitrap HRMS ThermoScientific","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"trichoderma;penicillium;fungi","pi":[{"name":"Niko Andriansyah","email":"niko.andriansyah1262@student.unri.ac.id","institution":"University of Riau","country":"Indonesia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"41700e308e8d4c09bf529664bd83031e","id":"2257"}, {"dataset":"MSV000095226","datasetNum":"95226","title":"Proteogenomic analysis of hiPSC cultures from a healthy donor","user":"jakub_vasicek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1720008468000","created":"Jul. 3, 2024, 5:07 AM","description":"Proteogenomic analysis of three stem cell samples from a healthy donor. The cell lines used here are commercially available as induced pluripotent stem cells (iPSC) via retroviral reprogramming of skin fibroblasts isolated from the PGP1 donor from the Personal Genome Project (PGP) (Coriell, GM23338). hiPSC cultures were maintained as previously described [doi.org\/10.1387\/ijdb.230220lg]. Cell lysis, protein extraction, trypsin digestion, and peptide desalting were performed using the AccelerOme automated system from Thermo Fisher Scientific according to the manufacturer's instructions.\n\nPeptides were separated on a 110 cm micro-PAC HPLC column (Thermo Fisher Scientific) with a Vanquish Neo HPLC system (Thermo Fisher Scientific) coupled through a nano-electrospray source to a Tribrid Ascend mass spectrometer (Thermo Fisher Scientific) with a non-linear gradient of 1 - 50 % buffer B (0.1 % formic acid, 80 % acetonitrile) at a flow rate of 300 nL\/min over 160min. The column temperature was kept at 50 C. Samples were acquired using a DDA MS2 data acquisition, where the Tribrid mass spectrometer was switching between a full scan (120 K resolution, Auto max. injection time, AGC target 100%), to a data-dependent (Top-20) MS\/MS scans in the Orbitrap analyzer (15K resolution, 27 ms max. injection time, AGC target 400%). Isolation window was set to 1.4 (m\/z), and normalized collision energy to 25. Precursors were filtered by charge state of 2-6 and multiple sequencing of peptides was minimized by excluding the selected peptide candidates for 60 s.\n\nProtein sequence database was generated by ProHap [doi.org\/10.1101\/2023.12.24.572591] using the phased genotype of the healthy donor, available from [https:\/\/my.pgp-hms.org\/profile_public?hex=hu43860C]. ","fileCount":"22","fileSizeKB":"10718955","spectra":"0","psms":"293576","peptides":"85346","variants":"102014","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"proteogenomics;stem cells;hiPSC;iPSC;DDA","pi":[{"name":"Marc Vaudel","email":"marc.vaudel@uib.no","institution":"University of Bergen","country":"Norway"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD053601","task":"a79bd945a76a40b999c69b924961ce34","id":"2258"}, {"dataset":"MSV000095224","datasetNum":"95224","title":"microbeMASST try try try try try try try try 22","user":"yh0227","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719993016000","created":"Jul. 3, 2024, 12:50 AM","description":"sample001, sample002, microbeMASST, trial_2, 07.03.24","fileCount":"4","fileSizeKB":"4757","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ACQUITY UPLC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"dataset","pi":[{"name":"Yeonhee Kim","email":"yh0227@ncc.re.kr","institution":"National cancer center","country":"Republic of Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6393bf2ef6ce4d528164d173cb4c6f99","id":"2259"}, {"dataset":"MSV000095223","datasetNum":"95223","title":"GNPS - Cardiomyocyte-specific NAMPT Knockout Mice: Untargeted Metabolomics from Heart Ventricle Tissues (dataset2)","user":"Khanh_UPenn_Baur","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719988838000","created":"Jul. 2, 2024, 11:40 PM","description":"Untargeted metabolomics from heart ventricular tissues of wild-type (WT) and cardiomyocyte-specific conditional NAMPT knockout (cNKO) mice untreated or treated with nicotinamide riboside (cNKO-NR), harvested at 8-weeks post-NAMPT deletion. Mass spectrometer was operated in both negative (NEG, 70 to 1000 m\/z) and positive (POS, 50 to 117.9 m\/z) ion mode with the HILIC 25-minute method for the detection of metabolites.","fileCount":"33","fileSizeKB":"1089871","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"Heart, NAMPT, Cardiomyocyte, Metabolomics, NAD","pi":[{"name":"Joseph A. Baur","email":"baur@pennmedicine.upenn.edu","institution":"University of Pennsylvania","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ba0b2e33e51649859a229e612d6c9a5f","id":"2260"}, {"dataset":"MSV000095221","datasetNum":"95221","title":"Proteomic analysis of P21 DYRK1A-knockin mice","user":"yangyj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719982951000","created":"Jul. 2, 2024, 10:02 PM","description":"Dyrk1A deficiency is linked to various neurodevelopmental disorders, including developmental delays and autism spectrum disorders (ASD). Haploinsufficiency of Dyrk1a in mice leads to ASD-related phenotypes, although key pathological mechanisms remain unclear. In addition, human DYRK1A mutations have not been characterized in mice. Here we report Dyrk1a-knockin mice carrying a human mutation (Ile48LysfsX2; Dyrk1a-I48K mice). These mice display severe microcephaly, social and cognitive deficits, dendritic shrinkage, excitatory synaptic deficits, and altered phospho-proteome patterns enriched for multiple signaling pathways and synaptic proteins. Early chronic lithium treatment of newborn mutant mice rescues brain volume, behavior, dendrite, synapse, and signaling\/synapse phospho-proteome phenotypes at juvenile and adult stages. These results suggest that signaling\/synaptic alterations contribute to phenotypic alterations in Dyrk1a-I48K mice, and that early correction of these alterations by lithium treatment has long-lasting effects of preventing juvenile and adult-stage phenotypes. ","fileCount":"65","fileSizeKB":"58608572","spectra":"0","psms":"151927","peptides":"84860","variants":"108654","proteins":"7403","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Dyrk1a;ASD;Proteomics","pi":[{"name":"Jin Young Kim","email":"jinyoung@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep. of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053587","task":"d3d6e13551e149f4bf0531a6563a4463","id":"2261"}, {"dataset":"MSV000095220","datasetNum":"95220","title":"GNPS_CMMC_Bile_Salt_Hydrolase_Assay_6","user":"asund42","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719978756000","created":"Jul. 2, 2024, 8:52 PM","description":"MS\/MS fragmentation data of 2 BSH enzyme assays. One with taurylcholic acid and the other with glycocholic acid each with a mix of 43 amino compounds (Asparagine, Aspartic Acid, L-Glutamic Acid, Glutamine, Methionine, 4-aminophenol, Tryptamine, B-Alanine, L-Carnosine, Allantoin, 2-Phenylglycine, L-aspartyl-L-phenylalanine methyl ester, Isoniazid, DL-Proline, Creatine, Histamine. L-Alanine, L-Arginine, L-Cysteine, L-Leucine, Lysine, Phenylalanine, Serine, Tryptophan, Valine, 1,3-Diaminopropane, L-citrulline, 5-Aminovaleric Acid, Dopamine, Serotonin, Histidine, L-Homoserine, L(+)-Ornithine, gamma-Aminobutyric acid, L-Glutathione (oxidized form), trans-4-Hydroxy-L-proline, L(+)-Homoarginine, Glycyl-L-Valine, L-2-Aminoadipic Acid, L-Glutathione reduced, 3-methoxytyramine, Threonine, and Tyramine) acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"7","fileSizeKB":"8279443","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"BSH;Amino compounds;Assay","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"85f992bacfdf4be6966eab9b22bb0028","id":"2262"}, {"dataset":"MSV000095217","datasetNum":"95217","title":"GNPS - greene_MauiCoralTissueMetabolomes","user":"zquinlan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719947582000","created":"Jul. 2, 2024, 12:13 PM","description":"Coral tissue samples from the islands of Maui and Hawai'i collected by Dr. Austin Greene and Dr. Megan J. Donahue at the Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa. Samples were collected from both Porites lobata and Montipora capitata.","fileCount":"1844","fileSizeKB":"204427754","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Montipora capitata (NCBITaxon:46704);Porites lobata (NCBITaxon:104759)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Coral;tissue metabolomes;coral tissue","pi":[{"name":"Zachary A. Quinlan","email":"Zquinlan@gmail.com","institution":"University of Hawai'i at Manoa","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"d277a48055be4aaea329a333500bd697","id":"2263"}, {"dataset":"MSV000095216","datasetNum":"95216","title":"GNPS - CMMC_N_acyl_lipid_and_3_OH_acyl_lipids","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719945980000","created":"Jul. 2, 2024, 11:46 AM","description":"MS\/MS fragmentation data of acyl lipids acquired on Explores 240 - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"746","fileSizeKB":"16945826","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"acyl lipid","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a682622f3b464c7da6b130c62cd4c32e","id":"2264"}, {"dataset":"MSV000095215","datasetNum":"95215","title":"Mindbomb1 is a Novel Negative Regulator of BMP Signaling","user":"TKC008","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719938931000","created":"Jul. 2, 2024, 9:48 AM","description":"Mindbomb1 is a Novel Negative Regulator of BMP Signaling.","fileCount":"45","fileSizeKB":"24587900","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"TMTPro Global Proteome Phosphorylation Ubiquitinylation;Mindbomb1","pi":[{"name":"Christopher Rose","email":"rose.christopher@gene.com","institution":"Genentech","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a9c35204d5374cc4beae35fbed644f0c","id":"2265"}, {"dataset":"MSV000095213","datasetNum":"95213","title":"Optimizing SureQuant for Targeted Peptide Quantification: A Technical Comparison with PRM and SWATH-MS Methods","user":"antelo0000","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719935617000","created":"Jul. 2, 2024, 8:53 AM","description":"Bacterial infections are a major threat to human health worldwide. A better understanding of the properties and physiology of bacterial pathogens in human tissues is needed to develop urgently needed novel control strategies. Mass spectrometry-based proteomics could yield such data but identifying and quantifying scarce bacterial proteins against a preponderance of human proteins is challenging. Here, we explored the recently introduced SureQuant method for highly sensitive targeted mass spectrometry. Using a major human pathogen, the Gram-positive bacteria Staphylococcus aureus, as an example, we optimized several parameters, including the number of targets and intensity thresholds, for optimal qualitative and quantitative detection. We compared the results with widely used standard techniques (parallel reaction monitoring, PRM) and data-independent acquisition (DIA). We found that SureQuant achieved the same quantitative performance as PRM and allowed accurate and precise quantification of up to 400 targets, surpassing the sensitivity and quantification capabilities of global DIA. We provide optimized MS parameters for sensitive quantification of different peptide panel sizes. This study provides a foundation for the broader application of SureQuant in the analysis of clinical specimens containing trace amounts of bacterial proteins as well as other studies requiring ultrasensitive detection of low-abundant proteins.","fileCount":"491","fileSizeKB":"485229124","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus aureus (NCBITaxon:1280);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bacterial Infections;SureQuant;Targeted mass spectrometry;PRM;SWATH-MS;Method optimization","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"a339c19ace084174a6e254d1d2b34a2e","id":"2266"}, {"dataset":"MSV000095212","datasetNum":"95212","title":"Acetylomic and Lipidomic Profiling of Mice with Doxorubicin Induced Cardiomyopathy: A Cardiometabolic Disease Attenuated by Sirtuin-3","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719929526000","created":"Jul. 2, 2024, 7:12 AM","description":"Doxorubicin (DOX) is a chemotherapeutic agent known for dose-dependent cardiotoxicity. Sirtuin 3 (SIRT3), a lysine deacetylase, regulates enzymatic function within mitochondria. DOX decreases SIRT3 levels, causing differential acetylation of cardiac mitochondrial enzymes. In this study, we evaluated M3-SIRT3 (shortened, not mitochondrial targeted), M1-SIRT3 (full length, mitochondrial localized), and non-transgenic mice treated with DOX (8.0mg\/kg\/week). M1-SIRT3 expression reduced mitochondrial acetylation and prevented DOX-induced cardiac remodelling and dysfunction. Acetyl-proteomics identified altered acetylation of mitochondrial enzymes involved in fatty acid metabolism.","fileCount":"27","fileSizeKB":"985423","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"acetylation;chemotherapy;cardiotoxicity","pi":[{"name":"Vernon W. 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Using supervised machine learning (ML) of 450 hallmark protein markers from 16 subcellular niches, we further refined the subcellular information of 2083 proteins with high confidence. Our data validation focused on specific subcellular niches such as mitochondria, cell surface, cardiac dyad, and myofibril including heart tissue-enriched nuclear fraction, underscoring the significance of protein localisation in cardiac biology. 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However, the precise molecular composition underlying these mechanisms remains unclear. Our data show that inorganic polyphosphate (polyP), a polymer well-conserved throughout evolution, is a component of these mechanisms. In mammals, mitochondria exhibit a significant abundance of polyP, and both our research and that of others have already highlighted its potent regulatory effect on bioenergetics. Given the intimate connection between energy metabolism and protein homeostasis, the involvement of polyP in proteostasis has also been demonstrated in several organisms. For example, polyP is a bacterial primordial chaperone, and its role in amyloidogenesis has already been established. Here, using HEK293 cells, our study reveals that the depletion of mitochondrial polyP leads to increased protein aggregation within the organelle, following stress exposure. Furthermore, mitochondrial polyP is able to bind to proteins, and these proteins differ under control and stress conditions. The depletion of mitochondrial polyP significantly affects the proteome under both control and stress conditions, while also exerting regulatory control over gene expression. Our findings suggest that mitochondrial polyP is a previously unrecognized, and potent component of mitochondrial proteostasis. The mass spectrometric raw files for this study are deposited here. 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Kinases phosphorylate RNA Polymerase II and associated factors to control transitions between these steps and act as central gene regulatory nodes. Similarly, phosphatases that dephosphorylate these components are emerging as important regulators of transcription, though their roles remain less well understood. Here we discover that the PNUTS-PP1 phosphatase complex plays an essential role in controlling transcription pause release in addition to its previously described function in transcription termination. Transcription pause release by the PNUTS complex is essential for almost all RNA Pol II-dependent gene transcription, relies on its PP1 phosphatase subunit, and controls the phosphorylation of factors required for pause release and elongation. Together, this reveals an essential new role for a phosphatase complex in transcription pause release and shows that the PNUTS complex is essential for RNA Poll II-dependent transcription.","fileCount":"301","fileSizeKB":"74026684","spectra":"9703951","psms":"1540487","peptides":"886581","variants":"1148911","proteins":"16952","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos;Exactive Plus","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"PP1, PNUTS, transcription, phosphorylation, degron","pi":[{"name":"Arminja Nadine Kettenbach","email":"Arminja.N.Kettenbach@Dartmouth.edu","institution":"Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053493","task":"a0221d824d7e4f82860af06929157177","id":"2286"}, {"dataset":"MSV000095174","datasetNum":"95174","title":"Accessing the proteome of extracellular vesicles via rapid acoustic isolation of a minute human blood plasma sample","user":"havers_megan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719576823000","created":"Jun. 28, 2024, 5:13 AM","description":"Samples from raw human blood plasma or the same plasma enriched for extracellular vesicles by acoustic trapping.\nRaw files, spectral library generated from pooled samples and DIA-NN data provided.","fileCount":"48","fileSizeKB":"33549921","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:27 - 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PolyP, inorganic polyphosphate, mitochondria, HEK293","pi":[{"name":"Maria E Solesio","email":"m.solesio@rutgers.edu","institution":"Rutgers University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d591747893504d2b8a8b5ea497296d7f","id":"2288"}, {"dataset":"MSV000095167","datasetNum":"95167","title":"GNPS - Heat-induced Stress Modulates Cell Surface Glycans and Membrane Lipids of Coral Symbionts","user":"christianmartinhdz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719496888000","created":"Jun. 27, 2024, 7:01 AM","description":"Glycans and lipids change with stress in coral symbionts","fileCount":"235","fileSizeKB":"9308653","spectra":"455669","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Montipora capitata (NCBITaxon:46704)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Heat-stress;Coral Symbiont;Symbiodiniaceae;Montipora capitata;Cladocopium spp;Durusdinium spp","pi":[{"name":"Robert Quinn","email":"quinnr1234@gmail.com","institution":"Robert Quinn","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c4f26e3ca3934a16b97928f0c9a9ef77","id":"2289"}, {"dataset":"MSV000095163","datasetNum":"95163","title":"Nuclear Factor I family members are pioneering transcription factors that serve as key regulators of transcription","user":"dmpinar","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719468391000","created":"Jun. 26, 2024, 11:06 PM","description":"The Nuclear Factor I (NFI) family of transcription factors (TFs) plays key roles in cellular differentiation, proliferation, and homeostasis. As such, NFI family members engage in large number of interactions with other proteins and the chromatin. However, despite their well-established significance, the NFIs interactomes, their dynamics, and their functions have not been comprehensively examined. Here, we employed complementary omics-level techniques, i.e. interactomics (affinity purification mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID)), and chromatin immunoprecipitation sequencing (ChIP-Seq), to obtain a comprehensive view of the NFI proteins and their interactions. Our analyses included all four main NFI family members, and a less studied short isoform of NFIB (NFIB4), which lacks the DNA binding domain. We observed that, despite exhibiting some redundancy, each family member had unique high-confidence interactors and target genes, highlighting distinct roles within the transcriptional regulatory networks. The study revealed that NFIs interact with a large number of other TFs to co-regulate a broad range of regulatory networks and cellular processes. Notably, time-dependent proximity-labeling unveiled a highly dynamic nature of NFI protein-protein interaction networks and hinted at temporal modulation of NFI interactions. Furthermore, gene ontology (GO) enrichment analysis of NFI interactome and targetome revealed the involvement of NFIs in transcriptional regulation, chromatin organization, and cellular signaling pathways, and pathways related with cancer. Additionally, we observed that NFIB4 engages with proteins associated with mRNA regulation, which suggests that NFIs have roles beyond traditional DNA binding and transcriptional modulation. We propose that NFIs serve as pioneering TFs, playing critical roles in regulating other TFs and influencing a wide range of cellular processes. These insights into NFI protein-protein interactions and their dynamic, context-dependent nature provide a deeper understanding of gene regulation mechanisms and hint at the role of NFIs as master regulators.","fileCount":"3440","fileSizeKB":"147110564","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Nuclear Factor I, Transcription factors, Affinity purification, Proximity dependent biotinylation, BioID, Protein-protein interactions, transcriptional regulation, interaction proteomics, mass spectrometry, ChIP-Seq.","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d7fb1fe388814ba78fbfd6cc8525e196","id":"2290"}, {"dataset":"MSV000095162","datasetNum":"95162","title":"Cell Storage Conditions Impact Single-Cell Proteomic Landscape","user":"onatbora","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719466412000","created":"Jun. 26, 2024, 10:33 PM","description":"Three storage conditions were compared in 293T cells: (1) 37C (control), (2) 4C overnight, and (3) -80C storage followed by liquid nitrogen preservation. Either cold storage induced significant alterations in cell diameter, circularity, and proteome composition. This study highlights the importance of preserving cells under viable conditions to maintain the integrity of the proteome and underscore the necessity of optimizing cell storage protocols to ensure accurate representation of the cellular proteome, particularly in the context of SCP studies. By elucidating the intricate interplay between storage conditions, cellular morphology, and protein expression, this study contributes valuable insights towards advancing SCP methodologies and enhancing our understanding of cellular heterogeneity.","fileCount":"32","fileSizeKB":"478990479","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"SCP;Single Cell Proteomics;Storage;HEK293","pi":[{"name":"Jesse G. Meyer","email":"jessegmeyer@gmail.com","institution":"UW-Madison","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"11b2882779684bd28b8ee0e5e5dda3d1","id":"2291"}, {"dataset":"MSV000095160","datasetNum":"95160","title":"HDL proteomics in breast cancer - Santana 2024","user":"douglasrsjr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719445338000","created":"Jun. 26, 2024, 4:42 PM","description":"Dataset from breast cancer patients. Work is from University of Sao Paulo, Brazil.","fileCount":"1051","fileSizeKB":"207349638","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"data-independent acquisition;high-density lipoprotein;breast cancer","pi":[{"name":"Marisa Passarelli","email":"mpassere@usp.br","institution":"Faculdade de Medicina da Universidade de Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"8d6f566e4c9e4ae2ba008efad14c03aa","id":"2292"}, {"dataset":"MSV000095158","datasetNum":"95158","title":"Structural and functional validation of DCAF2 for targeted protein degradation","user":"acioffi3","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719442611000","created":"Jun. 26, 2024, 3:56 PM","description":"Proteomics data for submitted publication entitled \"Structural and functional validation of DCAF2 for targeted protein degradation\"","fileCount":"15","fileSizeKB":"9121597","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"DCAF2;DTL;isoTOP-ABPP","pi":[{"name":"Robert Everley","email":"robert.everley@frontiermeds.com","institution":"Frontier Medicines Corporation","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b5b6234701ff44af91d8d9edae40af4b","id":"2293"}, {"dataset":"MSV000095157","datasetNum":"95157","title":"GNPS - ISB Gut Statin Stool Metabolomics ","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719441454000","created":"Jun. 26, 2024, 3:37 PM","description":"Metabolomics data of ISB Gut Statin stool samples in collaboration with the Microbiome Core at UCSD. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). ","fileCount":"154","fileSizeKB":"9151492","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;fecal;stool","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ae8480f5e7fc429a9cba3974fb23e161","id":"2294"}, {"dataset":"MSV000095156","datasetNum":"95156","title":"GNPS - APOE Haddad Obesity Study Metabolomics","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719441124000","created":"Jun. 26, 2024, 3:32 PM","description":"Untargeted LC\/MS metabolomics of samples from Haddad lab re-run on 6\/17\/2024. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany).","fileCount":"442","fileSizeKB":"25034508","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"obesity;metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f610b196224a41058dc21ad719d5960c","id":"2295"}, {"dataset":"MSV000095151","datasetNum":"95151","title":"Inactivation of DET1 causes neurological defects and lethality 1 in mice and humans","user":"sklaeger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719416369000","created":"Jun. 26, 2024, 8:39 AM","description":"COP1 and DET1 are components of an E3 ubiquitin ligase that is conserved from plants to humans. Mammalian COP1 binds to DET1 and is a substrate adaptor for the CUL4A-DDB1-RBX1 RING E3 ligase. Its transcription factor substrates, including c-Jun, ETV4, and ETV5, are targeted for proteasomal degradation to effect rapid transcriptional changes in response to cues such as growth factor deprivation. Here we show that a homozygous DET1R26W mutation that is linked to lethal developmental abnormalities in humans disrupts DET1 binding to DDB1 and compromises E3 ligase function. Human-induced pluripotent stem cells bearing the homozygous DET1R26W mutation expressed ETV4 and ETV5 highly, had alterations in mitochondrial protein expression, and exhibited impaired neuronal differentiation. Mice lacking Det1 died during embryogenesis, while Det1 deletion just in neural stem cells elicited hydrocephalus, cerebellar dysplasia, and neonatal lethality. Our findings highlight an important role for DET1 in the neurological development of mice and humans.\n\n","fileCount":"63","fileSizeKB":"26757525","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"DET1, COP1, E3 ubiquitin ligase, neurodevelopment","pi":[{"name":"Susan Klaeger","email":"klaeger.susan@gene.com","institution":"Genentech, Inc.","country":"USA"}],"complete":"false","quant_analysis":"Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053433","task":"b758f88cd2ce4df6988c282c0f91244f","id":"2296"}, {"dataset":"MSV000095148","datasetNum":"95148","title":"GNPS - Non-targeted Metabolomics Plant Microbiome Screen","user":"TSchramm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719357800000","created":"Jun. 25, 2024, 4:23 PM","description":"Non-targeted LC-MS\/MS based Metabolomics of Plant Microbiome strain for natural product Screening","fileCount":"33","fileSizeKB":"3786068","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental sample (NCBITaxon:282508)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Flavia;Natural Products;Bacteria","pi":[{"name":"Caroline Roper ","email":"mcroper@ucr.edu","institution":"UC Riverside","country":"USA"},{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"UC Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"059b84d6b2804c92a327733019ecafa6","id":"2297"}, {"dataset":"MSV000095147","datasetNum":"95147","title":"GNPS - Scripps Pier Time Series 2024","user":"rrtorres","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719353530000","created":"Jun. 25, 2024, 3:12 PM","description":"Non-targeted LC-MS\/MS analysis of PPL extracts from dissolved organic matter at the Scripps Pier. Positive and Negative mode data. ","fileCount":"1323","fileSizeKB":"120613763","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Marine;Dissolved Organic Matter","pi":[{"name":"Lihini Aluwihare","email":"laluwihare@ucsd.edu","institution":"UCSD SIO","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4da8463fc6824cf192fd0c3f369bc8d6","id":"2298"}, {"dataset":"MSV000095146","datasetNum":"95146","title":"Metallosphaera sedula bifurcates into two sizes when it is cultured mixotrophically on soluble iron","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719351648000","created":"Jun. 25, 2024, 2:40 PM","description":"In situ kinetic measurements were conducted on Metallosphaera sedula as it respired aerobically on extracellular soluble iron. Cells cultured on the same organic nutrients in the absence or the presence of soluble iron exhibited the same level of respiratory activity, suggesting that the responsible proteins were expressed constitutively. The unexpected and novel observation was that cells cultured in the presence of iron comprised equal numbers of two types of cells, one larger and one smaller than the relatively uniform cells that were cultured in the absence of iron. Proteomic studies were conducted on cell-free extracts of cells that were cultured in the absence or the presence of soluble iron. The only relevant proteomic observation was that the enzymes of the TCA cycle were expressed in higher numbers in the cells that were cultured in the absence of soluble iron.","fileCount":"67","fileSizeKB":"25539988","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Metallosphaera sedula (NCBITaxon:43687)","instrument":"LTQ Orbitrap Velos;Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"in situ kinetics;phenotypic heterogeneity","pi":[{"name":"Robert C. Blake II","email":"rblake@xula.edu","institution":"Xavier University of Louisiana","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d034f9f6fddc4877bf305c7479181017","id":"2299"}, {"dataset":"MSV000095145","datasetNum":"95145","title":"Kiriakopulos_CISTR_BioID_P124_6600","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719338392000","created":"Jun. 25, 2024, 10:59 AM","description":"This dataset consists of 12 raw MS files and associated peak lists and results files, acquired on a ABSciex TripleTOF6600 mass spectrometer operated in Data Dependent Acquisition mode. \nSamples were generated by Katerina Kiriakopulos. Affinity purifications were performed by Katerina Kiriakopulos and Cassandra Wong. Mass spectrometry acquisition was performed by Cassandra Wong. Analysis was performed by Katerina Kiriakopulos, Philipp Maass, and Cassandra Wong. \nThe files are associated with a manuscript submitted for publication by Katerina Kiriakopulos et al. The main goal of this paper was to profile the proximity interactome CISTR-ACT, a lncRNA. This dataset identifies the important proteins that interact with CISTR-ACT to facilitate trans-regulation of cell size genes. \nPhilipp G. Maass is the corresponding author of the manuscript (Philipp.maass@sickkids.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 4 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence (as per iProphet)\nTable 3 lists the SAINTexpress interactions for SAINTID 6346\nTable 4 lists the SAINTexpress interactions for SAINTID 6390\n","fileCount":"68","fileSizeKB":"35480032","spectra":"0","psms":"266556","peptides":"41083","variants":"48682","proteins":"30294","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;proximity-dependent biotinylation;CISTR-ACT;cell size","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053402","task":"93593cfa0ab446fead50314a05bb45e0","id":"2300"}, {"dataset":"MSV000095144","datasetNum":"95144","title":"GNPS - LIVIA_SOMAN_RESEARCH_GROUP_MICROBIAL_METABOLITES_LC_MS","user":"liviasoman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719338392000","created":"Jun. 25, 2024, 10:59 AM","description":"Data from microbial metabolites produced by investigated fungi of Livia Soman Research Group. Natural Products.","fileCount":"422","fileSizeKB":"1483061","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Setophoma sp. (NCBITaxon:1868165);Talaromyces wortmannii (NCBITaxon:28567);Penicillium sp. (NCBITaxon:5081)","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fungal metabolites","pi":[{"name":"Livia Soman","email":"livia.soman@unifesp.br","institution":"UNIFESP","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"684c665a0a0c4d2c95f5b20b47a6777b","id":"2301"}, {"dataset":"MSV000095143","datasetNum":"95143","title":"GNPS - OAI cohort study (serum samples)","user":"helenamrusso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719337181000","created":"Jun. 25, 2024, 10:39 AM","description":"Untargeted LC-MS\/MS data for serum samples from patients with knee osteoarthritis (OAI cohort). OAI subcohorts:\n- progression: patients with clinically significant KOA at t0 followed for worsening of disease during the follow-up;\n- incidence: patients without clinically significant knee OA at baseline, but selected based on having specific characteristics which give them an increased risk of developing incident symptomatic knee OA during the study;\n- non-exposed: reference control group whose participants did not have either symptomatic knee OA or risk factors at t0\n\n","fileCount":"2430","fileSizeKB":"424303048","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"serum;osteoarthritis","pi":[{"name":"Monica Guma","email":"mguma@ucsd.edu","institution":"UCSD","country":"USA"},{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8addef860e34449fab06ff7c623b0166","id":"2302"}, {"dataset":"MSV000095141","datasetNum":"95141","title":"Label Free BioID interaction datasets, Soderling Lab","user":"es3064","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719335924000","created":"Jun. 25, 2024, 10:18 AM","description":"Quantitative LC\/MS\/MS was performed on 2 uL (1 ug) of each sample, using a nanoAcquity UPLC system (Waters Corp) coupled to a Thermo Orbitrap Fusion Lumos high resolution accurate mass tandem mass spectrometer (Thermo) equipped with a FAIMSPro device via a nanoelectrospray ionization source. Briefly, the sample was first trapped on a Symmetry C18 20 mm x 180 um trapping column (5 ul\/min at 99.9\/0.1 v\/v water\/acetonitrile), after which the analytical separation was performed using a 1.8 um Acquity HSS T3 C18 75 um x 250 mm column (Waters Corp.) with a 90-min linear gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 400 nanoliters\/minute (nL\/min) with a column temperature of 55C. Data collection on the Fusion Lumos mass spectrometer was performed for three difference compensation voltages (-40v, -60v, -80v). Within each CV, a data-dependent acquisition (DDA) mode of acquisition with a r 120,000 (m\/z 200) full MS scan from m\/z 375 - 1500 with a target AGC value of 4e5 ions was performed. MS\/MS scans were acquired in the Orbitrap at r 50,000 ( m\/z 200) from m\/z 100 with a target AGC value of 1e5 and max fill time of 35 ms. The total cycle time for each CV was 1s, with total cycle times of 3 sec between like full MS scans. A 20s dynamic exclusion was employed to increase depth of coverage. The total analysis cycle time for each sample injection was approximately 2 hours","fileCount":"130","fileSizeKB":"177068753","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"label free, bioid, interaction","pi":[{"name":"Scott Soderling","email":"scott.soderling@duke.edu","institution":"Duke University, Dept of Cell Biology","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"38f8bce0536e4b64841257f2c1d08a2a","id":"2303"}, {"dataset":"MSV000095140","datasetNum":"95140","title":"Quantitative Proteomics of Axon Regeneration in Danio rerio with Regen V Standardization","user":"sbhattacharya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719332593000","created":"Jun. 25, 2024, 9:23 AM","description":"Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration, unlike mammals. Optic nerve regeneration is frequently studied using optic nerve crush (ONC). For ONC, animals were deeply anesthetized in 0.033% tricaine methane-sulfonate (MS-222). The right optic nerve was exposed by gently removing the connective tissue on the dorsal half of the eye and rotating the eye ventrally out of the orbit with a pair of number 5 forceps. A nerve crush was then performed using number 5 forceps to crush the nerve ~0.5 to 1 mm from the optic nerve head for 5 seconds. Success of crush was assessed by identifying the generation of a translucent stripe in the nerve that completely separated two areas of white myelination with no bleeding. Fish were then revived in fresh aquatic system water in individual tanks. After 1 hour the tanks were returned to the fish system and animals were maintained normally with daily feeding until 3 days post injury.\nFemale and male (6 month to 1 year old) Zebrafish optic nerves (right side\/OD) were crushed and collected three days after. The associated retinas and tecta were also collected under the same conditions. Contralateral, uninjured optic nerves, retinas and tecta were collected as controls. For tissue collection, animals were euthanized by overdose of MS-222 (>400mg\/L) followed by dissection. The tissue was collected from the optic nerve head to the optic chiasm. The tissues were immediately frozen on dry ice. Optic nerve samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 31 to obtain sufficient protein concentrations for analysis (pooled optic nerves served as one sample). Retina and tectum samples were pooled using the same categories (female crush, female control, male crush, male control) at n = 10-12 (pooled tissue served as one sample).\nProtein extraction was carried out by homogenizing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic peptide standards (Regen III) were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 48uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 50ug\/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. All samples were labelled using 2 sets of 14 tags from a 18plex TMT (Tandem Mass Tag) kit (A52045: Thermo Fisher Scientific, Waltham, MA) for quantification. After combination and drying of all peptide samples, the samples were fractionated into 9 fractions using Pierce High pH Reversed-Phase Peptide Fractionation Kit (84868: Thermo Fisher Scientific, Waltham, MA). After fractionation and drying of all peptide samples, each fractionated TMT sample was spiked with two additional peptide standards (Regen II) containing isobaric labels. The final concentration of the post extraction spiked peptides was 54uM per plex. These standards (Regen II) were spiked directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards serve as a normalization method that may be used to compare protein abundance data across multiple datasets. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Raw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The Danio rerio proteome was downloaded from UniProt and used as the target database for protein identification. Max missed cleavage site was set to 2 and minimum peptide length to 6 . Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. The Normalization was set to total peptide amount and confidence to low. Two additional local databases were created for the pre- and post- extraction peptides and ran separately from experimental protein identification.","fileCount":"72","fileSizeKB":"90638477","spectra":"0","psms":"164625","peptides":"91449","variants":"101618","proteins":"26320","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Q Exactive","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Axon Regeneration, Quantitative Proteomics, Standardization, Regen V, Zebrafish, TMT Label","pi":[{"name":"Sanjoy Bhattacharya","email":"sbhattacharya@med.miami.edu","institution":"University of Miami","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053400","task":"6d1d656ac97f430097614dd72ce2a824","id":"2304"}, {"dataset":"MSV000095138","datasetNum":"95138","title":"AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics","user":"wallmann","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719266577000","created":"Jun. 24, 2024, 3:02 PM","description":"Mass spectrometry (MS)-based proteomics continues to evolve rapidly, opening more and more application areas. The scale of data generated on novel instrumentation and acquisition strategies pose a challenge to bioinformatic analysis. Search engines need to make optimal use of the data for biological discoveries while remaining statistically rigorous, transparent and performant. Here we present alphaDIA, a modular open-source search framework for data independent acquisition (DIA) proteomics. We developed a feature-free identification algorithm particularly suited for detecting patterns in data produced by sensitive time-of-flight instruments. It naturally adapts to novel, more efficient scan modes that are not yet accessible to previous algorithms. Rigorous benchmarking demonstrates competitive identification and quantification performance. While supporting empirical spectral libraries, we propose a new search strategy named end-to-end transfer learning using fully predicted libraries. This entails continuously optimizing a deep neural network for predicting machine and experiment specific properties, enabling the generic DIA analysis of any post-translational modification (PTM). AlphaDIA provides a high performance and accessible framework running locally or in the cloud, opening DIA analysis to the community. ","fileCount":"96","fileSizeKB":"234570642","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Escherichia coli (NCBITaxon:562);Saccharomyces cerevisiae (NCBITaxon:4932);Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Astral;timsTOF Ultra;ZenoTOF 7600","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"DIA;Search Engine;Bioinformatics;Machine Learning","pi":[{"name":"Matthias Mann","email":"mmann@biochem.mpg.de","institution":"Proteomics and Signal Transduction, Max Planck Institute of Biochemistry","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"fd207f2b50fb41c4b7bec2b564b515ff","id":"2305"}, {"dataset":"MSV000095137","datasetNum":"95137","title":"diaPASEF for HLA-I peptide analysis enables quantification of common cancer neoantigens","user":"sklaeger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719265296000","created":"Jun. 24, 2024, 2:41 PM","description":"Human leukocyte antigen class I (HLA-I) molecules present short peptide sequences from endogenous or foreign proteins to cytotoxic T cells. Low abundance of HLA-I peptides poses significant technical challenges for their identification and accurate quantification. While mass spectrometry (MS) is currently a method of choice for direct system-wide identification of cellular immunopeptidome, there is still a need for enhanced sensitivity in detecting and quantifying tumor specific epitopes. As gas phase separation in data dependent MS data acquisition (DDA) increased HLA-I peptide detection by up to 50%, here, we aimed to evaluate the performance of data independent acquisition (DIA) in combination with ion mobility (diaPASEF) for high sensitivity identification of HLA presented peptides. Our streamlined diaPASEF workflow enabled identification of 11,412 unique peptides from 12.5 million A375 cells and 3,426 8-11mers from as low as 500,000 cells with high reproducibility. By taking advantage of HLA binder-specific in-silico predicted spectral libraries, we were able to further increase the number of identified HLA-I peptides. We applied SILAC-DIA to a mixture of labeled HLA-I peptides, calculated heavy to light ratios for 7,742 peptides across 5 conditions and demonstrated that diaPASEF achieves high quantitative accuracy up to 4-fold dilution. Finally, we identified and quantified shared neoantigens in a monoallelic C1R cell line model. By spiking in heavy synthetic peptides, we verified identification of the peptide sequence and calculated relative abundances for 13 neoantigens. Taken together, diaPASEF analysis workflows for HLA-I peptides can increase the peptidome coverage for lower sample amounts. The sensitivity and quantitative accuracy provided by DIA can enable the detection and quantification of less abundant peptide species such as neoantigens across samples from the same background. ","fileCount":"297","fileSizeKB":"236158050","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:312 - \\\"Cysteinylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"immunopeptidomics, DIA, HLA, MHC","pi":[{"name":"Susan Klaeger","email":"klaeger.susan@gene.com","institution":"Genentech, Inc.","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053374","task":"b02664b23209471a89105bbd11401345","id":"2306"}, {"dataset":"MSV000095135","datasetNum":"95135","title":"GNPS - Monotropa_MS2 Analysis for Molecular Networking","user":"kellogglab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719262464000","created":"Jun. 24, 2024, 1:54 PM","description":"Untargeted LC-MS profiling of M. uniflora in the positive and negative modes for MS2 molecular networking and annotation.","fileCount":"175","fileSizeKB":"40096094","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Monotropa uniflora (NCBITaxon:50148)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Monotropa;uniflora;Ghost pipe;Monotropa uniflora","pi":[{"name":"Josh Kellogg","email":"jjk6146@psu.edu","institution":"Pennsylvania State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"118a114fc4f6418da374e23d5b8e3799","id":"2307"}, {"dataset":"MSV000095134","datasetNum":"95134","title":"Histone H3.3 lysine 9 and 27 control repressive chromatin states at cryptic cis-regulatory elements and bivalent promoters in mouse embryonic stem cells","user":"trovato","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719259430000","created":"Jun. 24, 2024, 1:03 PM","description":"Histone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutated histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleashed cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupted deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal level of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states at cis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.","fileCount":"18","fileSizeKB":"4965400","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\"","keywords":"H3.3;histone modifications;chromatin;transcriptional regulation;endogenous retroviruses;mouse embryonic stem cells","pi":[{"name":"Kyung-Min Noh","email":"kyung.min.noh@embl.de","institution":"European Molecular Biology Laboratory (EMBL)","country":"Germany"},{"name":"Matteo Trovato","email":"matteo.trovato@embl.de","institution":"European Molecular Biology Laboratory (EMBL)","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053371","task":"8e79b8b059514359bb3bc6f232f69656","id":"2308"}, {"dataset":"MSV000095129","datasetNum":"95129","title":"BRA006 (Micromonospora sp.), BRA010 (Streptomyces sp.) and BRA177 (Actinomadura sp.) metabolome obtained in LC-MS\/MS with a scheduled precursor list (SPL)","user":"gsarini","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719247604000","created":"Jun. 24, 2024, 9:46 AM","description":"Data obtained by LC-MS\/MS of methanolic extracts (methanol:water) for the actinomycetes BRA006 (Micromonospora sp.), BRA010 (Streptomyces sp.) and BRA177 (Actinomadura sp.), where the precursor ions were guided by a scheduled precursor list (SPL). ","fileCount":"13","fileSizeKB":"2605380","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Micromonospora sp. (NCBITaxon:1876);Streptomyces sp. (NCBITaxon:1931);Actinomadura sp. (NCBITaxon:1989)","instrument":"Impact II QToF Bruker Daltonics","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Actinomycetes","pi":[{"name":"Ricardo Roberto da Silva","email":"ridasilva@usp.br","institution":"University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"09049b6e91f54c07a525a2861b36fdbd","id":"2309"}, {"dataset":"MSV000095128","datasetNum":"95128","title":"Enhanced payload localization in antibody-drug conjugates using a middle-down mass spectrometry approach with proton transfer charge reduction ","user":"Fornelli_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719246373000","created":"Jun. 24, 2024, 9:26 AM","description":"Here, we present an MD MS strategy relying on the use of PTCR to investigate an ADC with variable drug-to-antibody ratio, targeting the unambiguous localization of payload conjugation sites. Unlike traditional tandem MS experiments (MS2), which were largely ineffective, a single PTCR-based experiment (MS3) proved to be sufficient to achieve this goal across all modified ADC subunits.","fileCount":"9","fileSizeKB":"13308733","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"antibody drug conjugate","instrument":"Orbitrap Ascend","modification":"UNIMOD:305 - \\\"Fucosylated biantennary (-2 galactose).\\\";UNIMOD:307 - \\\"Fucosylated biantennary (-1 galactose).\\\";payload attachment","keywords":"middle down mass spectrometry;antibody drug conjugate;biotherapeutics ;proton transfer charge reduction;electron transfer dissociation ;ultraviolet photodissociation ;Orbitrap","pi":[{"name":"Luca Fornelli","email":"luca.fornelli@ou.edu","institution":"University of Oklahoma","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a2989460fd984bde8fd326fd25318b81","id":"2310"}, {"dataset":"MSV000095124","datasetNum":"95124","title":"GNPS - High mass resolution lipid MALDI imaging of rat brain ","user":"yutinlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719190606000","created":"Jun. 23, 2024, 5:56 PM","description":"Rat brain tissues for imaging mass spectrometry were removed from animal organs, frozen on dry ice, and then stored at -80-degree C until analysis. 10-micrometer rat brain tissues were sectioned using a Leica CM 3050S Research Cryostat (Leica Biosystems, Wetzlar, Germany), prior to thaw mounting onto indium tin oxide-coated microscope slides (Delta Technologies, Loveland, CO, USA). 1,5-diaminonaphthalene (DAN) MALDI matrix layer was sublimated to the microscope slide using an in-house sublimation apparatus. MALDI imaging mass spectrometry was performed on a 7T solariX Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a dynamically harmonized ParaCell XR (Bruker Daltonics, Bremen, Germany). Analysis was performed in negative ion mode from m\/z 400 to 2000 with ~0.5 s time-domain transient length, resulting in a resolution of ~35,000 FWHM at m\/z ~760. The MALDI source is equipped with a Smartbeam II Nd:YAG MALDI laser and was used to sample at a pixel spacing of 100 micrometers in the x and y dimensions using 200 laser shots per pixel (large laser focus, 2 kHz frequency) with Smart Walk enabled.","fileCount":"3","fileSizeKB":"140886357","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus rattus","instrument":"7T solariX FT-ICR","modification":"N\\\/A","keywords":"Rat brain;MALDI;imaging mass spectrometry;mass spectrometry imaging","pi":[{"name":"Boone M. Prentice","email":"booneprentice@chem.ufl.edu","institution":"University of Florida","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f03ace32c11e417fac2029e26ab413ca","id":"2311"}, {"dataset":"MSV000095123","datasetNum":"95123","title":"GNPS - Multi-ROI, multi-condition, and multi-replicate metabolite MALDI imaging of mouse heart and pancreas ","user":"yutinlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719190250000","created":"Jun. 23, 2024, 5:50 PM","description":"Mouse heart and pancreas tissues for imaging mass spectrometry were removed from animal organs, frozen on dry ice, and then stored at -80-degree C until analysis. 12-micrometer mouse heart tissues were sectioned using a Leica CM 3050S Research Cryostat (Leica Biosystems, Wetzlar, Germany) using -25-degree C chamber temperature and -23-degree C object temperature, prior to thaw mounting onto indium tin oxide-coated microscope slides (Delta Technologies, Loveland, CO, USA). A 10 mg\/mL solution of 1,5-diaminonaphthalene (DAN) MALDI matrix layer was applied to the microscope slide using an HTX M5 TM Sprayer (HTX Technologies, LLC, Chapel Hill, NC, USA) with 0.1 mL\/min flow rate over 4, 6, or 8 passes. MALDI imaging mass spectrometry was performed on a 7T solariX Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a dynamically harmonized ParaCell XR (Bruker Daltonics, Bremen, Germany). Analysis was performed in negative ion mode from m\/z 75 to 500 with a 1 megaword transient (~0.4 s ICR transient length). A 117 (+\/-) 75 m\/z continuous accumulation of selected ions (CASI) window was used to perform gas-phase enrichment of low m\/z metabolites. The MALDI source is equipped with a Smartbeam II Nd:YAG MALDI laser and was used to sample at a pixel spacing of 200 micrometers in the x and y dimensions using 200 laser shots per pixel (minimum laser focus, 2 kHz frequency) with Smart Walk enabled","fileCount":"13","fileSizeKB":"536222794","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus","instrument":"7T solariX FT-ICR","modification":"N\\\/A","keywords":"mouse heart;mouse pancreas;MALDI;imaging mass spectrometry;mass spectrometry imaging","pi":[{"name":"Boone M. Prentice","email":"booneprentice@chem.ufl.edu","institution":"University of Florida","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"332dca24fe4b4fbdb8e1f3ae73c9544e","id":"2312"}, {"dataset":"MSV000095122","datasetNum":"95122","title":"GNPS - LIVIA_SOMAN_RESEARCH_GROUP_MICROBIAL_METABOLITES_LC_MS","user":"liviasoman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719180150000","created":"Jun. 23, 2024, 3:02 PM","description":"Data from microbial metabolites produced by investigated fungi of Livia Soman Research Group. 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The samples were fractionated in RP. The crude extracts and fractions ","fileCount":"107","fileSizeKB":"1586744","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"fungi","instrument":"micrOTOF-Q","modification":"none","keywords":"fungi","pi":[{"name":"Denise Brentan da Silva","email":"denise.brentan@ufms.br","institution":"UFMS","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0e1d8545a8a84e0bb8c59742502fccf7","id":"2315"}, {"dataset":"MSV000095115","datasetNum":"95115","title":"GNPS Germ-Free Mice Gavage with Ruminococcus gnavus (ATCC 29149) and Lactobacillus rhamnosus GG (ATCC 53103): Fecal Sample Collection at Pre-gavage, Day 3, and Day 21","user":"jma429njms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1719004540000","created":"Jun. 21, 2024, 2:15 PM","description":"The study involved Germ-Free (GF) mice subjected to gavage with two bacterial strains: Ruminococcus gnavus (ATCC 29149) and Lactobacillus rhamnosus GG (ATCC 53103). Fecal samples were collected at three time points: pre-gavage, day 3 post-gavage, and day 21 post-gavage. Fecal samples were analyzed for polar metabolites using Liquid Chromatography-Mass Spectrometry (LC-MS) in both positive and negative ionization modes.","fileCount":"97","fileSizeKB":"27647932","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Germ free;Lactobacillus rhamnosus;Feces;Ruminococcus gnavus","pi":[{"name":"Nan Gao","email":"ngao@newark.rutgers.edu","institution":"Rutgers University, Newark","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6942a429e6024be3bba3dce983452ed4","id":"2316"}, {"dataset":"MSV000095110","datasetNum":"95110","title":"Presynaptic Rac1 Interactome in vivo BioID Soderling and Kim","user":"es3064","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718997526000","created":"Jun. 21, 2024, 12:18 PM","description":"Quantitative LC\/MS\/MS was performed on 2 uL of each sample, using a Vanquish Neo UPLC system (Thermo) coupled to a Thermo Orbitrap Astral high resolution accurate mass tandem mass spectrometer (Thermo). Briefly, the sample was first trapped on a Symmetry C18 20 mm x 180 um trapping column (5 ul\/min at 99.9\/0.1 v\/v water\/acetonitrile), after which the analytical separation was performed using a 1.5 um EvoSep 150um ID x 8cm performance (EveoSep) column with a 30 min gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 500 nanoliters\/minute (nL\/min) with a column temperature of 50C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r 240,000 (m\/z 200) full MS scan from m\/z 380-980 with a target AGC value of 4e5 ions. Fixed DIA windows of 4 m\/z from m\/z 380 to 980 DIA MS\/MS scans were acquired in the Astral with a target AGC value of 5e4 and max fill time of 6 ms. HCD collision energy setting of 27% was used for all MS2 scans.The total analysis cycle time for each sample injection was approximately 35 min.","fileCount":"11","fileSizeKB":"80348657","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"bioID, astral, label free","pi":[{"name":"Scott Soderling","email":"scott.soderling@duke.edu","institution":"Duke University, Dept of Cell Biology","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d509aa19025a410c88ffba12e4499f70","id":"2317"}, {"dataset":"MSV000095108","datasetNum":"95108","title":"PhpNF-Y transcription factor infiltrates repressive heterochromatin to generate transcripts crucial for spliceosome-dependent small RNA production","user":"monei004","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718990302000","created":"Jun. 21, 2024, 10:18 AM","description":"The assembly of repressive heterochromatin domains in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA-based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeat elements are transcribed has been unclear. Using fission yeast, we show that the conserved trimeric transcription factor (TF) PhpCNF-Y complex, which includes histone fold domain proteins, can infiltrate constitutive heterochromatin to transcribe repeat elements. PhpCNF-Y collaborates with a Zn-finger containing TF to bind heterochromatic repeat promoter regions with CCAAT boxes. Mutating either the TFs or the CCAAT binding site disrupts the transcription of heterochromatic repeats. Although repeat elements are transcribed from both strands, PhpCNF-Y-dependent transcripts originate from only one strand. These TF-driven transcripts contain cryptic introns that are processed via a mechanism requiring the spliceosome to generate small interfering RNAs (siRNAs) by the RNAi machinery. Our analyses show that siRNA production by this TF-mediated transcription pathway is critical for nucleation of heterochromatin at target repeat loci. This study reveals a mechanism by which heterochromatic repeats are transcribed, initiating their own silencing by triggering a primary cascade that produces siRNAs necessary for heterochromatin nucleation.\n\n","fileCount":"57","fileSizeKB":"28928202","spectra":"702409","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Schizosaccharomyces pombe (NCBITaxon:4896)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Heterochromatin, RNAi, siRNA, histone methylation, centromeric repeats, spliceosome, transcription factor","pi":[{"name":"Shiv Grewal","email":"grewals@mail.nih.gov","institution":"National Cancer Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a95da1fb2c874c93914b6bc406e6478b","id":"2318"}, {"dataset":"MSV000095107","datasetNum":"95107","title":" Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy","user":"aartigues","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718984995000","created":"Jun. 21, 2024, 8:49 AM","description":" Hepatocyte knockout of O-GlcNAc Transferase causes aneuploidy after partial liver hepatectomy.","fileCount":"213","fileSizeKB":"490271317","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"O-GlcNAc;Phosphorylation (T, S Y);Deamidation (N, Q);Oxidation (M);Carboxymethyl C","keywords":"O-GlcNAcyltion;hepatectomy;aneoploidy;Proteomics;Mass spectrometry;multi-Omics","pi":[{"name":"Chad Slawson","email":"cslawson@kumc.edu","institution":"University of Kansas Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053285","task":"1de1e8f3cc514b88bd9184eb43bc8c7e","id":"2319"}, {"dataset":"MSV000095105","datasetNum":"95105","title":"GNPS Germ-Free Mice Gavage with Ruminococcus gnavus ATCC 29149: Fecal Sample Collection at Pre-gavage, Day 5, and Day 13","user":"jma429njms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718979430000","created":"Jun. 21, 2024, 7:17 AM","description":"In this study, germ-free mice were administered a gavage containing Ruminococcus gnavus ATCC 29149. Fecal samples were collected at three time points: before gavage (Pre), 5 days post-gavage, and 13 days post-gavage. These samples underwent polar metabolite extraction and were analyzed using liquid chromatography-mass spectrometry (LC-MS) in both positive and negative modes.","fileCount":"37","fileSizeKB":"9983565","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Ruminococcus gnavus ATCC 29149;Germ free;Fecal metabolites","pi":[{"name":"Nan Gao","email":"ngao@newark.rutgers.edu","institution":"Rutgers University, Newark","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9d435a87af704090a37ccb38ee873a74","id":"2320"}, {"dataset":"MSV000095103","datasetNum":"95103","title":"The proteomic landscape of blood monocytes in community-acquired pneumonia","user":"Valdemaras","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718961203000","created":"Jun. 21, 2024, 2:13 AM","description":"This repository contains the raw proteomics data and Spectronaut search results and settings form the manuscript referenced in the title. ","fileCount":"89","fileSizeKB":"222469531","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Monocytes, Pneumonia","pi":[{"name":"Tom van der Poll ","email":"t.vanderpoll@amsterdamumc.nl","institution":"University of Amsterdam","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"83410976f3f448f2b143b55073459aef","id":"2321"}, {"dataset":"MSV000095101","datasetNum":"95101","title":"IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport ","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718957108000","created":"Jun. 21, 2024, 1:05 AM","description":"Mutations in the IER3IP1 (Immediate Early Response-3 Interacting Protein 1) gene can give rise to MEDS1 (Microcephaly with Simplified Gyral Pattern, Epilepsy, and Permanent Neonatal Diabetes Syndrome-1), a severe condition leading to early childhood mortality. The small endoplasmic reticulum (ER)-membrane protein IER3IP1 plays a non-essential role in ER-Golgi transport. Here, we employed secretome and cell-surface proteomics to demonstrate that the absence of IER3IP1 or the presence of the pathogenic p.L78P mutation results in the retention of specific cell-surface receptors and secreted proteins crucial for neuronal migration within the ER. This phenomenon correlates with the distension of ER membranes and increased lysosomal activity. Notably, the trafficking of cargo receptor ERGIC53 and KDEL-receptor 2 is compromised, with the latter leading to the anomalous secretion of ER-localized chaperones. Our investigation extended to in-utero knock-down of Ier3ip1 in mouse embryo brains, revealing a morphological phenotype in newborn neurons. In summary, our findings provide insights into how the loss or mutation of a 10 kDa small ER-membrane protein can cause a fatal syndrome.","fileCount":"25","fileSizeKB":"18068967","spectra":"255711","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"endoplasmic reticulum, COPII, anterograde transport, microcephaly, diabetes, axon pathfinding, cortical development","pi":[{"name":"Christoph Kaether","email":"Christoph.Kaether@leibniz-fli.de","institution":"Leibniz Institute on Aging, Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053277","task":"e21fd2257b874eb1904ee6d6a5867661","id":"2322"}, {"dataset":"MSV000095097","datasetNum":"95097","title":"GNPS - Lipidomics-based algorithms can enhance prediction of obstructive coronary artery disease","user":"mousthomai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718928209000","created":"Jun. 20, 2024, 5:03 PM","description":"Lipidomics-based algorithms can enhance prediction of obstructive coronary artery disease","fileCount":"357","fileSizeKB":"25951036","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Biological Samples","instrument":"Orbitrap Exploris 240","modification":"None","keywords":"Lipidomics","pi":[{"name":"Helen Gika","email":"gkikae@auth.gr","institution":"Aristotle University of Thessaloniki","country":"Greece"},{"name":"Maria Fedorova","email":"maria.fedorova@bbz.uni-leipzig.de","institution":"Leipzig University","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e7b886639c35473282097024a47a531f","id":"2323"}, {"dataset":"MSV000095096","datasetNum":"95096","title":"Characterization of PROTAC specificity and endogenous protein interactomes using ProtacID","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718927996000","created":"Jun. 20, 2024, 4:59 PM","description":"Data deposited contain results from proximity-dependent biotinylation LC-MS (BioID) experiments in which T-REx Flp-In HEK293, 697 and HAP1 cells expressing the E3 ligase VHL protein fused to miniTurbo biotin carboxylase were treated with either DMSO or various protacs with or without proteasome inhibitors.","fileCount":"709","fileSizeKB":"246008506","spectra":"0","psms":"8895795","peptides":"276591","variants":"475575","proteins":"67988","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"BioID, miniTurbo, protac, E3 ligase, LC-MS, VHL, BAF, SMARCA;ProtacID","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053263","task":"27365aa7aa87450e93b171f6c7e5de9d","id":"2324"}, {"dataset":"MSV000095095","datasetNum":"95095","title":"GNPS - Metabolomics and Microbiome of 3 Artemisia species","user":"pwpgomes","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718923377000","created":"Jun. 20, 2024, 3:42 PM","description":"This study assesses the biotransformation of plant metabolites by microbes. This dataset contains LC-MS\/MS data from crude extracts from 3 Artemisia species and extracts inoculated with human fecal culture. This study was led by Dr. Christine Tara Peterson and Dr. Paulo Wender Portal Gomes.","fileCount":"145","fileSizeKB":"85802387","spectra":"68550","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Artemisia absinthium (NCBITaxon:72332);Artemisia californica (NCBITaxon:86309);Artemisia annua (NCBITaxon:35608)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Artemisia;LC-MS\/MS;16S rRNA;Metabolomics;Microbiome;Plants","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7f3929cf08024099a2f4414c4d016ad7","id":"2325"}, {"dataset":"MSV000095094","datasetNum":"95094","title":"HCMV strain- and cell type-specific alterations in membrane contact sites point to the convergent regulation of organelle remodeling","user":"Krystallum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718913097000","created":"Jun. 20, 2024, 12:51 PM","description":"Data-independent acquisition assessment of human fibroblasts and epithelial cells infected with different strains of human cytomegalovirus (HCMV). Viruses are ubiquitous entities that infect organisms across the kingdoms of life. While viruses can infect a range of cells, tissues, and organisms, this aspect is often not explored in cell culture analyses. There is limited information about which infection-induced changes are shared or distinct in different cellular environments. The prevalent pathogen HCMV remodels the structure and function of subcellular organelles and their interconnected networks formed by membrane contact sites (MCSs). A large portion of this knowledge has been derived from fibroblasts infected with a lab-adapted HCMV strain. Here, we assess strain- and cell type-specific alterations in MCSs and organelle remodeling induced by HCMV. Integrating quantitative mass spectrometry, super-resolution microscopy, and molecular virology assays, we compare infections with lab-adapted and low-passage HCMV strains in fibroblast and epithelial cells. We determine that, despite baseline proteome disparities between uninfected fibroblast and epithelial cells, infection induces convergent changes and is remarkably similar. We show that hallmarks of HCMV infection in fibroblasts, mitochondria-ER encapsulations (MENCs) and peroxisome proliferation, are also conserved in infected epithelial and macrophage-like cells. Exploring cell type-specific differences, we demonstrate that fibroblasts rely on endosomal cholesterol transport while epithelial cells rely on cholesterol from the Golgi. Despite these mechanistic differences, infections in both cell types result in phenotypically similar cholesterol accumulation at the viral assembly complex. Our findings highlight the adaptability of HCMV, in that infections can be tailored to the initial cell state by inducing both shared and unique proteome alterations, ultimately promoting a unified pro-viral environment.","fileCount":"10","fileSizeKB":"246864210","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Ultra","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Proteomics, HCMV, Herpesvirus, Organelle remodeling, Membrane Contact Sites, Data-independent acquisition","pi":[{"name":"Ileana M. 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Following incubation, the spent media from each strain underwent polar metabolite analysis using liquid chromatography-mass spectrometry (LC-MS) in positive ion mode.\n\n","fileCount":"42","fileSizeKB":"22071359","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruminococcus gnavus ATCC 29149 (NCBITaxon:411470);Ruminococcus gnavus ATCC 35913;Mediterraneibacter gnavus H2_28;Mediterraneibacter gnavus AGR2154","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mediterraneibacter gnavus;Ruminococcus gnavus;porcine mucus;sialic acid","pi":[{"name":"Nan Gao","email":"ngao@newark.rutgers.edu","institution":"Rutgers University, Newark","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"68b2ef8678254deb8178b3c5089158a6","id":"2327"}, {"dataset":"MSV000095092","datasetNum":"95092","title":"GNPS - Fourier transform-Ion Mobility-Charge Detection-Mass Spectrometry","user":"michaelmarty","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718904810000","created":"Jun. 20, 2024, 10:33 AM","description":"Fourier transform-ion mobility separations interfaced with charge detection-mass spectrometry detection. 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Data is included for beta galactosidase alone, in a mixture with GroEL, and for a high mass enriched E. coli lysate mixture","fileCount":"529","fileSizeKB":"22009985","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive UHMR","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Charge Detection;Native MS;Multiplexed;Online SEC","pi":[{"name":"Michael Marty","email":"mtmarty@arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"87c596b5bd0646e0ac5237699b774ba4","id":"2329"}, {"dataset":"MSV000095090","datasetNum":"95090","title":"GNPS Ruminococcus gnavus Strains","user":"jma429njms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718897868000","created":"Jun. 20, 2024, 8:37 AM","description":"Strains of Ruminococcus gnavus, specifically ATCC 29149, ATCC 35913, H2-28, and Mediterraneibacter gnavus AGR 2154 (previously known as Ruminococcus gnavus), were cultured under three different conditions:\n\nMeat Broth (CNTRL)\nMeat Broth with Sialic Acid (SIALIC)\nMeat Broth with 1% Porcine Mucin (PORCINE)\n\nThe cultures were incubated for 3 hours. Following incubation, the spent media of the strains underwent polar metabolite analysis using liquid chromatography-mass spectrometry (LC-MS) in negative ion mode.","fileCount":"42","fileSizeKB":"16167816","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruminococcus gnavus ATCC 29149 (NCBITaxon:411470);Ruminococcus gnavus AGR 2154;Ruminococcus gnavus H2-28;Ruminococcus gnavus ATCC 35913","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"porcine mucin;sialic acid;meat broth","pi":[{"name":"Nan Gao","email":"ngao@newark.rutgers.edu","institution":"Rutgers University, Newark","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1a31267f3d894425ad61eae074091d86","id":"2330"}, {"dataset":"MSV000095089","datasetNum":"95089","title":"GNPS Ruminococcus gnavus ATCC 29149","user":"jma429njms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718890253000","created":"Jun. 20, 2024, 6:30 AM","description":"This study investigates the growth of Ruminococcus gnavus strain ATCC 29149 under two different conditions over a period of 3 hours. The experimental conditions include:\n\nRG (Ruminococcus gnavus in Meat Broth): R. gnavus grown in standard meat broth.\nRS-SA (Ruminococcus gnavus in Meat Broth with Sialic Acid): R. gnavus grown in meat broth supplemented with sialic acid.\nControl conditions were also established for comparison:\n\nCT (Control in Meat Broth): Standard meat broth without R. gnavus.\nCT-SA (Control in Meat Broth with Sialic Acid): Meat broth with sialic acid, also without R. gnavus.","fileCount":"16","fileSizeKB":"3723756","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruminococcus gnavus ATCC 29149 (NCBITaxon:411470)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sialic acid;Ruminococcus gnavus;Metabolites","pi":[{"name":"Nan Gao","email":"ngao@newark.rutgers.edu","institution":"Rutgers University, Newark","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0d1f0b7e4c64447797426bca930c7580","id":"2331"}, {"dataset":"MSV000095088","datasetNum":"95088","title":"GNPS-FAIMS Shotgun Lipidomics for Enhanced Class- and Charge-State Separation Complemented by Automated Ganglioside Annotation","user":"KathiHw","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718886077000","created":"Jun. 20, 2024, 5:21 AM","description":"Shotgun and shotgun FAIMS data of a pooled ganglioside (PGS) standard and the Avanti total porcine brain extract (BE) as (1) raw files (2) zipped raw files and (3) zipped LDA results.\r\n","fileCount":"67","fileSizeKB":"1939403","spectra":"5342","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gangliosides in pooled standards and porcine brain;Sus scrofa (NCBITaxon:9823);Bos taurus (NCBITaxon:9913)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Gangliosides, Glycosphingolipids, shotgun, FAIMS, LDA","pi":[{"name":"Evelyn Rampler","email":"evelyn.rampler@univie.ac.at","institution":"University of Vienna","country":"Austria"},{"name":"Katharina Hohenwallner","email":"katharina.hohenwallner@univie.ac.at","institution":"University of Vienna","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"937cc140cdee49b491b4cc26e3eeb70d","id":"2332"}, {"dataset":"MSV000095087","datasetNum":"95087","title":"Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation","user":"kojiode","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718846078000","created":"Jun. 19, 2024, 6:14 PM","description":"This dataset is the raw data for the quantification of the T286 phosphorylation level of CaMKIIa expressed downstream of the E11 enhancer, as presented in the paper \"Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation.\" The datasets ending in \"P\" are from samples that underwent phosphopeptide enrichment and were used to quantify phosphorylated T286 peptides. The datasets ending in \"NP\" are from samples that did not undergo phosphopeptide enrichment and were used to estimate the total amount of CaMKIIa.","fileCount":"85","fileSizeKB":"236777650","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:199 - \\\"DiMethyl-CHD2.\\\"","keywords":"CaMKII;T286;PV;parvalbumin neurons;sleep","pi":[{"name":"Hiroki R Ueda","email":"uedah-tky@umin.ac.jp","institution":"The University of Tokyo","country":"Japan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5f4cd89bc07c46ec9d4838cb6b92a9b1","id":"2333"}, {"dataset":"MSV000095086","datasetNum":"95086","title":"Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics","user":"jfhorner","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718826247000","created":"Jun. 19, 2024, 12:44 PM","description":"Raw data for the manuscript entitled \"Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics\"","fileCount":"167","fileSizeKB":"308315811","spectra":"1180050","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"top-down proteomics;proteoforms;nanoparticles;protein corona;plasma","pi":[{"name":"Neil L Kelleher","email":"neil.kelleher@norwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aeb6d7b51ebd4c8daaeef73cd099f777","id":"2334"}, {"dataset":"MSV000095082","datasetNum":"95082","title":"Assessment of data-independent acquisition mass spectrometry (DIA-MS) for the identification of single amino acid variants.","user":"klemens_froehlich","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718802160000","created":"Jun. 19, 2024, 6:02 AM","description":"Proteogenomics integrates genomic and proteomic data to elucidate cellular processes by identifying variant peptides, including single amino acid variants (SAAVs). In this study, we assessed the capability of data-independent acquisition mass spectrometry (DIA-MS) to identify SAAV peptides in HeLa cells using various search engine pipelines. We developed a customised sequence database incorporating SAAV sequences from the HeLa genome and conducted searches using DIA-NN, Spectronaut, and Fragpipe-MSFragger. Our evaluation focused on identifying true positive SAAV peptides and false positives through entrapment databases. The study revealed that DIA-MS provides reproducible and comprehensive coverage of the proteome, identifying a substantial proportion of SAAV peptides. Notably, DIA-MS searches maintained consistent identification of SAAV peptides despite varying sizes of the entrapment database. Comparative analysis showed that Fragpipe-MSFragger (FP-DIA) demonstrated the most conservative and effective performance, exhibiting the lowest false discovery match ratio (FDMR). Additionally, integrating DIA and data-dependent acquisition (DDA) MS data search outputs enhanced SAAV peptide identification, with a lower false discovery rate (FDR) observed in DDA searches. Validation using stable isotope dilution and parallel reaction monitoring (SID-PRM) confirmed SAAV peptides identified by DIA-MS and DDA-MS searches, highlighting the reliability of our approach. Our findings underscore the effectiveness of DIA-MS in proteogenomic workflows for identifying SAAV peptides, offering insights into optimising search engine pipelines and database construction for accurate proteomics analysis. These methodologies advance the understanding of proteome variability, contributing to cancer research and the identification of novel therapeutic targets.","fileCount":"38","fileSizeKB":"27845053","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Eclipse","modification":"oxidation M;UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"single amino acid variants;SAAV;entrapment search;DIA workflow;Proteogenomics;proteomic search platforms;DIA;DDA","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum","country":"Schweiz"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6187e10f539047e0a744cd3a9ea81c80","id":"2335"}, {"dataset":"MSV000095080","datasetNum":"95080","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718795658000","created":"Jun. 19, 2024, 4:14 AM","description":"Ribosome profiling on killifish brains coming from adult and old animals. Fractions have been pulled as described in the M&M and analysed by DIA proteomics.","fileCount":"24","fileSizeKB":"28185245","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Ribosome profiling;killifish;aging;brain","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053239","task":"be20c0d421fe4022bb49920fcbceb4ae","id":"2336"}, {"dataset":"MSV000095079","datasetNum":"95079","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718794569000","created":"Jun. 19, 2024, 3:56 AM","description":"DIA protein candidates validation via PRM in killifish brain aging","fileCount":"34","fileSizeKB":"11836258","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"PRM;Killifish;Brain;Aging;Nothobranchius","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053235","task":"42ea9268687949d39f9344916d7b2c51","id":"2337"}, {"dataset":"MSV000095078","datasetNum":"95078","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718792640000","created":"Jun. 19, 2024, 3:24 AM","description":"Proteome DIA analysis of brain tissue from old (32 weeks old) killifish treated for 3 weeks with bortezomib to reduce the proteasome activity or DMSO as control.","fileCount":"26","fileSizeKB":"70502921","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Bortezomib;Killifish;Aging;brain;proteasome inhibition","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053232","task":"d610a7eb7da749e89a7314e49684cb9d","id":"2338"}, {"dataset":"MSV000095077","datasetNum":"95077","title":"Serum Proteomics Reveals Survival-Associated Biomarkers in Pancreatic Cancer Patients Treated with Chemoimmunotherapy","user":"roland_bruderer","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718790702000","created":"Jun. 19, 2024, 2:51 AM","description":"Immunotherapy has transformed the landscape of cancer treatment but remains largely ineffective for patients with pancreatic ductal adenocarcinoma (PDAC). Some patients, however, show improved outcomes when treated with a combination of immunotherapy and chemotherapy. Here, we conducted deep serum proteome analysis to investigate the protein profiles of PDAC patients and changes during this combinatorial treatment. Utilizing an advanced serum workflow, we quantified 1,011 proteins across 211 samples from 62 patients. Glycolytic enzymes were associated with survival in anti-PD-1 treated patients, with their abundances significantly correlating with expression levels in tumor biopsies. Notably, a set of protein biomarkers was found to be highly predictive of survival in anti-PD-1-treated patients (AUC = 0.91). Overall, our data demonstrate the potential of deep serum proteomics for precision medicine, offering a powerful tool to guide patient selection for treatment through minimally invasive serum protein biomarker measurements.","fileCount":"626","fileSizeKB":"1923500163","spectra":"22786267","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:366 - \\\"Deamidation in presence of O18.\\\"","keywords":"plasma;cancer;biomarker;immunotherapy;chemotherapy;pancreatic ductal adenocarcinoma","pi":[{"name":"Christoph B. Messner","email":"christoph.messner@siaf.uzh.ch","institution":"Swiss Institute of Bioinformatics (SIB), 1005 Lausanne","country":"Switzerland"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053231","task":"ce08240616dd4e35bf9795dd5aac1d95","id":"2339"}, {"dataset":"MSV000095074","datasetNum":"95074","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718786356000","created":"Jun. 19, 2024, 1:39 AM","description":"Proteome DIA analysis of muscle tissue in young, adult and old killifish (Nothobranchius furzeri)","fileCount":"38","fileSizeKB":"166782161","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Killifish;Muscle;Aging;Nothobranchius;furzeri","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053229","task":"22a919edb51b417db7f1664961c0ff6e","id":"2340"}, {"dataset":"MSV000095072","datasetNum":"95072","title":"Single-cell proteomics of Arabidopsis leaf mesophyll protoplasts in the context of drought stress","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718759163000","created":"Jun. 18, 2024, 6:06 PM","description":"We followed the Arabidopsis tape-sandwich protocol to isolate the leaf protoplast enriched with palisade mesophyll cells. Briefly, control and WD-stressed Arabidopsis rosette leaves were placed on 3M tape, and abaxial cell layers were peeled off by gently removing the tape, thereby exposing the adaxial side with enriched palisade mesophyll cells. The exposed leaf (n=6) from control and WD stress conditions was placed in a petri plate, and 20 mL of protoplasting enzyme solution was added. The enzyme solution contained 1% cellulase (CELLULYSIN) and 0.25% macerozyme R10 dissolved in a buffer made of 0.4M mannitol, 20 mM potassium chloride, 20 mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer and adjusted to pH 5.7. The enzyme solution was heated at 55 deg C for 10 mins to dissolve the enzymes into the buffer followed by cooling the solution on ice for 5 minutes. Following that, 10 mM calcium chloride was added to the enzyme solution, and it was used for protoplast isolation. The leaf tissue was incubated with the enzyme solution for 45 minutes and kept on a rotatory shaker maintained at 150 rpm at 25 deg C in the dark to allow the enzymes to digest the cell walls to liberate the protoplasts. Three batches of protoplast isolation were performed from control and WD-stressed leaf tissue to yield sufficient protoplasts for single-cell proteomics workflow. After enzymatic digestion, the protoplast solution was carefully transferred to 50 mL falcon tubes and centrifuged at 13 G at room temperature using an IEC Centra MP4R refrigerated centrifuge. The protoplast pellet was gently washed two times using the same buffer used to dissolve enzymes (without mannitol) and filtered using a 0.45 um filter to remove the cell debris. The filtered leaf protoplasts were counted using a hemocytometer then immediately sorted using the cellenONE. \n\nWe employed an in-house assembled nanoPOTS autosampler for LC-MS\/MS analysis. The autosampler contains a custom packed SPE column (100 um i.d., 4 cm, 5 um particle size, 300 A pore size C18 material, Phenomenex) and analytical LC column (50 um i.d., 25 cm long, 1.7 um particle size, 190 A pore size C18 material, Waters) with a self-pack picofrit (cat. no. PF360-50-10-N-5, New Objective, Littleton, MA). The analytical column was heated to 50 deg C using an AgileSleeve column heater (Analytical Sales and services, Inc., Flanders, NJ). Briefly, samples were dissolved with Buffer A (0.1% formic acid in water) on the chip, then trapped on the SPE column for 5 min. After washing the peptides, samples were eluted at 100 nL\/min and separated using a 30 min gradient from 8% to 35% Buffer B (0.1% formic acid in acetonitrile). An Orbitrap Lumos Tribrid MS (ThermoFisher Scientific) with FAIMS, operated in data-dependent acquisition mode, was used for all analyses. Source settings included a spray voltage of 2,400 V, ion transfer tube temperature of 200 deg C, and carrier gas flow of 4.6 L\/min. For TIFF method16 samples, ionized peptides were fractionated by the FAIMS interface using internal compensation voltage stepping (-45, -60, and -75 V) with a total cycle time of 0.8 s per compensation voltage. Fractionated ions within a mass range 350-1600 m\/z were acquired at 120,000 resolution with a max injection time of 500 ms, AGC target of 1E6, RF lens of 30%. Tandem mass spectra were collected in the ion trap with an AGC target of 20,000, a \"rapid\" ion trap scan rate, an isolation window of 1.4 m\/z, a maximum injection time of 120 ms, and a HCD collision energy of 30%. For the TIFF library samples, a single compensation voltage was used for each LC-MS run with slight modifications to the above method where cycle time was increased to 2 s and maximum injection time was set to 118 ms. Precursor ions with a minimum intensity of 1E4 were selected for fragmentation by 30% HCD and scanned in an ion trap with an AGC of 2E4 and an IT of 150 ms. Precursor ions with intensities > 1E4 were fragmented by 30% HCD and scanned with an AGC of 2E4 and an IT of 254 ms. Downstream analysis was performed in FragPipe.","fileCount":"343","fileSizeKB":"59563717","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion Lumos;Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"protoplasts;drought;water stress;scProteomics;nanoPOTS","pi":[{"name":"James M. Fulcher","email":"james.fulcher@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"acf11dede0d3456e91662c0c95b3e023","id":"2341"}, {"dataset":"MSV000095071","datasetNum":"95071","title":"De novo gene synthesis by an antiviral reverse transcriptase","user":"mj2794","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718739962000","created":"Jun. 18, 2024, 12:46 PM","description":"Bacteria defend themselves from viral infection using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands in DRT2-expressing cells revealed that reverse transcription generates concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this DNA product is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.","fileCount":"25","fileSizeKB":"27360486","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"bacterial immmunity;bacterial defense;DRT;defense-associated reverse transcriptase;DRT2;bacterial reverse transcriptases;E. coli","pi":[{"name":"Marko Jovanovic","email":"mj2794@columbia.edu","institution":"Columbia University","country":"USA"},{"name":"Samuel H. Sternberg","email":"shsternberg@gmail.com","institution":"Columbia University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cf606b81b8a545a396259a5997b1f0f4","id":"2342"}, {"dataset":"MSV000095070","datasetNum":"95070","title":"GNPS - CMMC_n_acyl_lipids_reaction_codes_20_21_29_30_31_32_33_36_37_38_40_41_42_43_44_45","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718735261000","created":"Jun. 18, 2024, 11:27 AM","description":"MS\/MS fragmentation data of n acyl lipids acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"33","fileSizeKB":"7121348","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"n acyl lipid","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3641e725ac014aceb01d587bcd1fb639","id":"2343"}, {"dataset":"MSV000095069","datasetNum":"95069","title":"GNPS Human AKR1C3 Binds Agonists of GPR84 and Participates in an Expanded Polyamine Pathway (tandem MS files of murine type I fatty acid synthase NADPH assay for alpha-pyrone biosynthesis)","user":"ndudkina","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718730488000","created":"Jun. 18, 2024, 10:08 AM","description":"Representative tandem MS files generated from mouse type I fatty acid synthase biochemical assay with NADPH titration. \n\nProtocol description: Mouse FAS was enriched using dual-affinity chromatography (Ni-NTA, nitrilotriacetic acid, Strep-Tactin XT Sepharose from Cytiva) and subjected to in vitro enzymatic assays. In this assay, we titrated different amounts of NADPH (0-350 uM) in the reaction mixture containing malonyl-CoA (175 uM), acetyl-CoA (25 uM), and enriched mFAS (6.2 mg\/mL) in PBS buffer (pH 7.4) After 50 minutes of incubation, the reactions were quenched with acetonitrile, and the mixtures were centrifuged and subjected to HPLC-HR-QTOF-MS analysis (positive mode). We observed that with no NADPH we got the highest production of TAL (triacetic acid lactone), with high NADPH (350 uM) we got the highest production of palmitate, and that middle ranges of NADPH would variably generate the alpha-pyrone family. \nFile description: \nin-vitro-NADPH-0-1msms: a representative tandem MS file of alpha pyrones from mFAS in vitro biochemical assay (as described above) titrated with 0 uM NADPH co-factor.\nin-vitro-NADPH-100-1msms: a representative tandem MS file of alpha pyrones from mFAS in vitro biochemical assay (as described above) titrated with 100 uM NADPH co-factor.\nin-vitro-NADPH-200-1msms: a representative tandem MS file of alpha pyrones from mFAS in vitro biochemical assay (as described above) titrated with 200 uM NADPH co-factor.\nReversed-phase chromatography was performed with a Kinetex (Cat. # 00G-4601-E0) 5 um C18 100 A column (250 by 4.6 mm), using a water:acetonitrile gradient containing 0.1% formic acid at 0.7 mL\/min flow rate: 0-30 min, 10% to 100% acetonitrile. Positive mode (qTOF) ","fileCount":"4","fileSizeKB":"55825","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"murine type I fatty acid synthase, biochemical assay, NADPH titration, alpha pyrone biosynthesis, pyrone-211;tandem MS of alpha pyrones","pi":[{"name":"Jason Crawford","email":"jason.crawford@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"32dc3b76727647a0b0b359d96e319c93","id":"2344"}, {"dataset":"MSV000095067","datasetNum":"95067","title":"GNPS Human AKR1C3 Binds Agonists of GPR84 and Participates in an Expanded Polyamine Pathway (Pyrone Family Networking Analysis)","user":"ndudkina","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718728828000","created":"Jun. 18, 2024, 9:40 AM","description":"Files used for networking analysis of in vitro pulldown metabolomics with AKR1C3 recombinantly expressed and purified from E. coli BL21 (DE3). Alpha-Pyrone family was identified as pulldown products and networking analysis was performed with a representative tandem MS file (1 files from triplicates was chosen randomly). Corresponding conditions of 2 uploaded files: \nC3onlyoldmsms: Tandem MS file containing alpha pyrone family members (m\/z 127.0395, 237.1488, 239.1641, 265.1797, 267.1953, 293.2109 correspond to alpha-pyrones of varying fatty acid chain lengths and saturations) pull downed from enzyme (AKR1C3) only condition with NADPH co-factor added in PBS buffer and quenched with acetonitrile (30% final volume); \n211-natural-tandem: Tandem MS file of pyrone-211 metabolite pull downed from enzyme (AKR1C3) only condition with NADPH co-factor added in PBS buffer and quenched with acetonitrile (30% final volume);. \nReversed-phase chromatography was performed with a Kinetex (Cat. # 00G-4601-E0) 5 um C18 100 A column (250 by 4.6 mm), using a water:acetonitrile gradient containing 0.1% formic acid at 0.7 mL\/min flow rate: 0-30 min, 10% to 100% acetonitrile. Positive mode (qTOF)","fileCount":"3","fileSizeKB":"185318","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Homo sapiens (NCBITaxon:9606)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Networking analysis of AKR1C3 pulldown products, tandem MS file of alpha-pyrones, tandem MS file of pyrone-211","pi":[{"name":"Jason Crawford","email":"jason.crawford@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6e63e85a303b47bda997ed8ebbbca6b6","id":"2345"}, {"dataset":"MSV000095066","datasetNum":"95066","title":"Broadening the horizon of MS optimization for enzymatic digestions in proteomics","user":"reveszagnes","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718725897000","created":"Jun. 18, 2024, 8:51 AM","description":"Collision energy dependent measurements on human protein exctract and human blood plasma samples digested with various enzymes (trypsin, Arg-C, Glu-C, chymotrypsin, Asp-N) and performance assessment at optimized energies on Bruker QTof instruments","fileCount":"697","fileSizeKB":"106156741","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"maXis","modification":"[C] carbamidomethyl","keywords":"alternative enzymes;collision energy","pi":[{"name":"Agnes Revesz","email":"reveszagnes@ttk.hu","institution":"Research Centre for Natural Sciences, Budapest","country":"Hungary"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"34c95ed0ba5d452db3c41c75dc6f5279","id":"2346"}, {"dataset":"MSV000095065","datasetNum":"95065","title":"Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.","user":"jess_conforti1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718722131000","created":"Jun. 18, 2024, 7:48 AM","description":"Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remain unclear. This study investigated the role of OMVs and OMV-associated small RNA (sRNA) species from pathogenic and commensal Bacteroides fragilis (ETBF and NTBF respectively) in eliciting different immune responses from intestinal epithelial cells. To distinguish the differences in the sRNA profiles of the two strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting were conducted to identify enrichment of discrete sRNA species in OMVs, which were also differentially expressed between the two strains. To understand the effects of OMVs on pattern recognition receptors, Reporter cells of Toll-like receptor (TLR) activation were treated with OMVs, demonstrating activation of TLRs 2, 3, and 7. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8. Surprisingly, we discovered that degradation of RNase-accessible RNAs within ETBF OMVs, but not NTBF OMVs, resulted in vesicles with enhanced capacity to stimulate IL-8 expression, indicating that these extravesicular RNAs exert an immunosuppressive effect. This suggests a dual role for OMV-associated RNAs in modulating host immune responses, with implications for both bacterial pathogenesis and therapeutic applications. ","fileCount":"2062","fileSizeKB":"273235377","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis (NCBITaxon:817)","instrument":"Synapt G2-S HDMS;nanoACQUITY UPLC","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00046 - \\\"A protein modification that effectively converts an L-serine residue to O-phospho-L-serine.\\\";MOD:00047 - \\\"A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine.\\\";MOD:00048 - \\\"A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine.\\\"","keywords":"Bacteroides Fragilis;ETBF;NTBF","pi":[{"name":"Elyssia Gallagher","email":"elyssia_gallagher@baylor.edu","institution":"Baylor University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053204","task":"25d183a7fccb481ca2dfb7d6e41e81f6","id":"2347"}, {"dataset":"MSV000095063","datasetNum":"95063","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718719556000","created":"Jun. 18, 2024, 7:05 AM","description":"Proteome DIA analysis of Optic Tectum brain region in young, adult and old killifish (Nothobranchius furzeri)","fileCount":"49","fileSizeKB":"207894788","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Optic Tectum;Killifish;Aging;Brain;Nothobranchius;furzeri","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053202","task":"7f1894f448a94627b78905cf8a976735","id":"2348"}, {"dataset":"MSV000095062","datasetNum":"95062","title":"Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718714471000","created":"Jun. 18, 2024, 5:41 AM","description":"Proteome analysis of liver tissues coming from young, adult, and old Nothobranchius furzeri (killifish).","fileCount":"38","fileSizeKB":"213432963","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nothobranchius furzeri (NCBITaxon:105023)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:6 - \\\"Iodoacetic acid derivative.\\\"","keywords":"killifish;Liver;Aging;Nothobranchius;furzeri","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD053201","task":"5158c0e8d8724a91a82c44de429e0333","id":"2349"}, {"dataset":"MSV000095060","datasetNum":"95060","title":"DATASET - Mass Spectrometry - Snake venom proteomics of island and mainland V. ammodytes populations from North Macedonia","user":"MDamm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718696540000","created":"Jun. 18, 2024, 12:42 AM","description":"This DATASET collection includes the mass spectrometry files for proteomics venom investigation of island and mainland V. ammodytes populations from North Macedonia.\n\nSample list:\n\n1. Island - adult - male\n2. Island - adult - female\n3. Island - juvenile\n4. Island - subadult\n5. Mainland - adult\n6. Mainland - subadult\n7. Mainland - juvenile\n\nFolders 01-07 - BOTTOM-UP PROTEOMICS: The venom pools were investigated by the bottom-up \"snake venomics\" (labelled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o\/n tryptic digested. Samples submitted to HPLC-MS\/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS\/MS analytic w\/o further gel procession. Folders 01 to 07 include the MS and MS\/MS spectra of the V. ammodytes sample pools from different populations. Files are included as RAW and MZML format.\n\nUsed instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 x 150 mm; 5 um particle size) column.\n\nModifications: UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"\n\nUsed protein database: Uniprot_8750_serpentes_CanNIso_2674_entries_220210_cRAP_220210.fasta","fileCount":"2630","fileSizeKB":"45475860","spectra":"247616","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vipera ammodytes (NCBITaxon:8704);Vipera ammodytes montandoni (NCBITaxon:235554)","instrument":"LTQ Orbitrap XL","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"snake venomics;venom;snake;viper;snakebite;proteomics;mass spectrometry","pi":[{"name":"Maik Damm","email":"maik.damm@outlook.de","institution":"JLU Giessen","country":"Germany"},{"name":"Margareta Lakusic","email":"margareta.lakusic@cibio.up.pt","institution":"Centro de Investigacao em Biodiversidade e Recursos Geneticos (CIBIO)","country":"Portugal"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bb610d70a28b4319887a80bb2334ea5f","id":"2350"}, {"dataset":"MSV000095059","datasetNum":"95059","title":"GNPS Citrus Bacteria data 06172024","user":"malonekn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718667737000","created":"Jun. 17, 2024, 4:42 PM","description":"LC-MS\/MS data from crude extracts and fractions from assorted bacteria isolated from Citrus trees","fileCount":"1231","fileSizeKB":"7384224","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Assorted bacteria isolated from Citrus trees","instrument":"Agilent 6530 Q-ToF","modification":"n\\\/a","keywords":"Citrus, bacteria","pi":[{"name":"Katherine Maloney","email":"kmaloney@pointloma.edu","institution":"Point Loma Nazarene University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"81a7837dffc84342b997589796eae42f","id":"2351"}, {"dataset":"MSV000095058","datasetNum":"95058","title":"Effects Beta-hydroxybutyrate on human islet proteome","user":"Rogy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718663846000","created":"Jun. 17, 2024, 3:37 PM","description":"We measured changes in the human islet proteome following 72-hr exposure to 3 mM R-beta-hydroxybutyrate. Islets from 12 metabolically healthy human islet donors were obtained from the Alberta Diabetes Institute Islet Core","fileCount":"5533","fileSizeKB":"198321747","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Human islets;ketones;beta-hydroxybutyrate;diabetes","pi":[{"name":"James D. Johnson","email":"james.d.johnson@ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053179","task":"eaccb92de7c44c6880cbbae2b218e642","id":"2352"}, {"dataset":"MSV000095057","datasetNum":"95057","title":"Title: Site specific O-GlcNAcylation of progesterone receptor (PR) supports PR attenuation of interferon stimulated genes (ISGs) and tumor growth in breast cancer ","user":"aartigues","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718662149000","created":"Jun. 17, 2024, 3:09 PM","description":"Hormone receptor (HR) positive breast cancer, defined by expression of estrogen (ER) and\/or progesterone (PR) receptor expression, is the most commonly diagnosed type of breast cancer. PR alters the transcriptional landscape to support tumor growth in concert with or independent of ER. Understanding the mechanisms regulating PR function are critical to developing new strategies to treat HR+ breast cancer. O-GlcNAc is a post-translational modification responsible for nutrient sensing that fine tunes protein function. We have previously reported O-GlcNAcylation on PR. Although PR is heavily post translationally modified, primarily through phosphorylation, specific sites of O-GlcNAcylation on PR, and how they regulate PR action, have not been investigated. Using established PR-expressing breast cancer cell lines, we mapped the sites of O-GlcNAcylation on PR. RNA-sequencing revealed site-specific O-GlcNAcylation of PR is critical for ligand-independent suppression of interferon signaling, a regulatory function of PR previously studied in our lab. Furthermore, O-GlcNAcylation of PR enhances PR-driven tumor growth in vivo. We have delineated one mechanism regulating PR function in breast cancer that impacts tumor growth, and provided additional insight into the mechanism through which PR attenuates interferon signaling. 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Absolute quantification is typically a requirement for clinical assays and we explore the use of 15N labeled protein standards in a rapid, streamlined and generic manner. Our results indicate that Stellar MS can bridge the gap between proteomics discovery and routine clinical testing, enhancing the diagnostic and prognostic utility of protein biomarkers.","fileCount":"30","fileSizeKB":"130725101","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral;Stellar;Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plasma;targeted Proteomics;15N labeling","pi":[{"name":"Matthias Mann","email":"mmann@biochem.mpg.de","institution":"Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 D-82152 Martinsried","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053174","task":"8836c971f48343ca9ca910b7094135a6","id":"2355"}, {"dataset":"MSV000095049","datasetNum":"95049","title":"Multiplex genome editing eliminates the Warburg Effect without impacting growth rate in mammalian cells","user":"alejandro1018","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718609971000","created":"Jun. 17, 2024, 12:39 AM","description":"Peptide and phosphopeptide analysis of immunoprecipitated PDHA","fileCount":"28","fileSizeKB":"15554315","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Warburg effect;PDHA;Phosphorylation;lactate","pi":[{"name":"Nathan E Lewis","email":"n4lewis@eng.ucsd.edu","institution":"UC, San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"00a255399c074ab98ba47a0fdcaf37ee","id":"2356"}, {"dataset":"MSV000095047","datasetNum":"95047","title":"GNPS - Single cell amine metabolomics raw files","user":"JuhoH","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718461879000","created":"Jun. 15, 2024, 7:31 AM","description":"Targeted and untargeted single cell amine metabolomics raw files and metadata","fileCount":"38","fileSizeKB":"9067275","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics","pi":[{"name":"Jaakko Teppo","email":"jaakko.teppo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b69473af1b0c439eae5de32414a61cba","id":"2357"}, {"dataset":"MSV000095045","datasetNum":"95045","title":"Top-down mass spectrometry analysis of capsid proteins of recombinant adeno-associated virus using multiple ion activations and proton transfer charge reduction","user":"Fornelli_Lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718395334000","created":"Jun. 14, 2024, 1:02 PM","description":"Here, we present our investigation of the viral proteins of the capsid of adeno-associated viruses via top-down mass spectrometry on the LC timescale. 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Beyond these analytical insights, this study provides protein expression information on 11,000 proteins in >1,200 tumor samples from six cancer entities representing the first comprehensive pan-cancer proteome resource for FFPE material to date. The authors believe that the current study provides useful guidance for planning large-scale FFPE proteome projects and is also of immediate utility to the scientific community as the data is publicly accessible via a custom-built ShinyApp enabling a wide range of analysis. 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Low activity favors phospholipid synthesis, whereas high activity favors triacylglycerol synthesis. Pah1 function is controlled by its subcellular location as regulated by phosphorylation and dephosphorylation. Multiple protein kinases phosphorylate Pah1 for its inactivation in the cytosol; Pah1 is activated via recruitment and dephosphorylation by the protein phosphatase Nem1-Spo7 at the nuclear\/endoplasmic reticulum membrane where the PA phosphatase reaction occurs. Additionally, phosphorylation inhibits PA phosphatase activity and stabilizes Pah1 abundance, while dephosphorylation stimulates activity and destabilizes the enzyme abundance. Many of the protein kinases that phosphorylate Pah1 have yet to be characterized and their sites of phosphorylation defined. Here, we established Pah1 as a bona fide substrate of septin-associated Hsl1, a protein kinase involved in mitotic morphogenesis checkpoint signaling. Using Pah1 as substrate, Hsl1 activity was dependent on reaction time and the amounts of protein kinase, Pah1, and ATP. The phosphorylation occurred on Ser-748 and Ser-773, which together caused a 5-fold reduction in PA phosphatase catalytic efficiency. Analysis of cells expressing phosphorylation-deficient S748A and S773A mutant forms of Pah1 indicated that the Hsl1-mediated phosphorylation of Pah1 promoted membrane phospholipid synthesis at the expense of triacylglycerol, and ensured the dependence of Pah1 function on the Nem1-Spo7 protein phosphatase. This work advances understanding of how Hsl1 facilitates membrane phospholipid synthesis through the phosphorylation-mediated regulation of Pah1.","fileCount":"4","fileSizeKB":"1259845","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Pah1, phosphatidate phosphatase, Hsl1, protein kinase, phospholipid, triacylglycerol, yeast ","pi":[{"name":"George M. 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Cysteamine treatment delays the symptoms and improves the quality of life of the patients, but the patients depend on it for life. Furthermore, oral cysteamine treatment present undesirable side effects and fails in avoiding the end-stage renal failure that inevitably drives to kidney transplant. Our results will be helpful to understand, from a molecular point of view, the benefits, deficiencies, and detrimental effects of the cysteamine treatment.","fileCount":"256","fileSizeKB":"51594364","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ZenoTOF 7600","modification":"ALKYKATION Carbamidomethyl on cysteine C2H3NO [C] +57Da","keywords":"Lysosomal disease, metabolism, cystinosis, redox balance, rare disease","pi":[{"name":"Jesus Mateos","email":"jesusmateosmartin@gmail.com","institution":"Spanish Research Council CSIC","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5df720b803b44455be9556b914f0f1fd","id":"2370"}, {"dataset":"MSV000095018","datasetNum":"95018","title":"Proteomic and phosphoproteomic dataset of human FFPE lung adenocarcinomas with mutations","user":"BugyiFanni","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718278222000","created":"Jun. 13, 2024, 4:30 AM","description":"Mutations in key oncogenes have been identified as important genetic alterations in lung\nadenocarcinoma (LUAC), including genes encoding epidermal growth factor receptor (EGFR), Kirsten rat sarcoma viral oncogene homolog (KRAS), and anaplastic lymphoma kinase (ALK). These genetic mutations fundamentally determine the therapeutic options of the patients. Our aim was the characterization of the altered biological pathways and phosphorylation events in LUAC tumors harboring EGFR, KRAS, or ALK oncogenic mutation and triple wild-type (WT) LUAC tumors by MS-based quantitative proteomics and phosphoproteomics analyses of 84 formalin-fixed paraffin-embedded (FFPE) tissue sections. EGFR-mutated samples showed distinct proteomic profiles, while principal component analysis based on the phosphoproteomic experiments revealed considerable differences between the samples with different mutations. Additionally, 31 proteins and 60 phosphosites were identified with potentially mutation-specific values serving as potential therapeutic targets. Our results could provide significant insights for developing therapeutic strategies for LUAC.","fileCount":"5303","fileSizeKB":"118583539","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;timsTOF HT","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Phosphoproteomics;Proteomics;MS;Lung adenocarcinoma;FFPE tissue;Cancer research;Kinase-substrate enrichment analysis","pi":[{"name":"Lilla Turiak","email":"turiak.lilla@ttk.hu","institution":"MTA-TTK Lendulet (Momentum) Glycan Biomarker Research Group, HUN-REN Research Centre for Natural Sciences","country":"Hungary"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"b987ee3ba1d044f1964666c4a7d9f5aa","id":"2371"}, {"dataset":"MSV000095017","datasetNum":"95017","title":"Human IgG subclasses differ in structural elements of their N-glycosylation","user":"WeiweiWANG","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718269190000","created":"Jun. 13, 2024, 1:59 AM","description":"We tested tryptic plasma samples using HILIC-LC-MS\/MS, which included mixed human plasma as well as plasma from two healthy individuals collected at three different time points, approximately one month apart. Our focus was on the glycan structure of the Fc domain of IGG subclasses. The results indicated that each IGG subclass possesses a distinct glycan signature. Although there were slight variations between individuals, the glycan signature of IGG subclasses in individual plasma remained stable over time.","fileCount":"28","fileSizeKB":"58258366","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:137 - \\\"N-linked glycan core.\\\"","keywords":"IgG subclasses;human plasma","pi":[{"name":"Karli Reiding","email":"k.r.reiding@uu.nl","institution":"Utrecht University","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"73f400701b414cc580861d722c5904ce","id":"2372"}, {"dataset":"MSV000095016","datasetNum":"95016","title":"GNPS - Metabolomics-based LC-HRMS Analysis of Liquid Fermentation Co-culture of Penicillium sp. 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Algal species (Oophila amblystomatis) bloom outside the blastopore of the host. Pond water and rearing media samples are also included. Untargeted LC-MS\/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"118","fileSizeKB":"5265264","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ambystoma maculatum (NCBITaxon:43114);Oophila amblystomatis (NCBITaxon:1008953)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Salamander;Algal induction;MSCollaboratory","pi":[{"name":"Ryan Kerney","email":"rkerney@gettysburg.edu","institution":"Gettysburg College","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3a9690d1b53a40eca2593c1bb8332222","id":"2375"}, {"dataset":"MSV000095011","datasetNum":"95011","title":"Proteomic content in metabolomic samples cause post-extraction metabolite changes","user":"ryan_sheldon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718229571000","created":"Jun. 12, 2024, 2:59 PM","description":"Arising from efforts to improve extraction conditions for polar metabolomics, a proteomic landscape of over 1,000 proteins within metabolite extracts was discovered. This is a ubiquitous feature across several common extraction and sample types. A novel yet simple extraction workflow integrates 3kDa filtration for protein removal as a superior method for polar metabolomics.","fileCount":"110","fileSizeKB":"22204538","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240;Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;transaminase;glutathione;filter;inhibitor;aminooxyacetic acid;liver;brain;skeletal muscle;adipose;plasma;phoenix-AMPHO HEK293;Bligh-Dyer;4:4:2;40:40:20;Acetonitrile:Methanol:Water","pi":[{"name":"Ryan Sheldon","email":"ryan.sheldon@vai.org","institution":"Van Andel Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b204220ef95c400393f834ff70471b5a","id":"2376"}, {"dataset":"MSV000095010","datasetNum":"95010","title":"Proteomic content in metabolomic samples","user":"ryan_sheldon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718228256000","created":"Jun. 12, 2024, 2:37 PM","description":"Proteins remaining in the metabolomic extract from 3 common extraction modalities were quantified by DIA on the Oribtrap Eclipse following tryptic digest.","fileCount":"70","fileSizeKB":"50779770","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics;transaminase;glutathione;filter;liver;brain;skeletal muscle;adipose;plasma;phoenix-AMPHO HEK293;Bligh-Dyer;4:4:2;40:40:20;Acetonitrile:Methanol:Water","pi":[{"name":"Ryan Sheldon","email":"ryan.sheldon@vai.org","institution":"Van Andel Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD053052","task":"f67b54e690d141eda1dbd0d2cea1c652","id":"2377"}, {"dataset":"MSV000095009","datasetNum":"95009","title":"Filling the Gaps in Peptide Maps with a Platform Assay for Top-Down Characterization of Purified Protein Samples","user":"aobailey","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718221010000","created":"Jun. 12, 2024, 12:36 PM","description":"LC-MS intact mass analysis and LC-MS\/MS peptide mapping are foundational assays for developing biologic drugs and other commercial protein products. Certain PTM types, such as truncation and oxidation, increase the difficulty of precise proteoform characterization owing to inherent limitations in peptide and intact protein analyses. Top-down MS (TDMS) can resolve this ambiguity via fragmentation of specific proteoforms. We optimized our existing flow-programmed (fp) denaturing online buffer exchange (dOBE) approach to improve ESI sensitivity and increase TDMS sampling time for industrial applications. Using bovine alpha-lactalbumin (aLac), we tested data-dependent (DDA) and targeted strategies with 14 different MS\/MS scan types featuring combinations of collisional- and electron-based fragmentation as well as proton transfer charge reduction. This large dataset was processed using a new software platform, named TDAcquireX, that improves proteoform characterization through TDMS data aggregation. A DDA-based (fp)dOBE-TDMS workflow provided high confidence identification of aLac truncation proteoforms. Targeted TDMS data were analyzed using sliding window-based fragment ion deconvolution to generate composite proteoform spectral match (cPrSM) results. This strategy facilitated probability-based noise filtering of deconvoluted fragment results, simultaneously increasing the percentage of matched fragments while decreasing the total number of fragments reported. We used fragment noise filtering to characterize aLac oxidation positional isomers, finding that electron transfer dissociation (ETD) uniquely provided accurate relative occupancy data as a result of oxidation-specific technical challenges. 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We performed genomic, transcriptomic, and proteomic characterization on the primary prostate tumor, the metastatic brain NEPC, and an additional metastatic nodule in the dura with adenocarcinoma histology. These data are the proteomics result of this patient, with three replicates for each sample (primary prostate, dura adenocarcinoma, brain NEPC).","fileCount":"65","fileSizeKB":"26830241","spectra":"761426","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Proteomics;Prostate Cancer;Neuroendocrine;Adenocarcinoma;Biopsy Tissue;Brain Metastasis;Case Report","pi":[{"name":"Justin M. 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Our experiments uncover a novel, post-transcriptional mechanism of OR gene regulation that assures that the identity of the expressed OR can influence the identity of the OSN only at the onset of singular OR choice.","fileCount":"24","fileSizeKB":"13265678","spectra":"149172","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mex3a, IP, TMT","pi":[{"name":"Stavros Lomvardas","email":"sl682@cumc.columbia.edu","institution":"Columbia University","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"8db1dde776b0457a9cdb831d1f54fac1","id":"2380"}, {"dataset":"MSV000095004","datasetNum":"95004","title":"GNPS - Combrethum micranthum decoction metabolomic study","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718179737000","created":"Jun. 12, 2024, 1:08 AM","description":"This data correspond to the raw UHPLC-HRMS file and the dereplication results used in the study of a traditional devotion of Combrethum micranthum.","fileCount":"43","fileSizeKB":"2386021","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Combrethum micranthum","instrument":"Q Exactive","modification":"PRIDE:0000398","keywords":"Combrethum micranthum;decoction;medicinal chemistry","pi":[{"name":"Emerson Ferreira Queiroz","email":"Emerson.Ferreira@unige.ch","institution":"Universite de Geneve","country":"Suisse"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b218d9b20d5248fa883d7d7aed92dde9","id":"2381"}, {"dataset":"MSV000095003","datasetNum":"95003","title":"GNPS - Personal Care Product reference dataset positive ionization","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718155543000","created":"Jun. 11, 2024, 6:25 PM","description":"Personal Care Product extracted with 80:20 ACN\/H2O with sulfadimethoxine-d6 and cleaned up with EMR-Lipid SPE. 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Detailed information about the genetic backgrounds of the lines used in each experiment, as well as the results for all experiments, can be found in the spreadsheets labelled \"results_xxx\".","fileCount":"164","fileSizeKB":"22933848","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion Lumos;timsTOF HT","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"chromatin, SWI\/SNF, Arabidopsis, remodeling","pi":[{"name":"Javier Gallego-Bartolome","email":"jagalbar@ibmcp.upv.es","institution":"INSTITUTO DE BIOLOGIA MOLECULAR Y CELULAR DE PLANTAS IBMCP (UPV\/CSIC)","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2f76b69679cf42cca2c20866ffcf251c","id":"2393"}, {"dataset":"MSV000094980","datasetNum":"94980","title":"GNPS - Metabolomics data Hasil 11 Juni","user":"Niko160702","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718105834000","created":"Jun. 11, 2024, 4:37 AM","description":"metabaolomics analysis in co-culture fungi in Riau","fileCount":"21","fileSizeKB":"3494254","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichoderma asperellum (NCBITaxon:101201);Trichoderma asperelloides (NCBITaxon:702382);Penicillium citrinum (NCBITaxon:5077)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Penicillium citrinum","pi":[{"name":"Chen He","email":"hechen@cup.edu.cn","institution":"China University of Petroleum, Beijing","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da2816ca29024202beb7c78d48d11726","id":"2394"}, {"dataset":"MSV000094978","datasetNum":"94978","title":"Integrated Phosphoproteomics of Theileria annulata-Infected Cells: Unveiling Host and Parasite Kinase Networks and Signaling Pathways","user":"Dan_3072","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718088306000","created":"Jun. 10, 2024, 11:45 PM","description":"This study employs comparative phosphoproteomics to investigate the changes in protein phosphorylation (post-translational modifications) induced by Theileria annulata infection in host cells. Three groups are analyzed: bovine lymphocytes infected with T. annulata, uninfected control lymphocytes, and lymphocytes treated with buparvaquone, a drug that clears the parasite. The analysis aims to identify and compare the kinase networks and signaling pathways activated in both the host and the parasite during infection.","fileCount":"25","fileSizeKB":"38608381","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913);Theileria annulata (NCBITaxon:5874)","instrument":"LTQ Orbitrap","modification":"UNIMOD:260 - \\\"Thiophosphorylation.\\\"","keywords":"Apicomplexan, Theileria annulata, post-translational modification, kinase, Cancer","pi":[{"name":"Dr. Paresh Sharma","email":"paresh@niab.org.in","institution":"National Institute of Animal Biotechnology","country":"India"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"344f42a9b8f0433eb2b046254620aa36","id":"2395"}, {"dataset":"MSV000094977","datasetNum":"94977","title":"GNPS - 2024-Mobley-collaborative-project_Cu","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718078542000","created":"Jun. 10, 2024, 9:02 PM","description":"Proteus mirabilis WGLW4 were cultured, supernatant was extracted using HLB-SPE and 80% MeOH\/water and metabolome was analyzed with QExactive HF. 150uL,Cu","fileCount":"37","fileSizeKB":"7072162","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteus mirabilis WGLW4 (NCBITaxon:1125693)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metal binding","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"439543d4cb2546f681c6e5943aa99dc7","id":"2396"}, {"dataset":"MSV000094976","datasetNum":"94976","title":"GNPS - 2024-Mobley-collaborative-project_Zn","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718077548000","created":"Jun. 10, 2024, 8:45 PM","description":"roteus mirabilis WGLW4 were cultured, supernatant was extracted using HLB-SPE and 80% MeOH\/water and metabolome was analyzed with QExactive HF. 150uL, Zn","fileCount":"35","fileSizeKB":"6437792","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteus mirabilis WGLW4 (NCBITaxon:1125693)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metal binding","pi":[{"name":"Allegra Aron","email":"alaron@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7a1b3703334549eb93a93b2c2c660b9a","id":"2397"}, {"dataset":"MSV000094975","datasetNum":"94975","title":"GNPS_koolengroup_microorganisms_LCMSMS","user":"moyses","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718073003000","created":"Jun. 10, 2024, 7:30 PM","description":"LC-MS\/MS of fungi studied in the metabolomics and mass spectrometry research group (MMSRG) at the State University of Amazonas, Brazil.","fileCount":"352","fileSizeKB":"3260363","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fusarium (NCBITaxon:5506);Penicillium (NCBITaxon:5073);Talaromyces (NCBITaxon:5094);Trichoderma (NCBITaxon:5543);Arcopilus sp. 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Protein-protein interaction studies verified a BRD4:PLX-3618:DCAF11 ternary complex, and mutational studies provided further insights into the DCAF11-mediated degradation mechanism. 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Cells were treated with either vehicle (DMSO, 1:1000) or CHIR99021 (1 uM) in serum free media for 7 days followed by harvesting the conditioned lysate, concentration using an Amicon filter, and loading onto an SDS-PAGE gel. Total protein (unsolved, in the stacking gel) was stained with Coomassie Blue and the gel bands containing total secreted protein were excised and submitted to the Proteomics Core (UT Southwestern).","fileCount":"10","fileSizeKB":"9317533","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"EFEMP1;fibulin-3;extracellular matrix;CHIR99021;Doyne Honeycomb Retinal Dystrophy;Malattia Leventinese;age-related macular degeneration;GSK3;ARPE-19","pi":[{"name":"John D. 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By proteomic profiling of 55 biopsy specimens representing controls, Reflux- (GERD), Eosinophilic-(EoE), Crohns-(CD), and Herpes simplex (HSV)-esophagitis, as well as Candida albicans infection by LC-MS\/MS, we identified distinct signatures and functional networks. Our integrated AI-assisted morphoproteomic approach allows deeper insights in disease-specific molecular alterations and represents a promising tool in esophagitis-related precision medicine.\r\n\r\n\r\nThe FFPE samples were further processed including macrodissection, protein extraction, protein precipitation, protein digestion, and peptide clean up according to a previously published and modified protocol (Buczak et al., 2020). For further details, please refer to the Materials and Methods section of the manuscript. \r\n \r\nIn depth proteomic characterization of the samples a label free high-resolution LC-MS\/MS approach using an Orbitrap Tribrid Fusion mass spectrometer was chosen (operated in DIA mode). Tryptic peptides were loaded onto a µPAC Trapping Column with a pillar diameter of 5 µm, inter-pillar distance of 2.5 µm, pillar length\/bed depth of 18 µm, external porosity of 9%, bed channel width of 2 mm and length of 10 mm; pillars are superficially porous with a porous shell thickness of 300 nm and pore sizes in the order of 100 to 200 Å at a flow rate of 10 µl per min in 0.1% trifluoroacetic acid in HPLC-grade water. Peptides were eluted and separated on the PharmaFluidics µPAC nano-LC column: 50 cm µPAC C18 with a pillar diameter of 5 µm, inter-pillar distance of 2.5 µm, pillar length\/bed depth of 18 µm, external porosity of 59%, bed channel width of 315 µm and bed length of 50 cm; pillars are superficially porous with a porous shell thickness of 300 nm and pore sizes in the order of 100 to 200 Å by a linear gradient from 2% to 30 % of buffer B (80% acetonitrile and 0.08% formic acid in HPLC-grade water) in buffer A (2% acetonitrile and 0.1% formic acid in HPLC-grade water) at a flow rate of 300 nl per min. The remaining peptides were eluted by a short gradient of 10 minutes from 30% to 95% buffer B; followed by 25 minutes at 2% of buffer B, the total gradient run was 120 min. \r\nSpectra were acquired in DIA mode using 50 variable-width windows over the mass range 350-1500 m\/z. The Orbitrap was used for MS1 and MS2 detection, with an AGC target for MS1 set to 20x104 and a maximum injection time to 100 ms. MS2 scan range was set between 200 and 2000 m\/z, with a minimum of 6 points across the peak. Orbitrap resolution for MS2 was set to 30K, isolation window set to 1.6, AGC target to 50x104 and maximum injection time to 54 ms. MS1 and MS2 data were acquired in centroid mode.\r\nIn order to check for retention time (RT) stability, iRT standards (Biognosys) were spiked in each sample according to the manufacturer recommendations, the 11 iRT peptide sequences were manually added to the database and used during DIA-NN search to generate the precursor ion library used for MS data analysis. To reduce the possibility of carry over and cross contamination between the samples, two BSA washes were used between samples, and a trap column wash followed by 2 BSA washes was used every 10 samples sequence.\r\nThe above-mentioned workflow is schematically displayed in Fig. 1B. \r\nLC-MS\/MS was performed at the Proteome Center Tuebingen (PCT). Here, 250 ng of peptides were loaded onto an Easy-nLC 1200 system coupled to a quadrupole Orbitrap Exploris 480 mass spectrometer (all Thermo Fisher Scientific, Waltham, MA, USA) as previously described (Krauss et al, 2023).\r\n\r\nMS raw data files were analyzed using DIA-NN 1.8.1 (Demichev et al, 2020) in library-free mode against the human database (UniProt release March 2024, 20412 proteins). First, a precursor ion library was generated using FASTA digest for library-free search in combination with deep learning-based spectra prediction. An experimental library generated from the DIA-NN search was used for cross-run normalization and mass accuracy correction. Only high-accuracy spectra with a minimum precursor FDR of 0.01, and only tryptic peptides (2 missed Tryptic cleavages) were used for protein quantification. The match between runs option was activated and no shared spectra were used for protein identification. Similarly, Normal, HSV, and Candida samples were searched against reviewed entries of HSV1 (taxonomy id 10298, 125 entries), HSV2 (taxonomy id 10310, 95 entries), and C. albicans (taxonomy id 5476, 1412 entries) downloaded on 04.03.2024, in addition to the human database.\r\n\r\n","fileCount":"121","fileSizeKB":"72619141","spectra":"4484750","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Candida albicans (NCBITaxon:5476);Human alphaherpesvirus 1 (NCBITaxon:10298)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"FFPE-proteomics;precision medicine;mass spectrometry;targeted therapy;eosinophilic esophagitis;gastroesophageal reflux disease;Crohn esophagitis","pi":[{"name":"Prof. Dr. Stephan Singer","email":"stephan.singer@med.uni-tuebingen.de","institution":"Department of Pathology and Neuropathology, University Hospital Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD052961","task":"6102430d4adf4ad5a8b3daf7c1525c8a","id":"2402"}, {"dataset":"MSV000094965","datasetNum":"94965","title":"GNPS-fenziwangluo-hezao-20240610-neg","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718017932000","created":"Jun. 10, 2024, 4:12 AM","description":"Ecklonia cava UHPLC-Q-Orbitrap HRMS Identification of compounds","fileCount":"2","fileSizeKB":"131587","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ecklonia cava","instrument":"UHPLC-Q-Orbitrap HRMS","modification":"none","keywords":"Ecklonia cava","pi":[{"name":"liyu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1b8ee228f03f4eba9f66857e9c910e3b","id":"2403"}, {"dataset":"MSV000094964","datasetNum":"94964","title":"GNPS-fenziwangluo-huzhang-20240610-pos","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1718015311000","created":"Jun. 10, 2024, 3:28 AM","description":"Ecklonia cava UHPLC-Q-Orbitrap HRMS Identification of compounds","fileCount":"6","fileSizeKB":"652087","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ecklonia cava","instrument":"UHPLC-Q-Orbitrap HRMS","modification":"none","keywords":"Ecklonia cava","pi":[{"name":"liyu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6bd112c111db49d1b44573adf492205a","id":"2404"}, {"dataset":"MSV000094962","datasetNum":"94962","title":"GNPS - Obesity and GDM associated changes in placental and maternal blood lipidomic profile: evidence for sexual dimorphism","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717986456000","created":"Jun. 9, 2024, 7:27 PM","description":"This study assesses fatty acid composition of lipids in matched maternal plasma and placental tissue from lean, obese and gestational diabetes (GDM) women stratified by fetal sex. Obesity and GDM are associated with adverse pregnancy outcomes and program the offspring for cardiometabolic disease in a sexually dimorphic manner. We collected maternal plasma and placental villous tissue following elective cesarean section at term from women who were lean (pre-pregnancy BMI 18.5-24.9), Obese (BMI>30) and type A2 GDM (matched to obese BMI) with either a male or female fetus (n=4 each group). Lipids were extracted and fatty acid composition of different lipid classes were analyzed by LC-MS\/MS to find significant changes in GDM vs Obese, GDM vs Lean, and Obese vs Lean.","fileCount":"241","fileSizeKB":"8142413","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"placenta;lipidomics;gestational diabetes","pi":[{"name":"Kristin Burnum-Johnson","email":"Kristin.Burnum-Johnson@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a56cace958ba42a094c8d4a7d145223b","id":"2405"}, {"dataset":"MSV000094961","datasetNum":"94961","title":"GNPS TarvinETAL2024 Data and Result Files for Silverstoneia flotator and Eleutherodactylus cystignathoides","user":"jcole844","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717962407000","created":"Jun. 9, 2024, 12:46 PM","description":"mzXML files generated from metabolomic extracts of frog (Silverstoneia flotator and Eleutherodactylus cystignathoides) skins, supplementary files from these raw files (generated using SIRIUS v5.8.6, MZmine v.3.9.0, GNPS), and feature tables with curated data from all these softwares (generated on R4.2.2) are included.","fileCount":"135","fileSizeKB":"3036667","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Eleutherodactylus cystignathoides (NCBITaxon:122124);Silverstoneia flotator (NCBITaxon:384859)","instrument":"Thermo Fisher Scientific (MA, USA) Vanquish Horizon Duo ultra-high performance liquid chromatography (UHPLC) system with an Accucore C18 column with 150 mm length, 2.1 mm internal diameter, and 2.6 \\u00B5m particle size;Thermo Fisher Scientific (MA, USA) Q Exactive hybrid quadrupole-orbitrap mass spectrometer","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dendrobatidae;UHPLC-HESI-MSMS;alkaloids;metabolomics;Silverstoneia flotator;Eleutherodactylus cystignathoides;aposematic;inconspicuous;frog;skin;Eleutherodactylidae","pi":[{"name":"Brian E. Sedio","email":"sediob@utexas.edu","institution":"University of Texas at Austin","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f00df09ea7aa489a88a5cb0b1e9d72f2","id":"2406"}, {"dataset":"MSV000094959","datasetNum":"94959","title":"Untargeted proteomic analysis of simultaneously collected human liver tissue and plasma of patients with a histological diagnosis of metabolic dysfunction-associated steatotic liver disease.","user":"brettsp1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717792667000","created":"Jun. 7, 2024, 1:37 PM","description":"The liver tissue and plasma were collected from patients when undergoing liver biopsy for a diagnosis of metabolic dysfunction-associated steatotic liver disease (MASLD), along with controls who had no histological abnormalities. The study group included seven patients with no liver histological abnormalities and 64 patients with MASLD across its spectrum, including those with metabolic dysfunction-associated steatotic hepatitis (MASH) and those with cirrhosis. The data were compared between liver tissue and plasma, across various stages of MASLD, and for the detection of biomarkers for different stages of MASLD.","fileCount":"1227","fileSizeKB":"305758939","spectra":"8683050","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"liver;plasma;steatohepatitis;steatotic liver disease","pi":[{"name":"Achuthan Sourianarayanane","email":"asourianar@mcw.edu","institution":"Medical College of Wisconsin","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052937","task":"e264e0801df5421c84a98c34ae859e79","id":"2407"}, {"dataset":"MSV000094957","datasetNum":"94957","title":"GNPS - Deep metabolome annotation of model organism Daphnia magna","user":"tomnl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717767056000","created":"Jun. 7, 2024, 6:30 AM","description":"Deep metabolome annotation of model organism Daphnia magna","fileCount":"2795","fileSizeKB":"38716295","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Daphnia magna (NCBITaxon:35525)","instrument":"LTQ Orbitrap Elite;Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Metabolite annotation;Daphnia magna","pi":[{"name":"Professor Mark Viant ","email":"m.viant@bham.ac.uk","institution":"University of Birmingham","country":"UK"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c83f6d37b102448abcb8d654a8c14be3","id":"2408"}, {"dataset":"MSV000094956","datasetNum":"94956","title":"Proximity-Dependent Biotin Identification of NHL repeat containing 2 (NHLRC2) and FINCA disease variant(p.Asp148Tyr)","user":"AHILTUNEN","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717764995000","created":"Jun. 7, 2024, 5:56 AM","description":"BioID analysis was performed on wild type NHLRC2 and NHLRC2 containing a FINCA disease variant (pAsp148Tyr) tagged C-terminally with BirA-FLAG. Stable cells with the genomic insertion of recombinant wild type NHLRC2 and FINCA variant were generated as Flp-In 293 T-REx HEK 293 cell pools and expression of the recombinant protein was induced using tetracycline 24h before sample collection. The samples were collected as triplicates. The biotinylated proteins were isolated using Strep-Tactin beads and analysed using liquid chromatography-MS). \n\n\n","fileCount":"28","fileSizeKB":"6896399","spectra":"237730","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"NHLRC2;FINCA disease","pi":[{"name":"Reetta Hinttala","email":"reetta.hinttala@oulu.fi","institution":"University of Oulu","country":"Finland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"553b20fbd5d34039a818f7045051cdd7","id":"2409"}, {"dataset":"MSV000094955","datasetNum":"94955","title":"GNPS-fenziwangluo-hezao-20240606-pos","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717728263000","created":"Jun. 6, 2024, 7:44 PM","description":"compound,Ecklonia cava,UHPLC-Q-Orbitrap HRMS,representation,Identification","fileCount":"2","fileSizeKB":"181987","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ecklonia cava","instrument":"UHPLC-Q-Orbitrap HRMS","modification":"NoPTMsincludedinthedataset","keywords":"Ecklonia cava","pi":[{"name":"Li Yu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"100e73ae54764286acf045e235fd2324","id":"2410"}, {"dataset":"MSV000094954","datasetNum":"94954","title":"GNPS-fenziwangluo-hezao-20240606-neg","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717727713000","created":"Jun. 6, 2024, 7:35 PM","description":"compound,Ecklonia cava,UHPLC-Q-Orbitrap HRMS,representation,Identification","fileCount":"2","fileSizeKB":"131587","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ecklonia cava","instrument":"UHPLC-Q-Orbitrap HRMS","modification":"NoPTMsincludedinthedataset","keywords":"Ecklonia cava","pi":[{"name":"Li Yu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"81aab6c40c734002b42a3949896ef219","id":"2411"}, {"dataset":"MSV000094953","datasetNum":"94953","title":"de novo Protein Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination - Benchmark Study","user":"ChelseaReitzel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717726864000","created":"Jun. 6, 2024, 7:21 PM","description":"This dataset submission includes the raw files used to sequence a mix of 5 human monoclonal antibodies as a benchmark proof-of-concept study for the manuscript \"de novo Protein Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination\". Refer to the attached metafile for detailed descriptions of the experiments. Briefly, bottom-up data was generated by performing in-solution digestions on the monoclonal antibodies on their own and after mixing to generate a pseudo-polyclonal mix. Separation was performed using native gel and non-reducing SDS-PAGE (NRT), followed by in-gel digestion for heavy-light chain pairing. Lastly, C-terminal modification and EThcD fragmentation of in-solution digests allowed for I\/L determination. 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Experiments were performed from HeLa and A375 cells and MS files were acquired on an Orbitrap Fusion mass spectrometer. For questions, please contact Jean-Philippe Lambert (jean-philippe.lambert@crchudequebec.ulaval.ca).","fileCount":"103","fileSizeKB":"125382507","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Chromatin","pi":[{"name":"Jean-Philippe Lambert","email":"jean-philippe.lambert@crchudequebec.ulaval.ca","institution":"Universite Laval","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"03cdc863dd974216b6f052d7cf9bde4d","id":"2413"}, {"dataset":"MSV000094949","datasetNum":"94949","title":"Raw MS data - Proximity labeling of Sucrosomes","user":"AmraSaric","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717691111000","created":"Jun. 6, 2024, 9:25 AM","description":"Human iPSCs (WTC11 line) expressing Lamp1-APEX were treated with sucrose overnight to form sucrosomes, and half of the sucrose-treated cells were treated with invertase to shrink sucrosomes to cause lysosome tubulation. Proximity labeling was done of the lysosomal surface as 3 technical replicates per condition. Biotinylated proteins were captured with NeutrAvidin Beads and samples were run by SDS-PAGE until they entered 1\/4 the gel length. The short lanes were excised and processed for mass spectrometry by dissolving the gel and trypsin-digesting the samples. Label-free quantitation was performed.","fileCount":"7","fileSizeKB":"7986939","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:108 - \\\"N-ethylmaleimide on cysteines.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"sucrosome;invertase;lysosome","pi":[{"name":"Spencer Freeman","email":"spencer.freeman@sickkids.ca","institution":"The Hospital for Sick Children","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"327454621fae453d9df1e5e21bfa972e","id":"2414"}, {"dataset":"MSV000094944","datasetNum":"94944","title":"Effects of gradient lengths and acquisition frequency on the number of protein identifications in nanoflow LCMSMS of complex proteomic samples CHO","user":"Arman_Kulyyassov","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717656459000","created":"Jun. 5, 2024, 11:47 PM","description":"A liquid chromatography-tandem mass-spectrometry LC-MS\/MS is now an indispensable method for shotgun proteomics. The combination of chromatographic separation and MS\/MS identification provides valuable information about protein compositions from different biological samples. In this article, we examined the relationship between gradient length and MS acquisition on examples of three complex peptide mixtures. We found that combining long gradient and higher MS acquisitions resulted in more protein identifications for human plasma, Escherichia coli, and Chinese hamster ovary cell lines. 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We also evaluated the efficiency of Mascot and PEAKS proteomic tools for the analysis of LC-MS\/MS data.","fileCount":"52","fileSizeKB":"20012573","spectra":"0","psms":"64993","peptides":"1383","variants":"1858","proteins":"305","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"impact II","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Complex proteomics samples, data-dependent acquisition (DDA), liquid chromatography-tandem mass-spectrometry LC-MS\/MS, in-solution digestion","pi":[{"name":"Arman Kulyyassov","email":"kulyyasov@biocenter.kz","institution":"National Center for Biotechnology Ministry of Healthcare of the Republic of Kazakhstan","country":"Kazakhstan"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052860","task":"7208a066c5be4a8fa3d699bd8dc125fc","id":"2419"}, {"dataset":"MSV000094935","datasetNum":"94935","title":"Effects of gradient lengths and acquisition frequency on the number of protein identifications in nanoflow LCMSMS of complex proteomic sample Escherichia coli","user":"Arman_Kulyyassov","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717589847000","created":"Jun. 5, 2024, 5:17 AM","description":"A liquid chromatography-tandem mass-spectrometry LC-MS\/MS is now an indispensable method for shotgun proteomics. The combination of chromatographic separation and MS\/MS identification provides valuable information about protein compositions from different biological samples. In this article, we examined the relationship between gradient length and MS acquisition on examples of three complex peptide mixtures. We found that combining long gradient and higher MS acquisitions resulted in more protein identifications for human plasma, Escherichia coli, and Chinese hamster ovary cell lines. We also evaluated the efficiency of Mascot and PEAKS proteomic tools for the analysis of LC-MS\/MS data.","fileCount":"52","fileSizeKB":"15467700","spectra":"0","psms":"79216","peptides":"4079","variants":"5242","proteins":"957","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"impact II","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Complex proteomics samples, data-dependent acquisition (DDA), liquid chromatography-tandem mass-spectrometry LC-MS\/MS, in-solution digestion","pi":[{"name":"Arman Kulyyassov","email":"kulyyasov@biocenter.kz","institution":"National Center for Biotechnology Ministry of Healthcare of the Republic of Kazakhstan","country":"Kazakhstan"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052859","task":"e180a59935ba410d945aa03b55726245","id":"2420"}, {"dataset":"MSV000094934","datasetNum":"94934","title":"Alternatively spliced mini exon B in PTPRD regulates hippocampal excitatory synapses through trans synaptic PTPRD IL1RAP interaction","user":"yangyj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717564881000","created":"Jun. 4, 2024, 10:21 PM","description":"PTP?, encoded by PTPRD, is implicated in various neurological, psychiatric, and neurodevelopmental disorders, but the underlying mechanisms remain unclear. PTP? trans-synaptically interacts with multiple postsynaptic adhesion molecules, which involves its extracellular alternatively spliced mini-exons, meA and meB. While PTP?-meA functions have been studied in vivo, PTP?-meB has not been studied. Here, we report that, unlike homozygous PTP?-meA-mutant mice, homozygous PTP?-meB-mutant (Ptprd-meB\u2013\/\u2013) mice show markedly reduced early postnatal survival. Heterozygous Ptprd-meB+\/\u2013 male mice show behavioral abnormalities and decreased excitatory synaptic density and transmission in dentate gyrus granule cells (DG-GCs). Proteomic analyses identify decreased postsynaptic density levels of IL1RAP, a known trans-synaptic partner of meB-containing PTP?. Accordingly, IL1RAP-mutant mice show decreased excitatory synaptic transmission in DG-GCs. Ptprd-meB+\/\u2013 DG interneurons with minimal IL1RAP expression show increased excitatory synaptic density and transmission. Therefore, PTP?-meB is important for survival, synaptic, and behavioral phenotypes and regulates excitatory synapses in cell-type-specific and IL1RAP-dependent manners.","fileCount":"159","fileSizeKB":"179794221","spectra":"0","psms":"347346","peptides":"112153","variants":"143242","proteins":"8358","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Proteomics;PTPRD;hippocampal excitatory synapses;presynaptic adhesion molecule;neurodevelopmental disorders","pi":[{"name":"Jin Young Kim","email":"jinyoung@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep. of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052848","task":"43ef149aed3049ae9b781085ededf7ed","id":"2421"}, {"dataset":"MSV000094933","datasetNum":"94933","title":"An algicidal bacterium shapes the microbiome during outdoor diatom cultivation collapse","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717548830000","created":"Jun. 4, 2024, 5:53 PM","description":"Proteomic measurements for samples from 5 outdoor algal ponds over a time series; ponds were sampled during the fall of 2015. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline against FASTA files compiled from ponds sequenced metagenomes and proteomes of dominating algae Nannochloropsis salina and Phaeodactylum tricornutum.","fileCount":"59","fileSizeKB":"72533841","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phaeodactylum tricornutum (NCBITaxon:2850);Nannochloropsis salina (NCBITaxon:5749)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"diatom;microbiome;algal-bacterial interactions","pi":[{"name":"Ty Samo","email":"samo1@llnl.gov","institution":"Lawrence Livermore National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ff4d61d512ea470e959315ee884167b6","id":"2422"}, {"dataset":"MSV000094932","datasetNum":"94932","title":"Localized K63 ubiquitin signaling is regulated by VCP\/p97 during oxidative stress","user":"Gustavo_Silva_2024","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717547877000","created":"Jun. 4, 2024, 5:37 PM","description":"Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote these concerted response mechanisms remain understudied. Here, we show that K63-linked ubiquitin chains, known to promote proteasome-independent pathways, accumulate primarily in non-cytosolic compartments during oxidative stress induced by sodium arsenite in mammalian cells. Subcellular ubiquitin proteomic analyses of non-cytosolic compartments revealed thousands of proteins ubiquitinated during oxidative stress and involved in pathways related to immune signaling and translation control. Moreover, subcellular proteome analyses also revealed proteins that are recruited to non-cytosolic compartments under stress, including a significant enrichment of helper ubiquitin-binding adaptors of the ATPase VCP that processes ubiquitinated substrates for downstream signaling. We further show that VCP recruitment to non-cytosolic compartments under arsenite stress occurs in a ubiquitin-dependent manner mediated by its adaptor NPLOC4. Additionally, we show that VCP and NPLOC4 activities are critical to sustain low levels of non-cytosolic K63-linked ubiquitin chains, supporting a cyclical model of ubiquitin conjugation and removal that is disrupted by cellular exposure to reactive oxygen species. This work deepens our understanding of the role of localized ubiquitin and VCP signaling in the basic mechanisms of stress response and highlights new pathways and molecular players that are essential to reshape the composition and function of the human subcellular proteome under dynamic environments.","fileCount":"43","fileSizeKB":"174956400","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Astral;Orbitrap Fusion Lumos","modification":"Fixed carbamidomethyl (Cys), oxidation (Met) and acetylation (protein N-terminus);UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"oxidative stress;K63 ubiquitin;VCP;subcellular localization;human cells","pi":[{"name":"Gustavo Monteiro Silva","email":"gustavo.silva@duke.edu","institution":"Duke University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052838","task":"a715bcc295cf41d5902996859f7622eb","id":"2423"}, {"dataset":"MSV000094931","datasetNum":"94931","title":"Spns1 controls megalin dependent endocytosis via iron misregulation. 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Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1830","fileSizeKB":"116745501","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CSF;Metabolomics","pi":[{"name":"Robert K. Heaton","email":"rheaton@ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cbfb272d2a3148e89081ea685129894d","id":"2427"}, {"dataset":"MSV000094926","datasetNum":"94926","title":"Impact of Antibiotics on Membrane Vesicles in Group B Streptococcus","user":"pellmacy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717452398000","created":"Jun. 3, 2024, 3:06 PM","description":"Comparative proteomics of Group B Streptococcus membrane vesicles across different antibiotic treatment groups.","fileCount":"53","fileSizeKB":"3345275","spectra":"0","psms":"30965","peptides":"5035","variants":"6121","proteins":"492","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptococcus agalactiae GB00112 (NCBITaxon:1178526)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Group B Streptococcus;membrane vesicles;antibiotics","pi":[{"name":"Shannon D. 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(2024), available at https:\/\/doi.org\/10.1007\/s11306-024-02136-9. 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The Env gp120 and gp41 subunits mediate receptor binding and membrane fusion and are generated from the gp160 precursor by cellular furins. This cleavage event is required for viral entry. One approach to generate HIV-1 neutralizing antibodies following immunization is to express membrane-bound Env anchored on the cell-surface by genetic means using the natural HIV gp41 transmembrane (TM) spanning domain. To simplify the process of Env trimer membrane expression we sought to remove the need for Env precursor cleavage while maintaining native-like conformation following genetic expression. To accomplish these objectives, we selected our previously developed 'native flexibly linked' (NFL) stabilized soluble trimers that are both near native in conformation and cleavage-independent. We genetically fused the NFL construct to the HIV TM domain by using a short linker or by restoring the native membrane external proximal region, absent in soluble trimers, to express the full HIV Env ectodomain on the plasma membrane. Both forms of cell-surface NFL trimers, without and with the MPER, displayed favorable antigenic profiles by flow cytometry when expressed from plasmid DNA or mRNA. These results were consistent with the presence of well-ordered cell surface native-like trimeric Env, a necessary requirement to generate neutralizing antibodies by vaccination. Inoculation of rabbits with mRNA lipid nanoparticles (LNP) expressing membrane-bound stabilized HIV Env NFL trimers generated tier 2 neutralizing antibody serum titers in immunized animals. Multiple inoculations of mRNA LNPs generated similar neutralizing antibody titers compared to immunizations of matched NFL soluble proteins in adjuvant. Given the recent success of mRNA vaccines to prevent severe COVID, these are important developments for genetic expression of native-like HIV Env trimers in animals and potentially in humans.","fileCount":"63","fileSizeKB":"8599138","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:366 - \\\"Deamidation in presence of O18.\\\";UNIMOD:43 - \\\"N-Acetylhexosamine.\\\"","keywords":"HIV;Vaccine;mRNA;NFL;SOSIP;Env;Immunogenicity;N-glycan;DeGlyPHER","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD052769","task":"8ec484f2249049bcba32532c5e6a0fc1","id":"2435"}, {"dataset":"MSV000094914","datasetNum":"94914","title":"Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection","user":"mjr10","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717190588000","created":"May. 31, 2024, 2:23 PM","description":"This repository contains Waters .raw files from the manuscript entitled \"Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection\". The dataset contains positive and negative MS data for megapolipeptin A and B, as well as the positive MS data for the methyl ester derivatives of the two molecules. All data were aquired on a SYNAPT G2-Si in MSe mode.","fileCount":"102","fileSizeKB":"3687662","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2);Burkholderia (NCBITaxon:32008)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"genome mining;natural products","pi":[{"name":"Alessandra S Eustaquio","email":"ase@uic.edu","institution":"University of Illinois (UIC)","country":"United States of America"},{"name":"Roger Linington","email":"rliningt@sfu.ca","institution":"Simon Fraser University","country":"Canada"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"9a962f6421eb4a23a74c86f2b23a3f33","id":"2436"}, {"dataset":"MSV000094913","datasetNum":"94913","title":"Assessing and harnessing updated polyketide synthase module_6230TOF-Triplicate","user":"rayk212","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717190132000","created":"May. 31, 2024, 2:15 PM","description":"This data was acquired by engineering tri-,tetra- and pentaketide synthases using pikromycin synthase modules within K207-3 E. coli cells. The products were extracted with ethyl acetate, evaporate and re-suspended in 1:1 MeOH and H2O.","fileCount":"88","fileSizeKB":"1666066","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"E. coli K207-3","instrument":"6230A Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Polyketide","pi":[{"name":"Adrian Keatinge-Clay","email":"adriankc@utexas.edu","institution":"University of Texas at Austin","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"663dcc7b6ee740b484f1b731f5b80e28","id":"2437"}, {"dataset":"MSV000094912","datasetNum":"94912","title":"GNPS - CMMC_acyl_lipids_VD_2_RT_matching_UCSD","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717189672000","created":"May. 31, 2024, 2:07 PM","description":"MS\/MS fragmentation data of N acyl lipids 2 acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"21","fileSizeKB":"3194524","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"acyl lipid","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1f4ceb7578ee443f8d33a3f21b651ae2","id":"2438"}, {"dataset":"MSV000094911","datasetNum":"94911","title":"GNPS - CMMC_N_acyl_lipid_VD9_helenaRT","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717188199000","created":"May. 31, 2024, 1:43 PM","description":"MS\/MS fragmentation data of n acyl lipids acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"3","fileSizeKB":"62088","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"acyl lipid","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2f41c54913344dc7801a5ac67d7d61d3","id":"2439"}, {"dataset":"MSV000094904","datasetNum":"94904","title":"A workflow for targeted proteomics assay development using a versatile linear ion trap","user":"shannon225","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717160733000","created":"May. 31, 2024, 6:05 AM","description":"Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.","fileCount":"191","fileSizeKB":"232447610","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Stellar MS Ion Trap (Thermo Scientific Instrument Model) ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DIA;PRM;data-independent acquisition;parallel reaction monitoring;targeted proteomics;il-2;il-15;interleukins;proteomics;ion trap;LIT;Q-LIT;stellar;low input;low amounts","pi":[{"name":"Brian C Searle","email":"brian.searle@osumc.edu","institution":"The Ohio State University","country":"United States"},{"name":"Brian C. Searle","email":"bsearle@systemsbiology.org","institution":"Institute for Systems Biology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8ac4363109554ef6aa62dfcad211841e","id":"2440"}, {"dataset":"MSV000094900","datasetNum":"94900","title":"FAM122A ensures cell cycle interphase progression and checkpoint control as a SLiM-dependent substrate-competitive inhibitor to the B55a\/PP2A phosphatase","user":"madamo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717114286000","created":"May. 30, 2024, 5:11 PM","description":"The Ser\/Thr protein phosphatase 2A (PP2A) is a highly conserved collection of heterotrimeric holoenzymes responsible for the dephosphorylation of many regulated phosphoproteins. Substrate recognition and the integration of regulatory cues are mediated by B regulatory subunits that are complexed to the catalytic subunit (C) by a scaffold protein (A). PP2A\/B55 substrate recruitment was thought to be mediated by charge-charge interactions between the surface of B55a and its substrates. Challenging this view, we recently discovered a conserved SLiM [RK]-V-x-x-[VI]-R in a range of proteins, including substrates such as the retinoblastoma-related protein p107 and TAU (Fowle et al. eLife 2021;10:e63181). Here we report the identification of this SLiM in FAM122A, an inhibitor of B55a\/PP2A. This conserved SLiM is necessary for FAM122A binding to B55a in vitro and in cells. Computational structure prediction with AlphaFold-Multimer predicts an interaction consistent with the mutational and biochemical data and supports a mechanism whereby FAM122A uses the 'SLiM' in the form of a short a-helix (helix 1) to dock to the B55a top groove, thereby blocking substrate binding to the same site. In this model, FAM122A also spatially constrains substrate access by occluding the catalytic subunit with a second a-helix immediately adjacent to helix 1. Consistently, FAM122A functions as a competitive inhibitor as it prevents the binding of substrates in in vitro competition assays and the dephosphorylation of CDK substrates by B55a\/PP2A in cell lysates. The ablation of FAM122A in human cell lines reduces the rate of proliferation, progression through cell cycle transitions, and abrogates G1\/S and intra-S phase cell cycle checkpoints. FAM122A-KO in HEK293 cells results in attenuation of CHK1 and CHK2 activation in response to replication stress. Overall, these data strongly suggest that FAM122A is a short helical motif (SHeM)-dependent, substrate-competitive inhibitor of B55a\/PP2A that suppresses multiple functions of B55a in the DNA damage response and in timely progression through the cell cycle interphase.","fileCount":"47","fileSizeKB":"3740959","spectra":"85604","psms":"85370","peptides":"49223","variants":"52041","proteins":"14816","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"PP2A;FAM122A;B55;retinoblastoma;p107;TAU;SLiM;CDK;interphase","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"The Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052731","task":"7216b37288104812881bb97607f0fef7","id":"2441"}, {"dataset":"MSV000094899","datasetNum":"94899","title":"GNPS_20240530_ChemProp2_Non-targeted Metabolomics of Xenobiotic Biotransformations using synthetic gut bacterial community","user":"bciap01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717105469000","created":"May. 30, 2024, 2:44 PM","description":"ChemProp2 Dataset: Investigating potential biotransformations with a panel of 12 Drugs on Synthetic Community (Com20) for 9 timepoints (t0 - t8) to elucidate Drug-Microbiome-Host Dynamics","fileCount":"1613","fileSizeKB":"135079237","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic community","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gut bacteria;com20;longitudinal study;chemprop2","pi":[{"name":"Daniel Petras","email":"daniel.petras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c74fd3fd5b8c459caaf3fa6e2a94928b","id":"2442"}, {"dataset":"MSV000094898","datasetNum":"94898","title":"Longitudinal Analysis of the Lung Proteome Reveals Persistent Repair Months after Mild to Moderate COVID-19","user":"CCMD","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717105219000","created":"May. 30, 2024, 2:40 PM","description":"In order to assess the restoration of homeostasis in the lung proteome after COVID-19\ninfection, we performed bronchoalveolar lavage on 45 patients with mild to moderate\ndisease at three phases (acute, recovery, convalescence) over a year. Changes in\nproteins were assessed using a multimodal approach. During the acute phase,\ninflamed and uninflamed phenotypes were characterized by the expression of tissue\nrepair and host defense response molecules. With recovery, inflammatory and\nfibrogenic mediators declined and clinical symptoms abated. However, at nine months,\nquantified radiographic abnormalities had resolved in the majority of patients, and yet\ncompared to healthy persons, all showed ongoing activation of cellular repair\nprocesses and depression of the renin-kallikrein kinin-coagulation and complement\nsystems. This dissociation of prolonged reparative processes from symptom and\nradiographic resolution suggests that occult ongoing disruption of the lung proteome is\nunderrecognized and may be relevant to recovery from other serious viral pneumonias.","fileCount":"77","fileSizeKB":"125572810","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"no","keywords":"COVID-19; Proteomics; lung injury; SARS-CoV-2; data independent acquisition mass spectrometry; proximal extension assay; longitudinal","pi":[{"name":"Shreya Madisetty Kanth","email":"shreya.kanth@nih.gov","institution":"National Institutes of Health","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7ff6a3ee1f574904a9048e646f89b209","id":"2443"}, {"dataset":"MSV000094896","datasetNum":"94896","title":"Paralogue-selective degradation of the lysine acetyltransferase EP300","user":"kiallsuazo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717100666000","created":"May. 30, 2024, 1:24 PM","description":"This contains the raw data for global proteomic profiling described in the paper \"Paralogue-selective degradation of the lysine acetyltransferase EP300\"","fileCount":"34","fileSizeKB":"32283892","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"EP300 CREBBP acetylation ","pi":[{"name":"Jordan Meier","email":"jordan.meier@nih.gov","institution":"National Cancer Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"64aeaff36cad4d7e8127954d76cd5759","id":"2444"}, {"dataset":"MSV000094895","datasetNum":"94895","title":"GNPS - 2024-Mobley-collaborative-project_Fe","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717100419000","created":"May. 30, 2024, 1:20 PM","description":"Proteus mirabilis WGLW4 were cultured, supernatant was extracted using HLB-SPE and 80% MeOH\/water and metabolome was analyzed with QExactive HF. 150uL, Fe","fileCount":"37","fileSizeKB":"7227570","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteus mirabilis WGLW4 (NCBITaxon:1125693)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metal binding","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"639de51fc16b4b12a78ee486d5c4b5e4","id":"2445"}, {"dataset":"MSV000094894","datasetNum":"94894","title":"GNPS - MS for 2-aminobenzamide-actiphenol ","user":"donghui","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717097931000","created":"May. 30, 2024, 12:38 PM","description":"44321-A2 was streaked onto R2YE agar containing 5 g of yeast extract, 103 g of sucrose, 10 g of dextrose, 0.1 g of casamino acid, 0.25 g of potassium sulfate (K2SO4), 10.12 g of magnesium chloride hexahydrate (MgCl2.6H2O), 5.73 g of TES buffer, 2 mL of trace element solution (containing 10 mg of ammonium molybdate tetrahydrate ((NH4)6Mo7O24.4H2O), 10 mg of sodium tetraborate decahydrate (Na2B4O7.10H2O), 10 mg of manganese chloride tetrahydrate (MnCl2.4H2O), 10 mg of cupric chloride dihydrate (CuCl2.2H2O), 200 mg of ferric chloride hexahydrate (FeCl3.6H2O), 40 mg of zinc chloride (ZnCl2), and 1 L of deionized water, filter sterilized), 10 mL of 0.5% potassium dihydrogen phosphate (KH2PO4), 4 mL of 5 M calcium chloride dihydrate (CaCl2.2H2O), 5 mL of 20% L-proline, 7 mL of 1 N sodium hydroxide (NaOH), 25 micrograms\/mL nalidixic acid, 10 micrograms\/mL benomyl, 15 g of agar, and 1 L of double distilled water. Plates were incubated for 5-7 days at 28 C. For the strain, 3 mL seed cultures in 14 mL dual position cap tubes were inoculated with a loopful of vegetative cells from R2YE plates and incubated for 5 days at 28 C, 200 rpm; 3 mL seed cultures were then inoculated into 100 mL seed cultures in 250 mL baffled flasks and incubated for 7 days at 28 C, 200 rpm; 50 mL of seed cultures were inoculated into 1 liter of fermentation media in 2.8 liter baffled Fernbach flasks and grown for 7 days at 28 C, 200 rpm.","fileCount":"2","fileSizeKB":"490203","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces actiphen","instrument":" Agilent 1290 Infinity II UPLC ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces actiphen;seq2pks;2-aminobenzamide-actiphenol","pi":[{"name":"Ashu Tripathi","email":"ashlesha@umich.edu","institution":"University of","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"13868cb13f644048a40933d91a4f037f","id":"2446"}, {"dataset":"MSV000094892","datasetNum":"94892","title":"Assessing and harnessing updated polyketide synthase modules...Massive dataset","user":"rayk212","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1717081358000","created":"May. 30, 2024, 8:02 AM","description":"This data was acquired by engineering tri-, tetra- and pentaketide synthases using pikromycin synthase modules within K207-3 E. coli cells. The products were extracted with ethyl acetate, evaporated and resuspended in 1:1 MeOH and H2O. ","fileCount":"30","fileSizeKB":"1017471","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"E. Coli K207-3","instrument":"6230A Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Polyketide","pi":[{"name":"Adrian Keatinge-Clay","email":"adriankc@utexas.edu","institution":"University of Texas at Austin","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4986d3bd6c2f4be9a72fd4d1dad58ffc","id":"2447"}, {"dataset":"MSV000094888","datasetNum":"94888","title":"Extracellular matrices of stromal cell subtypes regulate phenotype and contribute to the stromal microenvironment in vivo","user":"Astone","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716996050000","created":"May. 29, 2024, 8:20 AM","description":"Comparison of secreted proteins from heterogeneous mesenchymal stromal cells.","fileCount":"11","fileSizeKB":"12727557","spectra":"0","psms":"103327","peptides":"12120","variants":"15122","proteins":"2218","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Bos taurus (NCBITaxon:9913)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Mesenchymal Stromal Cell;secretome","pi":[{"name":"Paul Genever","email":"Paul.genever@york.ac.uk","institution":"University of York","country":"UK"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052678","task":"948e260c8e1f4eb48490c004b65f583c","id":"2448"}, {"dataset":"MSV000094885","datasetNum":"94885","title":"GNPS - Cyanobacteria Pteridines purified from Synechococcus elongatus PCC 7942 extracts","user":"Nike","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716937171000","created":"May. 28, 2024, 3:59 PM","description":"Different pteridines were purified from cyanobacterial cell extract (Synechococcus elongatus PCC 7942) via HPLC","fileCount":"30","fileSizeKB":"2637603","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cyanobacteria;Pteridines;Synechococcus","pi":[{"name":"Danie Petras","email":"daniel.petras@uni-tuebingen.de","institution":"University of Tuebingen ","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5945856a4f4b42efb027af88018d2d9e","id":"2449"}, {"dataset":"MSV000094884","datasetNum":"94884","title":"GNPS - Metabolomic approach based on mass spectrometry in plant leaf extracts of Sarcostema glaucum","user":"ValeskaLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716936858000","created":"May. 28, 2024, 3:54 PM","description":"This study focuses on the application of an untargeted metabolomic approach, using mass spectrometry, to investigate potential metabolites present in Sarcostema glaucum leaf extracts. These extracts are obtained with three different solvents (acquous, 50% methanol, and 96% methanol), with the objective of identifying compounds with potential insecticidal activity. ","fileCount":"397","fileSizeKB":"1696533","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sarcostemma (NCBITaxon:126772);Sarcostemma glaucum","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plant extract;Bejuco del Diablo;Sarcostema glaucum;Metabolomics","pi":[{"name":"Ana Maria Vidal","email":"amvidalc@eafit.edu.co","institution":"Universidad EAFIT","country":"Colombia"},{"name":"Sebastian Zapata","email":"invfitopatologia@augura.com.co","institution":"AUGURA","country":"Colombia"},{"name":"Valeska Villegas Escobar ","email":"vvilleg2@eafit.edu.co","institution":"Universidad EAFIT","country":"Colombia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a9abbd347a7f42b5b3948d866215d3d3","id":"2450"}, {"dataset":"MSV000094883","datasetNum":"94883","title":"Molecular mechanism of Contactin 2 homophilic interaction","user":"Bill","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716924839000","created":"May. 28, 2024, 12:33 PM","description":"Contactin 2 (CNTN2), a neuronal guidance molecule, forms transient homodimers. Cryo-electron microscopy reveals that the CNTN2 homodimer forms a T-shaped particle composed of parallel, intertwined monomers. A central homodimeric stalk places headpieces, leveraged by CNTNs to bind heterophilic partners, on either side, indicating that homophilic and heterophilic binding mechanisms are distinct. ","fileCount":"5","fileSizeKB":"106852","spectra":"0","psms":"2304","peptides":"74","variants":"210","proteins":"9","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion ETD","modification":"DSSO","keywords":"crosslinking","pi":[{"name":"William Russell","email":"bill.russell@utmb.edu","institution":"UTMB","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"104298f2ce4344d598711d9c12573a15","id":"2451"}, {"dataset":"MSV000094882","datasetNum":"94882","title":"Dietary lipid is largely deposited in skin and rapidly affects insulating properties","user":"barrettwilt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716914781000","created":"May. 28, 2024, 9:46 AM","description":"Dietary fat is rapidly deposited in skin resulting in change in skin thermal properties. Skin was found to be the largest target of deposition of dietary fat. Lipidomic analysis was performed on skin, white adipose tissue, serum, and hair.","fileCount":"13551","fileSizeKB":"333351501","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6546 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"skin metabolism;lipidomics;dietary fat deposition","pi":[{"name":"Caroline Alexander","email":"cmalexander@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1590e6c16e4b43a3908ffbcffd6bbdda","id":"2452"}, {"dataset":"MSV000094881","datasetNum":"94881","title":"Proteomic and lipidomic analysis of Ground Demonstrator Model of ArtEMISS-C, MELiSSA Project on Limnospira indica PCC 8005 P3.","user":"CecRen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716904652000","created":"May. 28, 2024, 6:57 AM","description":"Proteomic and lipidomic analysis of Ground Demonstrator Model of ArtEMISS-C (Science Verification Test), MELiSSA Project on Limnospira indica PCC 8005 P3. \nProteomic analysis has been performed with AB Sciex TripleTOF 6600.\nLipidomic analysis has been performed with AB Sciex ZenoTOF 7600.","fileCount":"208","fileSizeKB":"28925490","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Limnospira indica (NCBITaxon:147322)","instrument":"TripleTOF 6600;ZenoTOF 7600","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Ground demonstration, light intensity, limnospira indica","pi":[{"name":"Cecile Renaud","email":"cecile.renaud@umons.ac.be","institution":"Umons","country":"Belgium"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1b53faa1eebf41cb829009422078cffd","id":"2453"}, {"dataset":"MSV000094880","datasetNum":"94880","title":"The extracellular serine protease from Staphylococcus epidermidis elicits a type 2-biased immune response in atopic dermatitis patients","user":"steill","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716887292000","created":"May. 28, 2024, 2:08 AM","description":"Background: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease with skin barrier defects and a misdirected type 2 immune response against harmless antigens. The skin microbiome in AD is characterized by a reduction in microbial diversity with a dominance of staphylococci, including Staphylococcus epidermidis (S. epidermidis). \nObjective: To assess whether S. epidermidis antigens play a role in AD, we screened for candidate allergens and studied the T-cell and humoral immune response against the extracellular serine protease (Esp). \nMethods: To identify candidate allergens, we analyzed the binding of human serum IgG4, as a surrogate of IgE, to S. epidermidis extracellular proteins using 2-dimensional immunoblotting and mass spectrometry. We then measured serum IgE and IgG1 binding to recombinant Esp by ELISA in healthy and AD individuals. We also stimulated T-cells from AD patients and control subjects with Esp and measured the secreted cytokines. Finally, we analyzed the proteolytic activity of Esp against IL-33 and determined the cleavage sites by mass spectrometry.\nResults: We identified Esp as the dominant candidate allergen of S. epidermidis. Esp-specific IgE was present in human serum; AD patients had higher concentrations than controls. T-cells reacting to Esp were detectable in both AD patients and healthy controls. The T-cell response in healthy adults was characterized by IL-17, IL-22, IFN-gamma, and IL-10, whereas the AD patients' T-cells lacked IL-17 production and released only low amounts of IL-22, IFN-gamma, and IL-10. In contrast, Th2 cytokine release was higher in T-cells from AD patients than from healthy controls. Mature Esp cleaved and activated the alarmin IL-33.\nConclusions: The extracellular serine protease Esp of S. epidermidis can activate IL-33. As an antigen, Esp elicits a type 2-biased antibody and T-cell response in AD patients. This suggests that S. epidermidis can aggravate AD through the allergenic properties of Esp.\n","fileCount":"12","fileSizeKB":"834015","spectra":"0","psms":"2632","peptides":"1846","variants":"1894","proteins":"1462","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Staphylococcus epidermidis (NCBITaxon:1282)","instrument":"LTQ Orbitrap Velos","modification":"UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:510 - \\\"DiMethyl-C13HD2.\\\"","keywords":"Esp, Staphylococcus epidermidis, atopic dermatitis, allergy, IgE, Th2, protease","pi":[{"name":"Dr. Leif Steil","email":"steil@uni-greifswald.de","institution":"Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald","country":"germany"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052619","task":"0a0983a3e3c84bb089f33d21eb0631b5","id":"2454"}, {"dataset":"MSV000094879","datasetNum":"94879","title":"Chemical crosslinking extends and complements UV crosslinking in analysis of RNA and DNA nucleic acid protein interactions by mass spectrometry ","user":"LuisaMWelp","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716881488000","created":"May. 28, 2024, 12:31 AM","description":"UV (ultra violet) crosslinking with mass spectrometry (XL MS) has been established for identifying RNA and DNA binding proteins along with their domains and amino acids involved. Here, we explore chemical XL MS, for RNA protein, DNA protein and nucleotide protein complexes in vitro and in vivo. We also introduce a novel nucleotide protein crosslink search engine, NuXL, for fast and robust identification of such crosslinks at amino-acid resolution. Chemical XL MS complements and extends UV XL MS by generating different crosslink species. The added spatial information facilitates integrative structural modelling of nucleic acid protein complexes. In vivo UV and chemical XL MS data from E. coli cells analysed by NuXL establish a comprehensive nucleic acid protein crosslink inventory at amino acid level. RNA crosslinks cover most RNA binding proteins DNA and RNA crosslinks are found in transcriptional repressors and activators. Our workflow adds spatial information to the RNA binding properties of enzymes, for which crosslinking sites are often observed close to their cofactor binding domains. ","fileCount":"498","fileSizeKB":"167120780","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Homo sapiens (NCBITaxon:9606);Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Crosslinking mass spectrometry;Chemical crosslinking;DNA;RNA;protein-RNA;protein-DNA;DDA;Structural mass spectrometry","pi":[{"name":"Prof. Henning Urlaub","email":"henning.urlaub@mpinat.mpg.de","institution":"Max Planck Institute for Multidisciplinary Sciences","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052614","task":"5ec7910378d24ffba34a7961273020bf","id":"2455"}, {"dataset":"MSV000094878","datasetNum":"94878","title":"Proteome and secretome analysis of human dorsal forebrain organoids reveals a time-dependent shift in the abundance of cell adhesion and extracellular matrix proteins","user":"Dali77","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716879187000","created":"May. 27, 2024, 11:53 PM","description":"Temporal dynamics of prenatal brain development are influenced by changes in the microenvironment. Particularly, extracellular proteins contribute to the dynamic niche that balances neural stem cell proliferation and differentiation. Here, we present a resource for proteome and secretome analysis of human induced pluripotent stem cell-derived dorsal forebrain organoids over the early developmental period. We used liquid chromatography-mass spectrometry to identify proteins found in whole organoid and secreted proteins at days 20, 35, and 50 of dorsal forebrain organoid differentiation. We show that the whole organoid proteome demonstrates progression in the neurodevelopmental trajectory with reduced proliferation and increased neural differentiation over time. However, secretome analysis revealed a unique signature for developmental progression. Cell adhesion molecules are enriched in the secretome of day 35 organoids, while secretome of day 50 organoids is enriched with extracellular matrix proteins, demonstrating a change in the extracellular interactions over time of organoid differentiation and maturation. We, therefore, show the relevance of secretome analysis for the thorough study of extracellular matrix-related proteins and the importance of time course study of neural organoids to understand the subtle changes that guide human neurodevelopment. 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For the control group, seedlings were continuously grown at 22C after being transferred to the ATS medium with the normal nitrogen source (14N-medium). \nRoot and shoot tissues were collected at different time points post-transfer and then subjected to differential centrifugation to isolate fractions enriched in organellar, soluble, or microsome-associated proteins for analysis by LC-MS\/MS.\n","fileCount":"110","fileSizeKB":"10004148","spectra":"0","psms":"11510","peptides":"1105","variants":"1451","proteins":"349","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"15N-stable isotope labeling, crop resilience, heat stress, protein turnover, proteomics","pi":[{"name":"Adrian D. 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In this study, we carried out a biological triplicate of quantitative proteomic and phosphoproteomic analyses on the pathogenic bacterium Streptococcus pneumoniae in the non-competent and the competent states. Competence is a developmental genetic program triggered by a signaling pathway that is key for natural genetic transformation and consequently bacterial horizontal gene transfer. We used dimethyl-tag labeling for the calculation of peptide abundance ratios between non-competent and competent samples, Titanium dioxide (TiO2) beads for phosphopeptide enrichment and LC-MS\/MS determination. Our proteome covers 62.7% of the total protein content of the bacteria with 75 proteins having different abundance ratios, including proteins not previously described to be involved in competence. 103 phosphopeptides were identified including 48 having different abundance ratios. Notably, the proteins with a change in phosphorylation in competent cells are different from the proteins with a change in expression, highlighting different pathways induced by competence and regulated by phosphorylation. This is the first report that phosphorylation of some proteins is regulated during competence in Streptococcus pneumoniae, a key pathway for the bacteria to evade vaccines or acquire antibiotic resistance.","fileCount":"25","fileSizeKB":"16572342","spectra":"0","psms":"592648","peptides":"15538","variants":"45481","proteins":"1285","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptococcus pneumoniae (NCBITaxon:1313)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Streptococcus pneumoniae;competence;phosphorylation;protein kinase;phosphoproteomic","pi":[{"name":"Christophe Grangeasse","email":"c.grangeasse@ibcp.fr","institution":"MMSB-UMR5086-CNRS","country":"France"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"69774eea6bbf4fbd92b527a299381229","id":"2480"}, {"dataset":"MSV000094839","datasetNum":"94839","title":"GNPS - Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system","user":"cjchen_01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716427167000","created":"May. 22, 2024, 6:19 PM","description":"LC-MS data of the reaction products from both Elizabethkingia anophelis and Anabaena sp. cyclases with nucleotides ","fileCount":"692","fileSizeKB":"65436","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Elizabethkingia anophelis (NCBITaxon:1117645);Anabaena sp. (NCBITaxon:1167)","instrument":"HCT","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS;nucleotide;anti-phage system","pi":[{"name":"Chao-Jung Chen","email":"cjchen@mail.cmu.edu.tw","institution":"China Medical University","country":"Taiwan"},{"name":"yeh chen","email":"chyeah6599@nchu.edu.tw","institution":"Department of Food Science and Biotechnology, National Chung Hsing University","country":"Taiwan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"faeba3b441d442849b1536ca3e7f79d4","id":"2481"}, {"dataset":"MSV000094838","datasetNum":"94838","title":"GNPS_CMMC_KV-9,KV-10,KV-11,KV-12","user":"kyvittali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716423377000","created":"May. 22, 2024, 5:16 PM","description":"MS\/MS fragmentation data of KV-9 (C2:0, C3:0, C5:0 with 2-aminoadipic acid, 3-methoxytyramine, 5-methoxy tryptamine, kynurenine, 3-hydroxy kynurenine); KV-10 (C5:0, C9:0, C3:1, C10:0, C14:0, C16:0 with norvaline, ornithine, glutathionine, phenethylamine, glutamine, alanine, phenylalanine); KV-11 (C10:1, C5:1, C11:1 with the 20 proteinogenic amino acids); KV-12 (C4:0 3-OH, C5:0 3-OH with the 20 proteinogenic amino acids) acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\n","fileCount":"9","fileSizeKB":"242243","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"n-acyl lipids; 3-hydroxy fatty acids;fatty acids","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"469d31101fe34e21be9b22a485456520","id":"2482"}, {"dataset":"MSV000094832","datasetNum":"94832","title":"Metaproteome analysis of the coral holobiont demonstrates algal symbiont quiescence under thermal stress","user":"enchiles","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716394452000","created":"May. 22, 2024, 9:14 AM","description":"Raw metabolomic Mass spectrometry data from thermal stress experiment on 3 corals from the Great Barrier Reef, Acropora hyacinthus , Porites lobata and Stylophora pistillata.","fileCount":"218","fileSizeKB":"19421055","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Acropora hyacinthus (NCBITaxon:55974);Porites lobata (NCBITaxon:104759);Stylophora pistillata (NCBITaxon:50429)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics, coral reefs, coral bleaching, Great Barrier Reef, coral holobiont, algal symbionts","pi":[{"name":"Debashish Bhattacharya","email":"d.bhattacharya@rutgers.edu","institution":"Rutgers","country":"USA"}],"complete":"false","quant_analysis":"Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"54947e09d02d41e8995fdbc01d88a4b5","id":"2483"}, {"dataset":"MSV000094829","datasetNum":"94829","title":"Single-nucleus proteomics identifies regulators of protein transport","user":"jderks","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716393281000","created":"May. 22, 2024, 8:54 AM","description":"Rapid advances in proteomics methods and technologies have enabled global and unbiased quantification of the molecular actuators of biological processes -- proteins -- in single-cells. By quantifying proteomic variability in single-cells, phenotypic inferences have been made to investigate the diversity of ostensibly homogeneous populations of cells, such as emergent polarizations in resting macrophages. Still, there remains an untapped potential to reverse these investigations, and instead use phenotypic variability from naturally heterogeneous cells to discover proteins novely associated with function. The variability of cellular responses, such as macrophages to an inflammatory stimulus, is likely explained by the variability in their respective initial proteomes. Here we demonstrate an approach that enables the inference of functional regulators of lipopolysacharide (LPS)-induced nucleocytoplasmic transport in THP-1 macrophages. We accomplished this by analyzing the proteomes of 3,412 single-macrophage nuclei before and up to 60 minutes after 1 ug\/mL LPS stimulation, thus yielding a distribution of initial nuclear proteomes and enabling the probabilistic quantification of nucleocytoplasmic protein transport in response to brief LPS stimulation. We found that simple biophysical constraints, such as the quantity of nuclear pores, partially explain the variability in LPS-induced nucleocytoplasmic transport (P < 1e-15, r = 0.48). However, many other proteins were highly associated with the response. We evaluated the single-nucleus derived associations for 16 proteins, and found them to be highly predictive of their functional effects in validations by genetic perturbation. Together these results demonstrate the potential for (sub-)single-cell proteomics to infer functional regulation.","fileCount":"56913","fileSizeKB":"6781651191","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"UNIMOD:888 - \\\"MTRAQ light.\\\";UNIMOD:889 - \\\"MTRAQ medium.\\\";UNIMOD:1302 - \\\"MTRAQ heavy.\\\"","keywords":"single-cell;single-nucleus;plexDIA;protein transport;macrophage","pi":[{"name":"Nikolai Slavov","email":"n.slavov@northeastern.edu","institution":"Northeastern University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"74b20742b1334685bcea0bb139f79188","id":"2484"}, {"dataset":"MSV000094828","datasetNum":"94828","title":"Human_MTHR_PhosphorylationMapping_MSMS_Dataset","user":"menjdoza","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716392082000","created":"May. 22, 2024, 8:34 AM","description":"Phosphorylation mapping data from MS\/MS analysis of human MTHFR, \"Structural basis of S-adenosylmethionine-dependent Allosteric Transition from Active to Inactive States in Methylenetetrahydrofolate Reductase\", Yamada et al. 2024","fileCount":"18","fileSizeKB":"2634150","spectra":"0","psms":"1566","peptides":"165","variants":"298","proteins":"43","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Phosphorylation;MTHFR;Allostery","pi":[{"name":"Markos Koutmos","email":"mkoutmos@umich.edu","institution":"University of Michigan","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052481","task":"2fb4988cff094610a7cc15d3c97766be","id":"2485"}, {"dataset":"MSV000094825","datasetNum":"94825","title":"Label-free quantification of 3D MCF10A cell culture proteome (DIA)","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716333167000","created":"May. 21, 2024, 4:12 PM","description":"Global shotgun proteomic analysis using data independent acquisition (DIA) and Spectronaut analysis on the input cell lysates before the enrichment step in proximity labeling experiments, specifically MCF10A cells stably expressing miniTurbo-BAD in 3D with biotin treatment (n=4)","fileCount":"9","fileSizeKB":"14319130","spectra":"281092","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - 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Invasive growth of cancer cells relates to high levels of compressive forces translating to relevant damage of the plasma membrane. However, functional implications of protein machineries required for plasma membrane repair in ccRCC are not yet completely elucidated. Given the membrane-associated localization of the large family of annexin proteins, we aimed for a global annotation annexin proteins, which led to the identification of ANXA4 selectively expressed in cancer cells of ccRCC. Interestingly, ANXA4 showed context-dependent distinct localization patterns including the plasma membrane as well as the nuclear compartment\/nuclear membrane. We investigated the functional role of ANXA4 in ccRCC employing genetic titration studies (knockdown, CRISPR\/Cas9 knockout and overexpression) and identified impaired acute plasma membrane repair as well as invasive capability in conditions of reduced ANXA4 expression. Utilizing computational segmentation of the tumor microenvironment (TME) of ccRCC samples revealed that ANXA4 low tumors exhibited a distinct TME composition compared to ANXA4 high cases. ANXA4 low tumors showed higher levels of tumor infiltrating lymphocytes accompanied by increased deposition of acellular extracellular matrix. Further transcriptomic analysis demonstrated major alterations in transcriptional signatures related to epithelial-mesenchymal transition (EMT) and immune signaling. Transcription factor enrichment analysis and further functional validation identified ELF3 as one central regulator of invasive properties. Our integrative approach including molecular analyses with advanced histopathological segmentation uncovered novel roles for ANXA4 in modulating acute membrane repair, transcriptional regulation, and shaping cellular composition of the ccRCC tumor microenvironment.","fileCount":"54","fileSizeKB":"34779333","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive","modification":"UNIMOD:518 - \\\"Diethylation, analogous to Dimethylation.\\\"","keywords":"cell conditioned medium","pi":[{"name":"Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"Institute of Surgical Pathology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"92de6c2316dd464cb89a59efa7941959","id":"2494"}, {"dataset":"MSV000094811","datasetNum":"94811","title":"GNPS - CMMC_Bile_Salt_Hydrolase_Rxn_5.1","user":"asund42","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1716246609000","created":"May. 20, 2024, 4:10 PM","description":"MS\/MS fragmentation data of BSH enzyme assay of taurylcholic acid with a mix of 10 amino acids (Phenylalanine, Alanine, Arginine, Asparagine, Cysteine, Glutamine, Histidine, Methionine, Lysine, and Isoleucine) acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"4","fileSizeKB":"95159","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"BSH;Bile Acid;Amino Acid","pi":[{"name":"Pieter C. 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The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m\/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved \"pseudo-MS\/MS\" spectra, facilitating direct (\"spectral-library free\") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. 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As a proof of concept, we treated cells with sodium butyrate, a histone deacetylase inhibitor, and demonstrate that our method can i) distinguish between treated and non-treated cells , ii) identify sub-populations of cells that respond differently to treatment, and iii) reveal how hPTM regulation differs in the context of drug treatment using covariation analysis. Overall, these experiments establish the applicability of our method to investigate chromatin heterogeneity at the single-cell level, which has important implications for understanding complex disease states like cancer and aging. 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Traditional biotinylation proteomics workflows suffer from complex sample preparation steps, non-specific bindings, limited throughput, and experimental variability. To address these critical challenges, we designed a two-proteome model, where yeast proteins were biotinylated in vitro and spiked in unlabeled human proteins, allowing us to distinguish true enrichment (yeast) from non-specific bindings (human) for comprehensively benchmarking of biotinylation proteomics methods. We also significantly optimized the entire workflow and reduced the sample preparation time from the traditional 3 days to just 9 hours, enabling a fully automated 96-well format sample processing for excellent reproducibility and throughput with minimized non-specific bindings. We then applied this optimized and automated workflow to proximity labeling proteomics and investigated the intricate interplay between mitochondria and lysosomes in living cells under both healthy state and mitochondrial damage. We demonstrated that mitochondrial damage led to an increased mitochondria-lysosome membrane contact and induced broad alternations in mitophagy-related proteins. We identified and quantified biotinylated proteins and precise amino acid residues at mitochondria-lysosome contact sites and within the mitophagy pathway, revealing an elevated level of interaction between mitochondria and lysosomes and proteome-wide remodeling in response to mitochondrial damage.","fileCount":"352","fileSizeKB":"146035542","spectra":"4791005","psms":"1288196","peptides":"80509","variants":"106771","proteins":"14038","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"[M] oxidation;[K] biotinylation;[C] alkylation;[N-term] acetylation","keywords":"biotinylation;proximity labeling;HeLa cell","pi":[{"name":"Ling Hao","email":"linghao@email.gwu.edu","institution":"The George Washington University","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052357","task":"c221e885fef643fbb177343dc432daf9","id":"2505"}, {"dataset":"MSV000094794","datasetNum":"94794","title":"Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation","user":"mj2794","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715988686000","created":"May. 17, 2024, 4:31 PM","description":"RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc-finger families. We show that multiple ZFPs are previously unknown regulators of RNA splicing, alternative polyadenylation, stability, or translation. The examined ZFPs show widespread sequence-specific RNA binding and preferentially bind proximal to transcription start sites. Additionally, several ZFPs associate with their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DNA\/RNA-associated protein that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation.","fileCount":"10","fileSizeKB":"8010048","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ZNF;RBP;DBP","pi":[{"name":"Gene Yeo","email":"geneyeo@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"48b2ee31fad947e8b208e66b4675c207","id":"2506"}, {"dataset":"MSV000094793","datasetNum":"94793","title":"GNPS - CMMC_acyl_amide_VD9_through_VD19","user":"victoriadeleray","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715987446000","created":"May. 17, 2024, 4:10 PM","description":"MS\/MS fragmentation data of N-acyl amides VD9,VD10, VD11, VD12, VD13, VD15, VD16, VD17, VD18, VD19 acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"21","fileSizeKB":"9759816","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"amide, n-acyl-lipid, lipid","pi":[{"name":"Pieter C. 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In this work, we report the discovery and characterization of a widespread gene cluster family for the biosynthesis of briarane diterpenoids that number over 600 molecules distinct to corals. We sequenced five genomes from evolutionarily discrete families of briarane-producing octocorals, including the chromosomally resolved precious coral Corallium rubrum, and identified a common five-gene cluster composed of a terpene cyclase, three cytochrome P450s, and a short-chain dehydrogenase. Using Escherichia coli and Saccharomyces cerevisiae as hosts and homologous briarane biosynthesis genes from seven corals, we reconstituted the biosynthesis of cembrene B g-lactone, which contains the g-lactone structural feature distinctive of briarane diterpenoids. The discovery of the genomic basis of briarane biosynthesis not only allows for its biological examination across coral species but establishes that animals, like microbes and plants, also employ gene cluster families to produce specialized metabolites. 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The majority of nTDMS studies utilize purified recombinant proteins, with significant challenges hindering application to endogenous systems. To perform native top-down proteomics (nTDP), where endogenous proteins from complex biological systems are analyzed by nTDMS, it is essential to separate proteins under nondenaturing conditions. However, it remains difficult to achieve high resolution and MS-compatibility with online chromatography while preserving protein tertiary structure and noncovalent interactions. Herein, we report the use of online mixed-bed ion exchange chromatography (IEC) to enable separation of endogenous proteins from complex mixtures under nondenaturing conditions, preserving noncovalent interactions for nTDP analysis. We have successfully detected large proteins (>146 kDa) and identified endogenous metal-binding and oligomeric protein complexes in human heart tissue lysate. The use of a mixed-bed stationary phase allowed retention and elution of proteins over a wide range of isoelectric points without altering the sample or mobile phase pH. Overall, our method provides a simple online IEC-MS platform that can effectively separate proteins from complex mixtures under nondenaturing conditions and preserve higher-order structure for nTDP applications.","fileCount":"359","fileSizeKB":"4192939","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"maXis II","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"native;top-down proteomics;ion-exchange chromatography","pi":[{"name":"Ying Ge","email":"ying.ge@wisc.edu","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052354","task":"b5983707cbd74694beabffb0f1a0307d","id":"2512"}, {"dataset":"MSV000094784","datasetNum":"94784","title":"Paracrine secretion of monounsaturated fatty acids prevents ferroptosis in triple negative breast cancer and reveals selenocysteine synthesis dependency for metastatic seeding.","user":"dsumpton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715938495000","created":"May. 17, 2024, 2:34 AM","description":"The limited availability of therapeutic options for patients with triple-negative breast cancer (TNBC) contributes to the high rate of metastatic recurrence and poor prognosis. Ferroptosis is a cell death caused by iron-dependent lipid peroxidation counteracted by the antioxidant activity of selenoproteins. Here, we show that TNBC cells secrete an anti-ferroptotic factor in the extracellular environment when cultured at high cell densities but are primed to when forming colonies from single cells. We found that the secretion of the anti-ferroptotic factor, identified as monounsaturated fatty acids (MUFA) containing lipids, and the vulnerability to ferroptosis of single cells depend on the expression of stearyl-CoA desaturase (SCD) that is proportional to cell density. Finally, we show that the inhibition of tRNAsec selenocysteinilation, an essential step for selenoproteins production, causes ferroptosis and impairs the lung seeding of circulating TNBC cells no longer protected by the MUFA-rich environment of the primary tumour.","fileCount":"3225","fileSizeKB":"11622545","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus;7000A Triple Quadrupole GC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Ferroptosis;lipidomics;MUFA;selenocysteine synthesis ;fatty acids;triple negative breast cancer ","pi":[{"name":"David Sumpton","email":"d.sumpton@crukscotlandinstitute.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"},{"name":"Saverio Tardito","email":"saverio.tardito@glasgow.ac.uk","institution":"CRUK Scotland Insititue","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4b2d5832b1784cb7a771c9a2ce57bef6","id":"2513"}, {"dataset":"MSV000094783","datasetNum":"94783","title":"Barbatia virescens byssal filament proteins","user":"jiminchoi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715930897000","created":"May. 17, 2024, 12:28 AM","description":"ESI-LC-MSMS result of byssal filament proteins from Barbatia virescens. \nByssal filament proteins were obtained with the hydroxylamine extraction method.","fileCount":"6","fileSizeKB":"110931","spectra":"0","psms":"228","peptides":"46","variants":"82","proteins":"6","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Barbatia virescens (NCBITaxon:6559)","instrument":"Easy n-LC and LTQ Orbitrap XL mass spectrometers (both from Thermo Fisher, San Jose, CA, USA), each equipped with a nano-electrospray source, were used for nano LC-MS\\\/MS. ","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";automatic PTM search algorithm","keywords":"B. virescens; Byssus; Byssal filament proteins","pi":[{"name":"JIMIN CHOI","email":"jmjm334@postech.ac.kr","institution":"Pohang University of Science and Technology","country":"South Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052335","task":"ebe13a27f86441a2ab6b1f2d517746db","id":"2514"}, {"dataset":"MSV000094782","datasetNum":"94782","title":"GNPS - Improving bioenergy yield under drought stress from field to lab","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715908961000","created":"May. 16, 2024, 6:22 PM","description":"Part of the DOE\u2019s strategy to ensure American energy independence is to produce biofuels from dedicated biomass crops. Achieving DOE\u2019s ambitious goal of displacing 30 percent of 2004 gasoline demand with biofuels by 2030 will require major increases in plant productivity. Switchgrass has been championed as a promising bioenergy species, but few tools exist to facilitate its widespread commercial use. A major challenge has been its large, complex genome. As a close relative of agronomic switchgrass (Panicum virgatum) with a diploid genome and seed-to-seed time of 8 weeks, Panicum hallii offers researchers a model system for exploring Panicum genetics, genomics, and adaptation for agronomic improvement. Bacteria living in leaves and roots influence many aspects of plant health, especially rhizobacteria and mycorrhizae are known to impact plant aboveground phenotypes 1,2. To better understand P. halli-microbe ecosystems, we will conduct experiments at our Texas field site, in EcoCells at Desert Research Institute (DRI) and in growth chambers and the Ecopod at LBNL. Ecopods are enclosed environments that allow direct and intensive monitoring and manipulation of replicated plant-soil-microbe-atmosphere interactions over the complete plant life cycle. Specifically, we are interested in plant microbe ecosystem stress response with respect to soil drying. Despite its broad adaptation to marginal, droughty soils 3,4, a persistent issue in producing switchgrass has been the rapid and consistent establishment of strong stands, especially when drought occurs during implantation. The proposed study is aimed at disclosing biotic interactions modulating plant and microbial metabolism under globally relevant environmental conditions and provides an opportunity to benchmark the Ecopods at LBNL.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001211) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"799","fileSizeKB":"65961570","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Panicum hallii microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"rhizosphere;drought tolerance","pi":[{"name":"Esther Singer","email":"Esther.singer13@gmail.com","institution":"Lawrence Berkeley National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"af37545c949f4bb4b658f405beabdfda","id":"2515"}, {"dataset":"MSV000094781","datasetNum":"94781","title":"GNPS - Elucidating lignin catabolism in white rot fungi","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715908623000","created":"May. 16, 2024, 6:17 PM","description":"We propose to elucidate new metabolic pathways in fungi - with a special focus on white rot fungi (WRF)- involved in the catabolism of lignin-derived aromatic compounds. Basidiomycete fungi, in particular WRF, are the most efficient organisms for the depolymerization and mineralization of lignin to CO2 and H2O in Nature and thus, WRF play a pivotal role in carbon cycling. Lignin depolymerization by WRF is mediated by the action of extracellular oxidative ligninolytic enzymes, such as laccases and peroxidases, alongside other secreted metabolites. This extracellular process has been studied for decades via analysis of lignin modifications, ligninolytic enzyme activity in fungal broths, enzyme isolation and characterization, and more recently through multi-omics analyses. Despite the massive research effort directed toward understanding how WRF depolymerize lignin, almost no attention has been dedicated to the elucidation of the intracellular metabolism of WRF in catabolizing lignin. In fact, whether or not WRF are able to catabolize lignin remains a matter of discussion and debate.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001176) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"1836","fileSizeKB":"134407004","spectra":"2464577","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trametes versicolor; Ceriporiopsis subvermispora","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lignin degradation;white rot fungi","pi":[{"name":"Davinia Salvachua","email":"davinia.salvachua@nrel.gov","institution":"National Renewable Energy Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7db50b964a50409794ce684757acfae8","id":"2516"}, {"dataset":"MSV000094780","datasetNum":"94780","title":"GNPS - Using genomics to understand microbial adaptation to soil warming - drought tolerance in Actinobacteria","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715908062000","created":"May. 16, 2024, 6:07 PM","description":"The earth\u2019s climate is warming, and warming-induced biological feedbacks to climate threaten to further destabilize ecosystems. In a 30-year soil warming field experiment at the Harvard Forest in central Massachusetts, microbial isolates from heated (+5 degrees C above ambient) show signs of irreversible adaptation to warming in traits associated with altered soil biogeochemical cycling. Our labs have documented physiological adaptation in all three dimensions of microbial activities: growth, resource acquisition, and stress tolerance. We will use metabolomics to investigate the nature of adaptation due to long-term warming, where reduced soil organic matter, reduced soil water holding capacity and potentially increased niche partitioning may be a selective pressure. Specifically we hypothesize that increased drought tolerance of Actinobacteria exposed to long-term warming is due to production of more or different compatible solutes compared to isolates from controls.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008103) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"897","fileSizeKB":"71033778","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"soil incubated with Actinobacteria (specific genuses: Kitasatospora; Streptomyces; Leifsonia sp. BS71; Streptacidiphilus; Corynebacteria; Planotetraspora; Frankia; Catenulispora)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Harvard Forest;long-term warming;drought tolerance;Actinobacteria","pi":[{"name":"Kristen DeAngelis","email":"deangelis@microbio.umass.edu","institution":"University of Massachusets","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3adc265b1daa4e9da17ece64c6ff7a59","id":"2517"}, {"dataset":"MSV000094779","datasetNum":"94779","title":"Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance","user":"shaoen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715900461000","created":"May. 16, 2024, 4:01 PM","description":"Recently developed covalent inhibitors for RasG12C provide the first pharmacological tools to target mutant Ras-driven cancers. However, the rapid development of resistance to current clinical Ras G12C inhibitors is common. Presumably, a subpopulation of RasG12C-expressing cells adapt their signaling to evade these inhibitors and the mechanisms for this phenomenon are unclear due to the lack of tools that can measure signaling with single-cell resolution. Here, we utilized recently developed Ras sensors to profile the environment of active Ras and to measure the activity of endogenous Ras in order to pair structure (Ras signalosome) to function (Ras activity), respectively, at a single-cell level. With this approach, we identified a subpopulation of KRasG12C cells treated with RasG12C-GDP inhibitors underwent oncogenic signaling and metabolic changes driven by WT Ras at the golgi and mutant Ras at the mitochondria, respectively. Our Ras sensors identified Major Vault Protein (MVP) as a mediator of Ras activation at both compartments by scaffolding Ras signaling pathway components and metabolite channels. We found that recently developed RasG12C-GTP inhibitors also led to MVP-mediated WT Ras signaling at the golgi, demonstrating that this a general mechanism RasG12C inhibitor resistance. Overall, single-cell analysis of structure-function relationships enabled the discovery of a RasG12C inhibitor-resistant subpopulation driven by MVP, providing insight into the complex and heterogenous rewiring occurring during drug resistance in cancer.","fileCount":"78","fileSizeKB":"36760172","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Ras, signaling","pi":[{"name":"Dustin J Maly","email":"djmaly@uw.edu","institution":"University of Washington","country":"USA"},{"name":"Jason Z Zhang","email":"jzz0428@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052325","task":"d4076e33ad654e718ca4c300e1eccef9","id":"2518"}, {"dataset":"MSV000094778","datasetNum":"94778","title":"GNPS - Samples metabolomics, Solanaceae, GEME Max Planck","user":"EstevanGN","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715899161000","created":"May. 16, 2024, 3:39 PM","description":"LC-MS QTOF of methanolic extract from 3 mature leaves. Positive mode","fileCount":"295","fileSizeKB":"29036795","spectra":"482565","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Atropa belladonna (NCBITaxon:33113);Brugmansia sanguinea (NCBITaxon:540794);Brugmansia suaveolens (NCBITaxon:905076);Brugmansia vulcanicola (NCBITaxon:1689661);Lycianthes amatitlanensis (NCBITaxon:304106);Cuatresia sp. nov;Brugmansia insignis;Brugmansia versicolor;Brugmansia x candida;Brugmansia sanguinea x vulcanicola;Solanum mammosum (NCBITaxon:115667);Iochroma arborescens;Browallia americana (NCBITaxon:310462);Brugmansia aurea (NCBITaxon:374040);Datura stramonium (NCBITaxon:4076);Solanum pseudocapsicum (NCBITaxon:45837);Solanum crinitipes (NCBITaxon:205543);Cestrum imbricatum;Cestrum humboldtii (NCBITaxon:1689665);Jaltomata procumbens (NCBITaxon:45845);Solanum hazenii (NCBITaxon:1085554);Physalis peruviana (NCBITaxon:126903);Solanum seaforthianum (NCBITaxon:45840);Solanum jamaicense (NCBITaxon:115665);Witheringia solanacea (NCBITaxon:52874);Solanum juglandifolium (NCBITaxon:205559);Solanum pseudolulo (NCBITaxon:227724);Solanum americanum (NCBITaxon:109975);Solanum viarum (NCBITaxon:215581);Solanum rudepannum (NCBITaxon:744116);Solanum ovalifolium (NCBITaxon:1403689);Solanum marginatum (NCBITaxon:329785);Ipomoea purpurea (NCBITaxon:4121);Lycianthes sp..;Solanum sp..;Solanum stellatiglandulosum","instrument":"Exactive Orbitrap focus (Thermo Fisher Scientific)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Solanaceae;Leaves;UPLC-LC-MS;Positive mode","pi":[{"name":"Federico Roda Fornaguera","email":"frodaf@unal.edu.co","institution":"Universidad Nacional de Colombia, Bogota","country":"Colombia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e70d77be304b4c0e917a7cce20067b18","id":"2519"}, {"dataset":"MSV000094777","datasetNum":"94777","title":"GNPS - Gel-assisted mass spectromety imaging","user":"ychan60","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715892577000","created":"May. 16, 2024, 1:49 PM","description":"This dataset contains mass spectrometry data from 'Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics'.\r\n","fileCount":"32","fileSizeKB":"144308125","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"rapifleX;4800 Plus MALDI TOF\\\/TOF;timsTOF fleX MALDI-2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Expansion microscopy;Mass spectrometry imaging;Imaging mass spectrometry","pi":[{"name":"Ruixuan Gao","email":"gaor@uic.edu","institution":"University of Illinois Chicago","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cde35fae6e364027b97f8b0630f4f464","id":"2520"}, {"dataset":"MSV000094776","datasetNum":"94776","title":"A highly potent bi-thiazole inhibitor of LOX rewires collagen architecture and enhances chemoresponse in triple-negative breast cancer","user":"hbtaylor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715867620000","created":"May. 16, 2024, 6:53 AM","description":"Raw proteomic files\n\nMetin C, Saatci O, Rezaeian A-H, Rao CN, Beneker C, Taylor H, Pederson B, Chatzistamou I, Buckley B, Lessner S, Angel P, McInnes C, Sahin O. A highly potent bi-thiazole inhibitor of LOX rewires collagen architecture and enhances chemoresponse in triple-negative breast cancer. Cell Chem Biol ","fileCount":"25","fileSizeKB":"10531363","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:366 - \\\"Deamidation in presence of O18.\\\"","keywords":"LOX inhibitor;collagen architecture;Lysyl oxidase;TNBC chemoresistance","pi":[{"name":"Harrison Taylor","email":"taylorha@musc.edu","institution":"Medical University of South Carolina","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052315","task":"5b7ac248df8641329bd74e57595ed68e","id":"2521"}, {"dataset":"MSV000094773","datasetNum":"94773","title":"FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer","user":"zifeng_wang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715812808000","created":"May. 15, 2024, 3:40 PM","description":"For FLAG pull-down, protein extracts of cells stably expressing FLAG-tagged FOXA2 were incubated with FLAG-conjugated beads. To perform mass spectrometry analysis, we used at least 6 x 108 cells to map post-translational modification sites through Thermo EASY-nLC 1200 at the Proteomics Core of University of Massachusetts Boston","fileCount":"10","fileSizeKB":"2587281","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo EASY-nLC 1200","modification":"UNIMOD:34 - \\\"Methylation.\\\"","keywords":"FOXA2","pi":[{"name":"Changmeng Cai","email":"changmeng.cai@umb.edu","institution":"UMASS Boston","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052273","task":"1aace6c5bd344725b19d2e79f06eacc2","id":"2522"}, {"dataset":"MSV000094771","datasetNum":"94771","title":"Secretome Proteomic Analysis of GN11 Cells","user":"stweintraub","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715806651000","created":"May. 15, 2024, 1:57 PM","description":"Proteins secreted in the conditioned medium of mouse GN11 GnRH neuronal cells were analyzed by mass spectrometry","fileCount":"20","fileSizeKB":"4454240","spectra":"0","psms":"84361","peptides":"44861","variants":"54967","proteins":"19491","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"LTQ Orbitrap Velos Pro","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"GnRH neuron; secretome;proteomics","pi":[{"name":"Yuzuru Shiio, M.D., Ph.D.","email":"shiio@uthscsa.edu","institution":"Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio","country":"U.S.A."}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052271","task":"6cd02ca071bf4b35a310e51ae2c367ad","id":"2523"}, {"dataset":"MSV000094770","datasetNum":"94770","title":"GNPS - Dissolved lipidomes of three Chaetoceros diatom host virus systems","user":"edwardsbr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715805367000","created":"May. 15, 2024, 1:36 PM","description":"Dissolved lipidomes from three diatom host-virus pairs. At each time point (T=0, 1, 3, 4, and 21 days), ~20 mL of 0.2 um filtered sample was extracted using Waters HLB SPE cartridges. In 2016, the samples were run on a Q Exactive mass spec with all ion fragmentation. This data was used for quantification. In 2021, the samples were rerun on an Orbitrap ID-X with targeted ms2 for further annotation of putative oxylipins. Methods and interpretation of the oxylipin and free fatty acid data are presented in: Edwards, B.R.; Thamatrakoln, K.; Fredricks, H.F.; Bidle, K.D.; Van Mooy, B.A.S. Viral Infection Leads to a Unique Suite of Allelopathic Chemical Signals in Three Diatom Host Virus Pairs. Mar. Drugs 2024, 22, x. https:\/\/doi.org\/10.3390\/xxxxx\r\n","fileCount":"140","fileSizeKB":"7386276","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Chaetoceros socialis (NCBITaxon:163503);Chaetoceros socialis forma radians RNA virus 1 (NCBITaxon:2169725);Chaetoceros tenuissimus (NCBITaxon:426638);Chaetoceros tenuissimus DNA virus type-II (NCBITaxon:1516127);Chaetoceros tenuissimus RNA virus type-II (NCBITaxon:1516128)","instrument":"Exactive;Orbitrap ID-X","modification":"normalized to volume filtered;normalized to recovery of the internal standard","keywords":"oxylipins;LOFA;NVO;PUFA;lipidome;dissolved organic matter;DOM;SPE;orbitrap;diatom;diatom virus;phytoplankton;phytoplankton virus;stress;chemical signal","pi":[{"name":"Bethanie R Edwards","email":"bethanie_edwards@berkeley.edu","institution":"University of California, Berkeley","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"82e6ba9472cf4b8380fcf5f07103fcdf","id":"2524"}, {"dataset":"MSV000094769","datasetNum":"94769","title":"GNPS - LC-MS2 and BGC paired data from actinomycetes","user":"ACumsille","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715795944000","created":"May. 15, 2024, 10:59 AM","description":"Paired genomics (.fasta) and metabolomics (.mzML) from 320 actinomycetes strains ","fileCount":"4192","fileSizeKB":"157579790","spectra":"1041694","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinobacteria (NCBITaxon:1760)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Natural products;Actinobacteria;Streptomyces","pi":[{"name":"Andres Mauricio Caraballo Rodriguez","email":"amcaraballor@gmail.com","institution":"UCSD","country":"United States"},{"name":"Hosein Mohimani","email":"hoseinm@andrew.cmu.edu","institution":"Carnegie Mellon University","country":"United States of America"},{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f7e7bbedcca7492996f54a2debcea079","id":"2525"}, {"dataset":"MSV000094763","datasetNum":"94763","title":"GNPS - Metabolite release by marine nitrifiers","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715752319000","created":"May. 14, 2024, 10:51 PM","description":"Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the endo- and exometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death\/lysis. While both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, in particular glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcription patterns of nitrifiers grown axenically to those in co-culture. Particularly, B vitamins exhibited dynamic production and consumption patterns in co-cultures, including a higher release of pantothenic acid (vitamin B5) in both co-culture systems, and increased amounts of riboflavin (vitamin B2) and the vitamin B12 ligand dimethylbenzimidazole in co-cultures with N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely consumed the vitamin B7 precursor dethiobiotin in co-culture with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001318) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"614","fileSizeKB":"45837930","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nitrosopumilus adriaticus CCS1; Nitrospina gracilis Nb-211","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"chemoautotroph-heterotroph interactions","pi":[{"name":"Alyson Santoro","email":"asantoro@ucsb.edu","institution":"University of California Santa Barbara","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8e78dd9c93584d60a4c101c7e3b2d89c","id":"2526"}, {"dataset":"MSV000094762","datasetNum":"94762","title":"Characterization of engineered sorghum with reduced S-adenosyl-L-methionine (AdoMet) levels","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715752100000","created":"May. 14, 2024, 10:48 PM","description":"Lignin accumulates progressively in cell walls during plant development, therefore, we are interested in analyzing the transcriptome and metabolome of engineered sorghum lines at three developmental stages. Results from these analyses will help to understand the metabolic changes (if any) besides lignin synthesis in transgenics and anticipate plants' physiological responses during growth under natural environment in future field trials.\r\n\r\nThis project will analyze the transcriptome and metabolome in stems of low-lignin sorghum transgenic lines compared to wild-type (WT) control.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60008680) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"290","fileSizeKB":"25433381","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sorghum bicolor 'Wheatland'","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sorghum;lignin","pi":[{"name":"Aymerick Eudes","email":"ageudes@lbl.gov","institution":"JBEI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5b51c6f18a754447bb73c5dcdf51dc79","id":"2527"}, {"dataset":"MSV000094761","datasetNum":"94761","title":"Label-free quantitative data dependent (DDA) and independent (DIA) analysis of the I-Ab-MHCII peptidomes eluted from cervical and mesenteric dendritic cells (DCs) of B6 mice. ","user":"oriongalaxy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715746582000","created":"May. 14, 2024, 9:16 PM","description":"In Dendritic cells (DC), the MHC II eluted immunopeptidome reflects the antigenic composition of the microenvironment. Proteins are transported and processed into peptides in endosomal MHC II compartments through autophagy or phagocytosis; extracellular peptides can also directly bind MHC II proteins at the cell surface. Altogether, these mechanisms allow DC to sample both the intra and extracellular environment. To understand the contribution of the lymph proteome to the MHC-II immunopeptidome we eluted I-Ab complexes from DCs harvested from the deep cervical or mesenteric nodes and investigated whether the I-Ab presented peptidome reflects the anatomical distribution of the proteomes carried by the lymph collected from the same anatomical districts. Heatmap representation and cluster analysis indicated differences among the two immunopeptidome. Similarly, regression analysis showed a much higher regression coefficient among MHC II immunopeptidomes eluted from the same anatomical district (r=0.699) as compared to the one eluted from the two different anatomical districts (deep cervical, average r = 0.877 and mesenteric, average r = 0.937). Overall, all analyzed peptides displayed the expected I-Ab binding motives, binding affinity and expected range of peptide length. A combination of data dependent (DDA) and data independent (DIA) analysis indicated that around 36% of the eluted peptides were shared by both the cervical and mesenteric lymph nodes. The rest of the eluted peptides were distinct to each lymph node reflecting the qualitatively different proteome associated with each of the two anatomical districts: peptides unique to the cervical lymph nodes displayed many proteins known to be enriched in brain tissue, whereas those unique to mesenteric lymph nodes were enriched in mesenteric organ proteins. As such, the quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in distinct anatomical districts.","fileCount":"44","fileSizeKB":"10271183","spectra":"0","psms":"44284","peptides":"8108","variants":"14881","proteins":"1173","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion;Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"mouse MHCII I-Ab immunopeptidome; LC\/MS\/MS DDA and DIA","pi":[{"name":"Cristina Clement","email":"ccc4002@med.cornell.edu","institution":"Weill Cornell Medicine College","country":"United States"},{"name":"Laura Santambrogio","email":"las4011@med.cornell.edu","institution":"Weill Cornell Medicine College","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052267","task":"08a967bb642d4085b5e2ee5ab69a68df","id":"2528"}, {"dataset":"MSV000094760","datasetNum":"94760","title":"GNPS - Plasmalogen oxidation induces the generation of excited molecules and electrophilic lipid species","user":"miyamoto_lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715731238000","created":"May. 14, 2024, 5:00 PM","description":"Raw files of LC-MS analysis of plasmalogen photooxidation products. Data were acquired in data-dependent mode using the lipidomic analysis method described in PMID: 31406145.","fileCount":"133","fileSizeKB":"45583291","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not applicable","instrument":"TripleTOF 6600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Phospholipid, plasmalogen, photooxidation, singlet oxygen","pi":[{"name":"Sayuri Miyamoto","email":"miyamoto@iq.usp.br","institution":"Institute of Chemistry, University of Sao Paulo","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"45c68319cb41454db207f2bd985cc4d9","id":"2529"}, {"dataset":"MSV000094757","datasetNum":"94757","title":"GNPS - The influence of APOE4 on the pTau interactome in sporadic Alzheimers disease","user":"Trixi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715724010000","created":"May. 14, 2024, 3:00 PM","description":"APOE4 is the major genetic risk factor for sporadic Alzheimers disease (AD). Although APOE4 is well known to promote Abeta pathology, recent data also support an effect of APOE polymorphism on phosphorylated Tau (pTau) pathology. To elucidate these potential effects, the pTau interactome was analyzed across APOE genotypes in the frontal cortex of 10 advanced AD cases (n=5 APOE3 and n=5 APOE4), using a combination of anti-pTau PHF1 (pS396\/pS404) immunoprecipitation and mass spectrometry. This proteomic approach was complemented by a neuropathological analysis of anti-pTau PHF1 and anti-Abeta 4G8 immunohistochemistry, performed in the frontal cortex of 21 advanced AD cases (n=11 APOE3 and n=10 APOE4). Our dataset includes 1130 and 1330 proteins enriched in IPPHF1 samples from APOE3 and APOE4 groups (FC over 1.50, IPPHF1 versus IPIgG ctrl). We identified 80 and 68 proteins as strong pTau interactors in APOE3 and APOE4 groups, respectively (SAINT score above 0.80; FDR under 5%). A total of 47\/80 proteins were identified as strong pTau interactors only for APOE3 cases. Functional enrichment analyses showed that they were significantly associated with the nucleoplasm compartment and involved in RNA processing. In contrast, 35\/68 proteins were identified as strong pTau interactors only for APOE4 cases. They were significantly associated with the synaptic compartment and involved in cellular transport. A comprehensive characterization of Tau pathology in the frontal cortex showed a higher density of plaque-associated neuritic crowns, made of dystrophic axons and synapses, in APOE4 carriers. Cerebral amyloid angiopathy was more frequent and severe in APOE4 cases. Our study supports an influence of APOE genotype on pTau subcellular location in the human brain. These results are consistent with a facilitation of pTau progression to Abeta-affected brain regions of APOE4 carriers, paving the way to the identification of potential new therapeutic targets. This entry contains the mass spectrometric raw files for the immune purifications. ","fileCount":"21","fileSizeKB":"12879036","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Alzheimer's Disease;phosphorylated Tau;ApoE genotype;immuno purification","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyulangone.org","institution":"NYU School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052263","task":"a0c878e5b1274006bbca340b7fb4d9b3","id":"2530"}, {"dataset":"MSV000094756","datasetNum":"94756","title":"GNPS - CROT deficiency in mice leads to an increase of omega-3 fatty acids","user":"SASINGH","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715720855000","created":"May. 14, 2024, 2:07 PM","description":"Background \r\nCarnitine O-octanoyltransferase (CROT) is a well-established peroxisomal enzyme involved in liver fatty acid oxidation, but less is known about its recently discovered role in promoting vascular calcification, and whether CROT-dependent liver metabolism contributes to the latter. To date, CROT function in the context of calcification potential has been conducted in the dyslipidemic low-density lipoprotein receptor-deficient (Ldlr-\/-) mice.\r\n\r\nMethods and Results \r\nTo differentiate peroxisome and CROT-dependent lipid biology from that of lipoprotein-mediated lipid biology, we therefore conducted a metabolomic analysis of the liver and plasma of normolipidemic CROT-deficient (Crot-\/-) mice. We performed LC-MS-based metabolomics on liver and plasma derived from Crot-\/- and Crot+\/- mice and sibling Crot+\/+ mice, using a dual-phase metabolite extraction protocol, and multiple LC-MS acquisition strategies. We identified between 79 to 453 annotated metabolites from liver samples, and 117 to 424 annotated metabolites from plasma samples. Through differential abundance analysis, we determined that omega-3 fatty acids such as EPA, DPA, and DHA were higher in the liver of Crot-\/- and Crot+\/- mice than Crot+\/+ mice. EPA were higher in plasma of Crot-\/- mice than Crot+\/+ mice. We also determined that the anti-inflammatory dicarboxylic acids, tetradecanedioic acid and azelaic acid, were higher in the plasma of CROT-deficient mice. \r\n\r\nConclusions\r\nOur study associated genetic CROT deletion with increased levels of anti-inflammatory molecules in mouse liver and plasma. These results suggest a potential mechanism for anti-calcification effects of CROT suppression and the potential use of omega-3 fatty acids as biomarkers for future CROT inhibition therapies. \r\n","fileCount":"1511","fileSizeKB":"278319347","spectra":"1216931","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fatty acids;Metabolomics","pi":[{"name":"SASHA A SINGH","email":"SASINGH@BWH.HARVARD.EDU","institution":"BRIGHAM AND WOMEN'S HOSPITAL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dd04ba19dc004668ac64fd296f335669","id":"2531"}, {"dataset":"MSV000094754","datasetNum":"94754","title":"YjbH contributes to S. aureus skin pathology and immune response through Agr-mediated alpha-toxin regulation","user":"KUMC_Prot","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715701561000","created":"May. 14, 2024, 8:46 AM","description":"Staphylococcus aureus is a global health threat that can cause a multitude of diseases in many different areas of the body and is the leading cause of skin infections. This bacterium can produce a variety of proteins that contribute to virulence and disease progression. These virulence factors include alpha-hemolysin (Hla), which can kill many different cell types in the human body. In this study, we identified a new protein that contributes to Hla production, YjbH. It does so by controlling the activity of the Accessory Gene Regulator (Agr), a major player in the modulation of proteins produced in the bacterium. We demonstrate that without YjbH, S. aureus cultures produce less Hla, and this is corroborated during infection. Accordingly, when YjbH is present, tissue damage is greater during infection than when it is absent. Overall, our study sheds light on the complex regulation involved in virulence factor production by S. aureus and its ability to cause a wide range of diseases. ","fileCount":"21","fileSizeKB":"64732723","spectra":"0","psms":"82719","peptides":"856","variants":"1107","proteins":"173","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus aureus subsp. aureus USA300 (NCBITaxon:367830)","instrument":"Orbitrap Ascend","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"YjbH;alpha-toxin regulatioin","pi":[{"name":"Jeffrey L. Bose","email":"jbose@kumc.edu","institution":"University of Kansas Medical Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052262","task":"27c679eafc494f2796bcf3e65bc0319f","id":"2532"}, {"dataset":"MSV000094753","datasetNum":"94753","title":"YjbH contributes to S. aureus skin pathology and immune response through Agr-mediated alpha-toxin regulation","user":"KUMC_Prot","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715699016000","created":"May. 14, 2024, 8:03 AM","description":"Staphylococcus aureus is a global health threat that can cause a multitude of diseases in many different areas of the body and is the leading cause of skin infections. This bacterium can produce a variety of proteins that contribute to virulence and disease progression. These virulence factors include alpha-hemolysin (Hla), which can kill many different cell types in the human body. In this study, we identified a new protein that contributes to Hla production, YjbH. It does so by controlling the activity of the Accessory Gene Regulator (Agr), a major player in the modulation of proteins produced in the bacterium. We demonstrate that without YjbH, S. aureus cultures produce less Hla, and this is corroborated during infection. Accordingly, when YjbH is present, tissue damage is greater during infection than when it is absent. Overall, our study sheds light on the complex regulation involved in virulence factor production by S. aureus and its ability to cause a wide range of diseases. ","fileCount":"21","fileSizeKB":"64732724","spectra":"0","psms":"82719","peptides":"856","variants":"1107","proteins":"173","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus aureus subsp. aureus USA300 (NCBITaxon:367830)","instrument":"Orbitrap Ascend","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"YjbH;alpha-toxin regulation","pi":[{"name":"Jeffrey L. Bose","email":"jbose@kumc.edu","institution":"University of Kansas Medical Center","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052261","task":"389c4525d1054c6ea420a5e98cbb78f3","id":"2533"}, {"dataset":"MSV000094752","datasetNum":"94752","title":"Metabolite profile at single-embryo level of 0 to 3h old Drosophila embryos","user":"jperezmojica","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715682828000","created":"May. 14, 2024, 3:33 AM","description":"We used single-embryo metabolomics to characterize early developmental metabolism in Drosophila. We employed a multi-omics approach where samples were collected, homogenized in 80% methanol and the soluble fraction recover to perform targeted metabolomic whle RNA-seq was performed on the insoluble fraction to accurately stage each embryo. Then, this RNA-based staging was used to place single embryo metabolomes across the developmental trajectory. Thus, we are able to construct a highly detailed metabolomic map of embryonic development. Importantly, we validated our single-embryo metabolomics results in pools of 10 embryos. The data provide a continuous timeline of metabolite levels (and gene expression) during early development (0-3 hours) in Drosophila melanogaster. We used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males\/DGRP_352, females\/DGRP_737). RNA-seq data related to this dataset can be accessed at GEO under accession number GSE263568.","fileCount":"36544","fileSizeKB":"15784404","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"6470A Triple Quadrupole LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Development;Embryo metabolism;Maternal to zygotic transition;Single-cell multi-'omics","pi":[{"name":"Adelheid Lempradl","email":"Heidi.Lempradl@vai.org","institution":"Van Andel Institute","country":"United States of America"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"14bd442c7cd5428ead099ad2cdda7f41","id":"2534"}, {"dataset":"MSV000094749","datasetNum":"94749","title":"GNPS - Mass Spectrometry-Based Metabolomics for Siderophore Discovery","user":"marquisyazzie","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715629499000","created":"May. 13, 2024, 12:44 PM","description":"This dataset contains data-dependent aquisition .raw files, converted .mzML files, and mzmine feature finding results of lab standard of deferoxamine iron and water infusion. Method is outlined in Mass Spectrometry-Based Metabolomics for Siderophore Discovery manuscript. Feature finding was conducted in mzmine version 3.9.0.","fileCount":"15","fileSizeKB":"739320","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lab Standard","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Siderophore","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0a8c055768174473922c0eca8d6c384e","id":"2535"}, {"dataset":"MSV000094747","datasetNum":"94747","title":"Human Secretome Dependence on the Signal Recognition Particle","user":"stweintraub","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715623782000","created":"May. 13, 2024, 11:09 AM","description":"The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting secretory and membrane proteins to the endoplasmic reticulum (ER). SRP co-translationally recognizes secretory proteins via N-terminal signal sequences. SRP-independent protein targeting is also known. When SRP is not able to recognize signal peptides of SRP-dependent proteins (due to mutations, for instance), they do not become SRP-independent; instead, their mRNAs are degraded in the protein quality control RAPP. However, which proteins are SRP-dependent and SRP-independent, especially in mammals, is not known yet. In this work, we answer this fundamental question by mass spec and whole proteome analysis in SRP54 depleted human cells and medium. The analysis shows that the majority of secretory proteins in the medium have lower abundance, demonstrating their SRP dependence. Moreover, we identified new SRP-independent proteins as well. Surprisingly, detailed examination did not elucidate obvious differences of the SRP-dependent and SRP-independent proteins, suggesting other factors regulate this process. We also detect changes in the abundance of proteins that may be involved in the RAPP mechanism and in stress that is associated with defective SRP. Our study demonstrates the complexity of molecular mechanisms of protein sorting and quality control in human cells.","fileCount":"31","fileSizeKB":"20400358","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"secretome;signal recognition particle (SRP);signal peptide;protein targeting;protein transport;proteomics;secretory pathway","pi":[{"name":"Andrey L. Karamyshev, Ph.D.","email":"andrey.karamyshev@ttuhsc.edu","institution":"Texas Tech University Health Sciences Center","country":"U.S.A."}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052230","task":"5b634e186b734b67b435e3a900a2f1e6","id":"2536"}, {"dataset":"MSV000094744","datasetNum":"94744","title":"GNPS - Nose microbiota cultivated in a bioreactor under pre-established conditions ","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715601689000","created":"May. 13, 2024, 5:01 AM","description":"Non-targeted metabolomics of nose microbiota cultivated in a bioreactor under controlled conditions ","fileCount":"45","fileSizeKB":"6002103","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Microbiota (NCBITaxon:13613)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"nose;microbial community","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d2f147fcbdf9489286c4f53721a822e0","id":"2537"}, {"dataset":"MSV000094742","datasetNum":"94742","title":"Gauron_PKC_timsTOFPro2_P124_VS16","user":"LTRI_proteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715599766000","created":"May. 13, 2024, 4:29 AM","description":"This dataset consists of 12 raw MS files and associated peak lists and results files, acquired on a Bruker timsTOF Pro 2 operated in Data Dependent Acquisition mode. \nSamples were generated by Celeste Gauron. Affinity purification was performed by Laura McGary. Mass spectrometry acquisition was performed by Laura McGary. Analysis was performed by Celeste Gauron, Laura McGary, and Alexandra Newton. \nThe files are associated with a manuscript submitted for publication by Celeste Gauron et al. The main goal of this dataset was to identify aberrant signaling mechanisms of a missense mutation in protein kinase C eta (PRKCH gene), found to be associated with families affected by Alzheimers disease. \nRudolph Tanzi (tanzi@helix.mgh.harvard.edu) and Alexandra Newton (anewton@health.ucsd.edu) are the corresponding authors of the manuscript; Karen Colwill should be contacted for questions on this dataset (colwill@lunenfeld.ca)\n","fileCount":"517","fileSizeKB":"22884570","spectra":"0","psms":"374837","peptides":"35622","variants":"40797","proteins":"4848","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Proximity-dependent biotinylation;PRKCH;Alzheimer's disease","pi":[{"name":"Karen Colwill","email":"colwill@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052210","task":"5ab2a63937c04247b7714e09e9990e03","id":"2538"}, {"dataset":"MSV000094739","datasetNum":"94739","title":"GNPS_CMMC_KV_6_decarboxylated_amino_acids_with_various_chlorides","user":"kyvittali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715372851000","created":"May. 10, 2024, 1:27 PM","description":"MS\/MS fragmentation data of various amines with C2,3,5,7,8,9,10 chlorides acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\n","fileCount":"3","fileSizeKB":"98999","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"N-acyl lipids;amino acids","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e581a59442ca429780a6398a0fa268ba","id":"2539"}, {"dataset":"MSV000094738","datasetNum":"94738","title":"GNPS - Lipidomics of homeoviscous adaptation to low temperatures in Staphylococcus aureus utilizing exogenous straight-chain unsaturated fatty acids over biosynthesized endogenous branched-chain fatty acids","user":"kmhines5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715371627000","created":"May. 10, 2024, 1:07 PM","description":"It is well established that Staphylococcus aureus can incorporate exogenous straight-chain unsaturated fatty acids (SCUFAs) into membrane phospho- and glyco-lipids from various sources in supplemented culture media, and when growing in vivo in an infection. Given the enhancement of membrane fluidity when oleic acid (C18:1(9z)) is incorporated into lipids, we were prompted to examine the effect of medium supplementation with C18:1(9z) on growth at low temperatures. C18:1(9z) supported the growth of a cold-sensitive, branched-chain fatty acid (BCFA)-deficient mutant at 12C. Interestingly, we found similar results in the BCFA-sufficient parental strain. We show that incorporation of C18:1(9z) and its elongation product C20:1(9z) into membrane lipids was required for growth stimulation and relied on a functional FakAB incorporation system. Lipidomics analysis of the phosphatidylglycerol (PG) and diglycosyldiacylglycerol (DGDG) lipid classes revealed major impacts of C18:1(9z) and temperature on lipid species. Growth at 12C in the presence of C18:1(9z) also led to increased production of the carotenoid pigment staphyloxanthin; however, this was not an obligatory requirement for cold adaptation. Enhancement of growth by C18:1(9z) is an example of homeoviscous adaptation to low temperatures utilizing an exogenous fatty acid. This may be significant in the growth of S. aureus at low temperatures in foods that commonly contain C18:1(9z) and other SCUFAs in various forms.","fileCount":"628","fileSizeKB":"23548025","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Staphylococcus aureus (NCBITaxon:1280)","instrument":"Synapt XS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipids, lipidomics, staphylococcus aureus, oleic acid, low temperature","pi":[{"name":"Brian J. Wilkinson","email":"bjwilkin@ilstu.edu","institution":"Illinois State University","country":"USA"},{"name":"Kelly M. Hines","email":"kelly.hines@uga.edu","institution":"University of Georgia","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2fb2889dbaf04208b694056836905eba","id":"2540"}, {"dataset":"MSV000094736","datasetNum":"94736","title":"Targeting ERAP enhances anti-tumor immunity by disrupting the NKG2A\/HLA-E inhibitory checkpoint","user":"clauser","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715352536000","created":"May. 10, 2024, 7:48 AM","description":"Tsao H, Anderson S, Finn KJ, Perera J, Pass LF, Schneider EM, Jiang A, Fetterman R, Chuong CL, Kozuma K, Stickler MM, Creixell M, Klaeger S, Phulphagar KM, Rachimi S, Verzani EK, Olsson N, Dubrot J, Pech MF, Silkworth W, Lane-Reticker SK, Allen PM, Ibrahim K, Knudsen NH, Cheng AY, Long AH, Ebrahimi-Nik H, Kim SY, Du PP, Iracheta-Vellve A, Robitschek EJ, Suermondt JSMT, Davis TGR, Wolfe CH, Atluri T, Olander KE, Rush JS, Sundberg TB, McAllister FE, Abelin JG, Firestone A, Stokoe D, Carr SA, Harding FA, Yates KB, Manguso RT. 2024\nNew targets that enhance anti-tumor immunity must be identified to improve the efficacy of cancer immunotherapy. Here we show that loss of endoplasmic reticulum aminopeptidase (ERAP) family proteins improves anti-tumor immunity and synergizes with immune checkpoint blockade. Mechanistically, we show that loss of ERAP inactivates the HLA-E\/NKG2A checkpoint, which normally restrains tumor killing by both CD8+ T cells and NK cells. The inhibitory activity of HLA-E is dependent on its presentation of a restricted set of invariant epitopes which form the binding surface for the NKG2A\/CD94 receptor complex. Using genetic screening, in vivo models, cell-based assays, and immunopeptidomics, we show that loss of ERAP activity prevents the processing of these invariant peptides and alters the presented peptidome of both HLA-E and classical MHC-I. HLA-E neo-peptides presented after ERAP deletion are unable to bind the NKG2A\/CD94 receptor, rendering tumor cells highly susceptible to killing by NKG2A+ cytotoxic T and NK cells. Thus, loss of ERAP phenocopies the loss or inhibition of the HLA-E\/NKG2A pathway and represents an attractive therapeutic approach to inhibit this critical checkpoint. More broadly, this work identifies ERAP1\/2 as druggable intracellular enzymes that could be targeted using small molecules to inactivate a cell-surface inhibitory pathway and represents a novel approach to therapeutic modulation of immune responses.\n\n","fileCount":"26","fileSizeKB":"1841633","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"K-TMT11;C-carbamidomethylation;M-oxidation;N-deamidation;Q-pyro-glutamic acid","keywords":"ERAP;TMT11;immunopeptidomics;HLA-I","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052175","task":"444eafdacfa24e959736e11ec3bf5c1f","id":"2541"}, {"dataset":"MSV000094733","datasetNum":"94733","title":"A CRISPR-Cas13d screen uncovers Bckdk as a regulator of the maternal-to-zygotic transition in teleosts","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715309708000","created":"May. 9, 2024, 7:55 PM","description":"Samples were reduced by 5mM TECP at rt for 30min and carboxymethylated by 10mM 2-chloroacetamide for 30min in dark at rt. Pre-chilled acetone was added to precipitate proteins overnight. The precipitated proteins were collected and dissolved in 100ul of 50mM TEAB, MS grade trypsin (Promega Gold) was added at 1:40 w\/w at 37C overnight. Peptide amounts were measured by fluorometric peptide assay (Pierce). \n20ul of anhydrous acetonitrile (ACN) were added into each 0.5mg TMTpro 16plex reagents (Thermo Scientific). For each sample, 20ug peptides were added into TMT vials. The 4 replicate samples for the WT non-injection, WT cas13-injection, BCKDK cas13-injection, were labeled with TMTpro respectively. The 12 differentially labeled samples were combined and concentrated by SpeedVac concentrator (Savant) to less than 10ul.\nHigh-Select Fe-NTA Phosphopeptide Enrichment Kit (Thermo Scientific) was used for phosphopeptide enrichment. Lyophilized TMT labeled peptides were suspended in 200ul of binding buffer and loaded onto equilibrated Fe-NTA spin column. After 30min incubation, the supernatant was collected through centrifugation. Phosphopeptides were eluted by 100ul of elution buffer. Both supernatant and eluate were dried immediately to less than 10ul. \nThe dried supernatant TMT-labeled peptide mixture was resuspended in 300ul of 0.1% trifluoroacetic acid (TFA) and loaded onto the high pH fractionation cartridge (Pierce). 8 hpH RP fractions were collected by sequential elution using 300ul of 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 50% in 0.1% TFA. The solvents were evaporated to dryness using SpeedVac. Dried samples were resolubilized in buffer A (5% ACN in 0.1% formic acid, FA) before LC-MS analysis.\nTMT-labeled peptides were analyzed on Orbitrap Eclipse Tribrid Mass Spectrometer (Thermo Scientific) with a FAIMS Pro interface, coupled to a Dionex UltiMate 3000 RSCLnano System. Peptides (hpH RP fraction) were loaded on an Acclaim PepMap 100 C18 trap cartridge. A 75 um i.d. analytical capillary column was packed in-house with 250mm of 1.9um ReproSil-Pur C18-AQ resin (Dr. Masch). The organic solvent solutions were H2O:ACN:FA at 95:5:0.1 (v:v:v) for buffer A (pH 2.6) and 20:80:0.1 for buffer B. The chromatography gradient was a 30min equilibration step in 2%B; a 5-min ramp to reach 10%B; 90min from 10% to 40%B; 10min to reach 90%B; a 5min wash at 90%B; 0.1min to 2%B; followed by a 15min column re-equilibration step in 2%B. The nano pump flow rate was set to 0.180ul\/min. \nThe Orbitrap Eclipse was set up to run the TMT-SPS-MS3 method with three FAIMS. Briefly, peptides were scanned from 400-1600 m\/z in the Orbitrap at 120K and fragmented by CID at 35% and detected in ion trap. The supernatant from phosphorylation peptide enrichment was analyzed with real time search (RTS). During data acquisition, ddMS2 spectra was searched against a non-redundant Danio rerio sequence database (UniProt 2021-03) with common contaminants. Carbamidomethyl (C) and TMTpro16plex (Kn) were searched statically, while oxidation (M) was searched as a variable modification. TMT reporter ions were detected by MS3. \nThe MS dataset was processed using Proteome Discoverer 2.4 (Thermo Fisher Scientific). MS\/MS spectra were searched against a Danio rerio protein database with common contaminants. SEQUEST-HT implemented through PD was set up as: precursor ion mass tolerance 10 ppm, fragment mass tolerance 0.6 Dalton, up to two missed cleavage sites, static modification of C(+57.021), and K and peptide N-termini with TMT tag(+304.2071) and dynamic oxidation of M(+15.995), and phosphorylation of S, T, Y(+79.9663). \nLeucine and isoleucine (Sigma-Aldrich), 13C6-Leucine (Cambridge Isotopes) and samples were derivatized by dansyl chloride (Sigma-Aldrich). Dried samples and amino acids standards were dissolved in pH9.5 250mM sodium bicarbonate buffer, dansyl chloride was added and incubated at room temperature for 1hr respectively. Derivatized 13C6-Leucine was spiked into derivatized Leucine respectively, as well as each derivatized sample before LC\/MS analysis.\nAmino acid samples were analyzed on a Q-Exactive Plus Mass Spectrometer (Thermo Scientific) equipped with a Nanospray Flex Ion Source and coupled to a Dionex UltiMate 3000 RSCLnano System. A 75um i.d. analytical capillary column was packed in-house with 100mm of 1.9um ReproSil-Pur C18-AQ resin (Dr. Masch). The UPLC solutions were 0.1% FA in H2O for buffer A and 0.1% FA in ACN for buffer B. The chromatography gradient as a 5min loading time at 20%B, 23min from 20% to 35%B; 2min to reach 100%B; and 10min washing at 100%B. The nano pump flow rate was set to 0.5ul\/min. The Q-Exactive was set up to run PRM method with inclusion list as 371.1736 m\/z and 365.1535 m\/z. Each standard curve concentration points and each sample were analyzed in triplicates. The peak area ratio between leucine and 13C6-leucine was used to quantify the leucine amount in each sample. ","fileCount":"30","fileSizeKB":"24560729","spectra":"0","psms":"81716","peptides":"27008","variants":"34231","proteins":"5436","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Orbitrap Eclipse","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"TMTpro;phosphorylation","pi":[{"name":"Laurence Florens","email":"proteomicslab@stowers.org","institution":"Stowers Institute for Medical Research","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD052161","task":"d61b266ecc734e239f376f88533ec309","id":"2542"}, {"dataset":"MSV000094730","datasetNum":"94730","title":"Top-Down Proteomics of Malayan Pitviper Venom","user":"daniel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715286975000","created":"May. 9, 2024, 1:36 PM","description":"LC-MS\/MS based Top-Down Proteomics of reduced and native venom from juvenile and adult Malayan Pitviper specimens. ","fileCount":"13","fileSizeKB":"3031683","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Calloselasma rhodostoma (NCBITaxon:8717)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Malayan pit viper;Top-down venomics;top-down proteomics;venom","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052152","task":"1f88ff73e1e94c11b3606f9fb68c017c","id":"2543"}, {"dataset":"MSV000094724","datasetNum":"94724","title":"DATASET - Mass Spectrometry - Snake venom proteomics of three subspecies of the North African mountain viper (Vipera monticola, Saint-Girons 1954) from Morocco","user":"MDamm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715261512000","created":"May. 9, 2024, 6:31 AM","description":"This DATASET collection includes the mass spectrometry files for proteomics venom investigation of three subspecies of the North African mountain viper (Vipera monticola, Saint-Girons 1954) from Morocco.\n\nSpecies list:\n1. Vipera monticola monticola\n2. Vipera monticola atlantica\n3. Vipera monticola saintgironsi\n\nFolders 01-03 - BOTTOM-UP PROTEOMICS: The venom pools were investigated by the bottom-up \"snake venomics\" (labled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o\/n tryptic digested. Samples submitted to HPLC-MS\/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS\/MS analytic w\/o further gel procession. Folders 01 to 03 include the MS and MS\/MS spectra of the snake species 1-3, respectively. Files are included as RAW and MZML format.\n\nUsed instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 x 150 mm; 5 um particle size) column.\n\nModifications: UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"\n\nUsed protein database: Uniprot_8570_serpentes_reviewed_CandIso_2747_entries_230398.fasta","fileCount":"838","fileSizeKB":"16031044","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vipera monticola (NCBITaxon:1588684);Vipera monticola monticola;Vipera monticola atlantica;Vipera monticola saintgironsi","instrument":"LTQ Orbitrap XL","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"snake venomics;venom ;snake ;viper ;snakebite;proteomics;morocco","pi":[{"name":"Maik Damm","email":"maik.damm@outlook.de","institution":"JLU Giessen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c23a9c34b5604d8aafcd19f3c59c4ed5","id":"2544"}, {"dataset":"MSV000094721","datasetNum":"94721","title":"GNPS_CMMC_KV-5_20AminoAcids_with_C2,3,4,8","user":"kyvittali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715227373000","created":"May. 8, 2024, 9:02 PM","description":"MS\/MS fragmentation data of C2,3,4,8 conjugated with the 20 proteinogenic amino acids acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\n","fileCount":"3","fileSizeKB":"140878","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"N-acyl lipids;Amino Acids","pi":[{"name":" Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a28eed9616e94d0abe6fbfdf8e49c4dd","id":"2545"}, {"dataset":"MSV000094718","datasetNum":"94718","title":"GNPS - Vendor-dependent mobile phase contaminants affect neutral lipid analysis in lipidomics protocols","user":"joshuaroberts","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715201230000","created":"May. 8, 2024, 1:47 PM","description":"The same sample of bovine liver extract analyzed using a mobile phase with solvents purchased from different vendors. LC-MS grade water was purchased from Sigma, methanol and isopropanol are purchased from Sigma, Honeywell and Fisher Scientific. Vendor names are randomized and only listed as vendors 1, 2 and 3 in the filenames for confidentiality. The raw data is used in the following preprint: \"Vendor-dependent mobile phase contaminants affect neutral lipid analysis in lipidomics protocols\" (DOI 10.26434\/chemrxiv-2024-r67fv) ","fileCount":"94","fileSizeKB":"7068162","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913)","instrument":"6546 Q-TOF LC\\\/MS Agilent","modification":"Not Applicable","keywords":"Liver;Lipidomics;Vendor;Solvent;Mobile Phase","pi":[{"name":"Jeffrey C. Smith","email":"jeffcsmith@cunet.carleton.ca","institution":"Carleton University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"69694220719343aca0a57a03f09f9516","id":"2546"}, {"dataset":"MSV000094717","datasetNum":"94717","title":"GNPS Human AKR1C3 Binds Agonists of GPR84 and Participates in an Expanded Polyamine Pathway","user":"ndudkina","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715195990000","created":"May. 8, 2024, 12:19 PM","description":"In vitro metabolomics with AKR1C3 and HEPG2 Metabolome \n\nFiles and corresponding conditions: \n\nC3only: Enzyme (AKR1C3) only condition with NADPH co-factor added \n\nWTmed: this is medium only control containing HEPG2 extract and NADPH. \n\nWTmed+C3: this is a no-cofactor control containing enzyme and HEPG2 extract. \n\nWTmed+C3+PH: this is all components together with enzyme, HEPG2 extract and NADPH co-factor. \n\nReversed-phase chromatography was performed with a Kinetex (Cat. # 00G-4601-E0) 5 um C18 100 A column (250 by 4.6 mm), using a water:acetonitrile gradient containing 0.1% formic acid at 0.7 mL\/min flow rate: 0-30 min, 10% to 100% acetonitrile. \nPositive mode (qTOF)","fileCount":"23","fileSizeKB":"1045794","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"HEPG2 Metabolome, AKR1C3 In Vitro Metabolomics with HEPG2 Metabolome ","pi":[{"name":"Jason Crawford","email":"jason.crawford@yale.edu","institution":"Yale University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7ac407b98d854632a04bae7025827e80","id":"2547"}, {"dataset":"MSV000094716","datasetNum":"94716","title":"GNPS MS Self Service Metabolomics Spring 2024 ","user":"cmboot","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715183948000","created":"May. 8, 2024, 8:59 AM","description":"a comparison of small molecules found in black and earl grey tea","fileCount":"17","fileSizeKB":"455204","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Camellia sinensis (NCBITaxon:4442)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolomics, black tea, earl grey tea","pi":[{"name":"Claudia Boot","email":"claudia.boot@colostate.edu","institution":"Colorado State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1aa1f6746c15482aa2bedbd8de444b9c","id":"2548"}, {"dataset":"MSV000094715","datasetNum":"94715","title":"Shared sequence features of diverse oncofusions promote gain-of-function RNA Pol II partitioning to drive gene activation","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715182731000","created":"May. 8, 2024, 8:38 AM","description":"Translocation renal cell carcinoma is a rare but aggressive cancer driven by oncogenic fusions between the DNA-binding transcription factor TFE3 and diverse subunits. We have found that these diverse fusions promote condensate formation and activation of target genes. To investigate what the condensates formed by different TFE3 fusions partition we used a cell-free method relying on condensate reconstitution within a nuclear extract. Using recombinant purified PRCC-TFE3 or ASPL-TFE3, we reconstituted condensates in a soluble nuclear extract. The extract was then fractionated by centrifugation into a supernatant and pellet. For each fusion supernatant and pellet fractions were collected in triplicate. Samples were individually labeled using a 6-plex tandem mass tag (TMT) post-tryptic isobaric labeling strategy and the three supernatant and three pellet fractions of each fusion were mixed and analyzed by LC-MS to provide quantitative measurements of partitioning. In summary, we deposit 2 TMT 6-plex samples which represent triplicates for each PRCC-TFE3 (1071162 F1-8) and ASPL-TFE3 (1069084 F1-8).\n\nTMT labels 126, 127, 128: Sup\nTMT labels 129, 130, 131: Pellet","fileCount":"33","fileSizeKB":"93530611","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"oncogenic fusion;translocation;tRCC;biomolecular condensates;intrinsically disordered regions;selective partitioning;IDR specificity","pi":[{"name":"Benjamin Sabari","email":"Benjamin.sabari@utsoutwhestern.edu","institution":"UT Southwestern Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"06293384fc63451a9eced15a6d9cb62f","id":"2549"}, {"dataset":"MSV000094712","datasetNum":"94712","title":"Triple acquisition mass spectrometry (TRAM) combining targeted and non-targeted metabolomics in a single run","user":"lisap","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715158971000","created":"May. 8, 2024, 2:02 AM","description":"Data was acquired in TRAM (DDA+MRM), DDA-only, and MRM-only mode on a ZenoTOF 7600 with alkaline HILIC separation. ","fileCount":"349","fileSizeKB":"19167252","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Metabolite Standards","instrument":"ZenoTOF 7600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;TRAM;DDA;MRM;HILIC; SRM 1950;human plasma;human cerebrospinal fluid; meningioma","pi":[{"name":"Gunda Koellensperger","email":"gunda.koellensperger@univie.ac.at","institution":"University of Vienna","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8bba834c1a444daaba85c9a20d6a5ffc","id":"2550"}, {"dataset":"MSV000094711","datasetNum":"94711","title":"Nannochloropsis oceanica red body proteome","user":"johanAR","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715153172000","created":"May. 8, 2024, 12:26 AM","description":"Datasets contains the raw datasets from the proteomics analysis of the N. oceanica red body. These were used to generate the spectral count data for identification and qualitative quantification of N. oceanica proteins in the Red body.\n\nRed body paper authored by: Christopher W. Gee, Johan Andersen-Ranberg , Ethan Boynton, Rachel Z. Rosen, Danielle Jorgens, Patricia Groba, Hoi-Ying N. Holmane, Krishna K. Niyogi","fileCount":"13","fileSizeKB":"1487055","spectra":"72092","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nannochloropsis oceanica CCMP1779","instrument":"Thermo-Fisher LTQ XL ;Agilent 1200 HPLC ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Red Body;Microalgae;Extracellular proteome","pi":[{"name":"Krishna Niyogi","email":"niyogi@berkeley.edu","institution":"UC Berkeley, Department of Plant and Microbial Biology","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052104","task":"b962b5057f0e43d98105f659588d5c7b","id":"2551"}, {"dataset":"MSV000094709","datasetNum":"94709","title":"Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics","user":"melihyilmaz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715142612000","created":"May. 7, 2024, 9:30 PM","description":"Ocean microbiome dataset published by [May2016] and the corresponding database search results. The LC-MS\/MS spectra are from triplicate acquisitions of peptides, acquisitions 51-53 from the Bering Strait (BSt) and acquisitions 45-47 from the Chukchi Sea (CS). For each sampling location, there are two sets of spectrum identifications: one based on a metapeptide database specific to the location (metapeptides_BSt and metapeptides_CS) and one based on a non-redundant environmental database (env_nr). Spectrum identifications were obtained with Tide and Percolator as described in [Yilmaz2023]. Casanovo predictions for this dataset are provided in MSV000093980, alongside Casanovo predictions for other datasets. ________________________________ PUBLICATIONS: [May2016] May, D. H. et al. \"An Alignment-Free Metapeptide Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.\" Journal of Proteome Research. 2016. [Yilmaz2023] Yilmaz, Melih et al. \"Sequence-to-sequence translation from mass spectra to peptides with a transformer model.\" Nature Communications. 2024. ________________________________ SPECTRUM FILES: The dataset contains the following six spectrum files, three from the Chukchi Sea (2016_Jan_12_QE2_45.mzXML, 2016_Jan_12_QE2_46.mzXML, 2016_Jan_12_QE2_47.mzXML) and three from the Bering Strait (2016_Jan_12_QE3_51.mzXML, 2016_Jan_12_QE3_52.mzXML, 2016_Jan_12_QE3_53.mzXML). ________________________________ FASTA FILES: The dataset containes three protein fasta files: Bering Strait proteins in metapeptides_BSt.fasta, Chukchi Sea proteins in metapeptides_CS.fasta, and the environmental protein database in env_nr.fasta. ________________________________ SEARCH FILES: Associated with each FASTA file is a tide-index log file with names of the form .tide-index.log.txt. The dataset contains Tide output files for 12 searches (six spectrum files, each searched against two databases). For each search, the corresponding tide-search primary output files have names like ..tide-search.target.txt. There are also corresponding log files and parameter files with names like ..tide-search.log.txt and ..tide-search.params.txt. ________________________________ PERCOLATOR FILES: The dataset contains four sets of Percolator output files. The Percolator PSM-level output files are named ..percolator.target.psms.txt, where is \"BSt\" for Bering Strait and \"CS\" for Chukchi Sea, and is \"metapeptide_BSt\", \"metapeptide_CS\" or \"env_nr\". The peptide-level output files are ..percolator.target.peptides.txt. The corresponding log files are ..percolator.log.txt. And the lists of peptides accepted at 1% FDR are ..peptides.q01.txt. ________________________________ CASANOVO FILES: Casanovo peptide predictions for this dataset reside in MSV000093980, and they are organized into six mzTab files where each file is named after the corresponding spectrum file. 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The elution was performed with 1mg\/mL HA-peptide in Tris buffered saline (TBS with 150mM NaCl), pH 7.5 in a final volume of 100 microL and a concentration of 150-250 ng\/microL. Two samples were sent to the facility for analysis: HEK293T-sgC and sgPRKCI. \n","fileCount":"8","fileSizeKB":"1067555","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:260 - \\\"Thiophosphorylation.\\\"","keywords":"EZH2;PRKCI;Prostate Cancer","pi":[{"name":"Maria T. Diaz-Meco Conde","email":"mtd4001@med.cornell.edu","institution":"WEILL CORNELL MEDICINE","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD052093","task":"4e5e994b55114023a29c74ed52606323","id":"2554"}, {"dataset":"MSV000094705","datasetNum":"94705","title":"DiazMeco_Increased translation driven by a non-canonical EZH2 cistrome creates a synthetic vulnerability in enzalutamide-resistant prostate cancer_set2","user":"moscatdiazme","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715109137000","created":"May. 7, 2024, 12:12 PM","description":"Identification of phosphopeptides in EZH2 upon PRKCI treatment (kinase). In vitro kinase reactions were performed in buffer containing 25 mM HEPES, 15 mM MgCl2, and 1mM DTT. Two samples were sent to the facility for analysis, EZH2, and EZH2+PRKCI.","fileCount":"8","fileSizeKB":"641903","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:260 - \\\"Thiophosphorylation.\\\"","keywords":"EZH2;PRKCI;Prostate Cancer","pi":[{"name":"Maria T. Diaz-Meco Conde","email":"mtd4001@med.cornell.edu","institution":"WEILL CORNELL MEDICINE","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD052092","task":"0bf723684c074b98bac14456618a7f1e","id":"2555"}, {"dataset":"MSV000094704","datasetNum":"94704","title":"DiazMeco_Increased translation driven by a non-canonical EZH2 cistrome creates a synthetic vulnerability in enzalutamide-resistant prostate cancer_set1","user":"moscatdiazme","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715108766000","created":"May. 7, 2024, 12:06 PM","description":"Identification of interacting partners from immuno-precipitated HA-EZH2 samples. Endogenous Co-IP was performed using 1.5 mg of nuclear lysate with anti-HA antibody after transfecting HEK 293T cells with HA-EZH2 plasmid. Two IP-ed samples were submitted to the core for analysis, HEK293T-sgC and sgPRKCI.","fileCount":"8","fileSizeKB":"1345018","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"EZH2;PRKCI;Prostate Cancer","pi":[{"name":"Maria T. Diaz-Meco Conde","email":"mtd4001@med.cornell.edu","institution":"WEILL CORNELL MEDICINE","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD052091","task":"bf58e079f4dd451faadb9b4176a607fb","id":"2556"}, {"dataset":"MSV000094702","datasetNum":"94702","title":"Proteomics in blood brain barrier cells and hepatocytes","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715106564000","created":"May. 7, 2024, 11:29 AM","description":"Proteomics of human primary blood brain barrier cells and hepatocytes analyzed by diaPASEF as described in HN Wilkins 2024.","fileCount":"3044","fileSizeKB":"533823548","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"UNIMOD:39 - \\\"Beta-methylthiolation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"diaPASEF;Blood brain barrier","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD052088","task":"5846f3074fbe43418a527d3b6e81d26f","id":"2557"}, {"dataset":"MSV000094701","datasetNum":"94701","title":"Loss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715089377000","created":"May. 7, 2024, 6:42 AM","description":"Histone lysine methyltransferases KMT2C and KMT2D are among the most commonly mutated genes in the highly metastatic TNBC subtype of breast cancer. However, it is not known if mutations of either of these genes similarly effect epigenomic and transcriptomic landscape or if a specific downstream target might influence metastases. Here, we generated heterogenous Kmt2c or Kmt2d KO murine TNBC cell lines side-by-side and performed in vivo metastases assay in syngeneic immunocompetent mice. Deficiency for either Kmt2c or Kmt2d, both, induced brain metastases from formerly non-metastatic cells. scRNAseq showed activation of pro-inflammatory pathways but conversely also increase of immune checkpoint blocking genes. Interestingly, histone mass spectrometry revealed changes of H3K27 but not the main substrate H3K4. However, ChIPseq for both, H3K4 and H3K27 modifications showed significant changes compared to wildtype cells. Strikingly, genome occupancy of H3K27me3 was reduced while H3K27 demethylase KDM6A was enriched on genomes of KO cells. Integration with gene expression data revealed significant correlations with histone and KDM6A ChIPseq, identifying them as a main driver of Kmt2c or Kmt2d KO-specific gene regulation. Although our datasets revealed more unique than shared signatures, we found Mmp3 being a common target upon Kmt2c or Kmt2d KO. Indeed, downregulation of Mmp3 reversed induction of Kmt2c and Kmt2d KO-dependent brain metastases. Finally, we found that Kdm6a knockdown reduces Mmp3 levels, again, leading to reduction of brain metastases of Kmt2c or Kmt2d KO cells.","fileCount":"14","fileSizeKB":"4083930","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"K-monomethylation, K-dimethylation, K-trimethylation, K-acetylation, K-propionylation, N-terminal propionylation, S-phosphorylation, K-ubiquitination","keywords":"global chromatin profiling","pi":[{"name":"Kornelia Polyak","email":"Kornelia_Polyak@dfci.harvard.edu","institution":"Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052075","task":"5f5c2c292da242c69234948af56c4752","id":"2558"}, {"dataset":"MSV000094700","datasetNum":"94700","title":"Aged Mouse Muscle: Sedentary or Exercised Animals with or without Nicotinamide N-methyltransferase Inhibitor Treatment","user":"RidgelineTx","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715082580000","created":"May. 7, 2024, 4:49 AM","description":"Aged (22-mo) female mice (n=35), obtained from the US NIH National Institute on Aging (NIA) Aged Rodent Colony, were randomly assigned to one of four groups: saline-treated sedentary ( n=9), nicotinamide N-methyltransferase inhibitor (NNMTi)-treated sedentary (10 mg\/kg body weight; n=9), saline-treated progressive weighted wheel running (PoWeR; saline; n=10), and NNMTi-treated PoWeR (10 mg\/kg body weight; n=7) . Group-housed Sed cohorts were compared to singly-housed PoWeR cohorts that underwent a 1-week introduction to an unweighted wheel, followed by eight weeks of weighted wheel running. Forelimb grip strength was assessed by a single NNMTi treatment-blinded investigator during week six and averaged across 2-4 trials\/mouse. At the end of week 8, when mice were ~24.5-months-old, the strength of the right limb plantarflexor muscle complex was measured using an in vivo isometric peak tetanic torque technique and a fatigue test. After the fatigue test, mice were euthanized, and tissues were weighed and collected. Of note, hindlimb muscles from the right limb (the limb that underwent in vivo isometric peak tetanic torque and fatigue testing) were processed for immunohistochemistry to avoid acute effects of muscle functional testing on the proteome and metabolome. Hindlimb muscles from the left limb that did not undergo torque and fatigue testing were flash-frozen for proteome and metabolome analyses.","fileCount":"75","fileSizeKB":"60383991","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"exercise;gastrocnemius;nicotinamide N-methyltransferase inhibitor;5A-1MQ;RT001;MS2;MS3","pi":[{"name":"Stan Watowich","email":"watowich@ridgelinetherapeutics.com","institution":"Ridgeline Therapeutics","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD052072","task":"90189426e38d4ef5a94b4572842b4ec0","id":"2559"}, {"dataset":"MSV000094699","datasetNum":"94699","title":"GNPS - Untargeted metabolomics of ","user":"Paul_Lubrano","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715081976000","created":"May. 7, 2024, 4:39 AM","description":"Untargeted metabolomics dataset for the paper \"Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks \"\r\n\r\nThese are the raw files for metabolites of all 41 isolates in Figure 4b of the paper. ","fileCount":"5414","fileSizeKB":"7866144","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"6546 Q-TOF LC\\\/MS (Agilent instrument model) ","modification":"No PTMs are included in the dataset","keywords":"Untargeted metabolomics;Escherichia coli","pi":[{"name":"Prof. Hannes Link","email":"hannes.link@uni-tuebingen.de","institution":"University Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3a3e076019b24a0ca20122bdae93c514","id":"2560"}, {"dataset":"MSV000094698","datasetNum":"94698","title":"GNPS - Targeted metabolomics of ","user":"Paul_Lubrano","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715080508000","created":"May. 7, 2024, 4:15 AM","description":"Compilation of the targeted metabolomics data present in the associated paper: Metabolic mutations induce antibiotic resistance by pathway-specific bottlenecks. \r\nSee \"File names association\" table in \"supplementary files\" to link file names with paper figures. ","fileCount":"10697","fileSizeKB":"782806","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"6495A Triple Quadrupole LC\\\/MS","modification":"No PTMs are included in the dataset","keywords":"Escherichia coli;Targeted metabolomics","pi":[{"name":"Hannes Link","email":"hannes.link@uni-tuebingen.de","institution":"University of Tubingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dbf28826aebd4272a0743bf4ce3ae70a","id":"2561"}, {"dataset":"MSV000094696","datasetNum":"94696","title":"Development of a high-throughput (10 minute microflow gradient) platform for quantitation of histone modifications on a new QTOF instrument","user":"zahn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715031448000","created":"May. 6, 2024, 2:37 PM","description":"Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The 5 histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry based approaches, identification and quantification of modified histone peptides remains challenging due to factors such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks. Here we describe the development of a new high-throughput method to identify and quantitate over 150 modified histone peptides by liquid chromatography-mass spectrometry (LC-MS). Fast gradient microflow liquid chromatography and variable window SWATH data-independent acquisition on a new quadrupole time-of-flight platform is compared to a previous method using nanoflow LC-MS on an Orbitrap hybrid instrument. Histones extracted from cells treated with either a histone deacetylase inhibitor (HDACi) or TGF-beta 1 were analyzed by data-independent acquisition (DIA) on two mass spectrometers: an Orbitrap Exploris 240 with a 55 minute nanoflow LC gradient, and the SCIEX ZenoTOF 7600 with 5 and 10 minute microflow gradients, with data analyzed using newly developed in-house software. To demonstrate the reproducibility and speed advantage of the method, 100 consecutive injections of one sample were performed in less than 2 days on the QTOF platform. The result is the comprehensive characterization of histone PTMs achieved in less than 20 minutes of total run time using only 200 ng of sample. Results for histone PTMs extracted from cells treated with epigenetic drugs or undergoing cellular transformation are comparable to those produced by the previous method, but can be achieved using less than one-third of the instrument time and one-fifth of the sample amount.","fileCount":"679","fileSizeKB":"57049601","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ZenoTOF 7600","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"epigenetics","pi":[{"name":"Benjamin A. Garcia","email":"bagarcia@wustl.edu","institution":"Washington University School of Medicine in St. Louis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052029","task":"cfea29ee4e9e4d77903e12fb720ea4e8","id":"2562"}, {"dataset":"MSV000094695","datasetNum":"94695","title":"Development of a high-throughput (10 minute microflow gradient) platform for quantitation of histone modifications on a new QTOF instrument ","user":"zahn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1715030792000","created":"May. 6, 2024, 2:26 PM","description":"Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The 5 histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry based approaches, identification and quantification of modified histone peptides remains challenging due to factors such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks. Here we describe the development of a new high-throughput method to identify and quantitate over 150 modified histone peptides by liquid chromatography-mass spectrometry (LC-MS). Fast gradient microflow liquid chromatography and variable window SWATH data-independent acquisition on a new quadrupole time-of-flight platform is compared to a previous method using nanoflow LC-MS on an Orbitrap hybrid instrument. Histones extracted from cells treated with either a histone deacetylase inhibitor (HDACi) or TGF-beta 1 were analyzed by data-independent acquisition (DIA) on two mass spectrometers: an Orbitrap Exploris 240 with a 55 minute nanoflow LC gradient, and the SCIEX ZenoTOF 7600 with 5 and 10 minute microflow gradients, with data analyzed using newly developed in-house software. To demonstrate the reproducibility and speed advantage of the method, 100 consecutive injections of one sample were performed in less than 2 days on the QTOF platform. The result is the comprehensive characterization of histone PTMs achieved in less than 20 minutes of total run time using only 200 ng of sample. Results for histone PTMs extracted from cells treated with epigenetic drugs or undergoing cellular transformation are comparable to those produced by the previous method, but can be achieved using less than one-third of the instrument time and one-fifth of the sample amount.","fileCount":"29","fileSizeKB":"29031739","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"epigenetics","pi":[{"name":"Benjamin A. 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In this study, we used live 3D imaging, mass spectrometry proteomics, and 48 targeted perturbations to comprehensively investigate Ins2(GFP)HIGH and Ins2(GFP)LOW beta cell states. We found that the two Ins2 gene activity states exist in intact isolated islets, and that cells in the same state were more likely to be nearer to each other. We report the proteomes of pure beta cells to a depth of 5555 proteins, and show that beta cells with high Ins2 gene activity had increased transcriptional and mRNA processing factors, as well as increased translation. We identified activators of cAMP signaling (GLP1, IBMX) as powerful drivers of both GFP expression and transitions from Ins2(GFP)LOW to the Ins2(GFP)HIGH states. Okadaic acid and cyclosporine A had the opposite effects. 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The performance of this strategy was benchmarked by the analysis of whole lysates from PANC-1 (a pancreatic cancer cell line), in total 2831 O-GlcNAc sites were unambiguously identified, representing the largest O-GlcNAc dataset of an individual study reported so far. Unexpectedly, in addition to confirming known sites and discovering many novel sites of Ser\/Thr modification, O-GlcNAcylation was found on 121 tyrosine (Tyr) residues of 93 proteins. Through in vitro enzymatic assays, we revealed that OGT shows catalytic capacity to transfer O-GlcNAc onto Tyr residues of peptides and OGA can remove Tyr O-GlcNAcylation from peptides. Taken together, we discovered widespread O-GlcNAcylation on tyrosine residues of proteins and Tyr O-GlcNAcylation is mediated by OGT and OGA. As a novel form of glycosylation, Tyr O-GlcNAcylation may have important regulatory roles. 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However, it has low activity at temperatures below 37 C, which reduces its effectiveness in organisms growing at lower temperatures, such as budding yeast. Multiple derivatives of the enzymes have been engineered, but a comparison of these variations of biotin ligases has not been reported in Saccharomyces cerevisiae. Here, we designed a suite of vectors to compare the activities of biotin ligase enzymes in yeast. We found that the newer TurboID versions were the most effective at labeling proteins, but they displayed low constitutive activity from biotin contained in the culture medium. We describe a simple strategy to express free BioID enzymes in cells that can be used as an appropriate control in BioID studies to account for the promiscuous labeling of proteins caused by random interactions between bait-BioID enzymes in cells. We also describe chemically-induced BioID systems exploiting the rapamycin-stabilized FRB-FKBP interaction. Finally, we used the TurboID version of the enzyme to explore the interactome of different subunits of the Ccr4-Not gene regulatory complex. We find that Ccr4-Not predominantly labeled cytoplasmic mRNA regulators, consistent with its function in mRNA decay and translation quality control in this cell compartment.","fileCount":"24","fileSizeKB":"14881139","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Fusion Lumos;Orbitrap Exploris 480","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"BioID;proximity labeling;TurboID;Ccr4-Not;mRNA decay","pi":[{"name":"Amber L. 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We used a model of polycystic kidney disease (PKD) in mice to showcase this approach (KO -> PKD, vs WT). After protein extraction and reductive alkylation, samples were treated with TMT16plex for labelling of protein N-termini and cleavage events; then digested with trypsin. Measurements of this experiment were performed via Q-Exactive plus and searched using FragPipe. To evaluate the potential effect of protein extraction methods on the identification of cleavage events, we performed a pilot experiment with samples from the same PKD model. Tissues from 3 mice for each condition (KO or WT) were subjected to protein extraction using beat beating, and two sonication approaches. Then processed with trypsin and measured in label-free DIA model in a timsTOF flex and searched in Spectronaut.","fileCount":"96","fileSizeKB":"80075331","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus;timsTOF fleX","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"proteolysis;terminomics;data processing;polycystic kidney disease","pi":[{"name":"Prof. Oliver Schilling","email":"oliver.schilling@mol-med.uni-freiburg.de","institution":"Institute for Surgical Pathology, University Medical Center Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051940","task":"b30ccb66b638440494bf72dc2a28a6e0","id":"2586"}, {"dataset":"MSV000094658","datasetNum":"94658","title":"Affinity Purification of T. vaginalis and L. donovani","user":"ljliu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714633484000","created":"May. 2, 2024, 12:04 AM","description":"Affinity purification of pathogenic proteasomes using clickable probes","fileCount":"11","fileSizeKB":"7010213","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichomonas vaginalis (NCBITaxon:5722);Leishmania donovani (NCBITaxon:5661)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Affinity Purification;Parasite;proteasome","pi":[{"name":"Anthony ODonoghue","email":"ajodonoghue@ucsd.edu","institution":"University of California San Diego","country":"USA"},{"name":"Conor Caffrey ","email":"ccaffrey@ucsd.edu","institution":"UCSD","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"275178c54dcb4d25aed1210ab629c564","id":"2587"}, {"dataset":"MSV000094657","datasetNum":"94657","title":"Identification of proteolytic events during C2C12 myoblast differentiation","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714609709000","created":"May. 1, 2024, 5:28 PM","description":"Identification of product of proteolysis during C2C12 myoblast differentiation using subtiligase N-terminomics. Different cell populations collected during a time-course of differentiation (4 days) were used for N-terminal labeling in a forward degradomics approach (n=2). Day0 population= Myoblasts, Day1 populations= live cells and dead cells, Day4 populations= Myotubes and Reserve cells. Additionally, cleavages events generated by mouse caspase-3 at early stages of differentiation (Day 0 and 1) was evaluated using a reverse degradomics approach on myoblasts and live cells (n=2).","fileCount":"15","fileSizeKB":"46964359","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:01427 - \\\"OBSOLETE because redundant and identical to MOD:00819. Remap to MOD:00819.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Muscle differentiation;Degradomics;Caspases;Proteases;Subtiligase;N-terminomics;N-terminal labeling;C2C12;Myoblasts;Proteolysis;Differentiation;Muscle development","pi":[{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0af3c1d48f9940a3a976c68ea210d640","id":"2588"}, {"dataset":"MSV000094656","datasetNum":"94656","title":"Label-free quantification of proteomic changes during C2C12 myoblast differentiation ","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714607854000","created":"May. 1, 2024, 4:57 PM","description":"Global proteome comparison between five cell populations isolated during a 4-day differentiation process in C2C12 myoblasts. 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Day0 population= Myoblasts, Day1 populations= live cells and dead cells, Day4 populations= Myotubes and Reserve cells.","fileCount":"26","fileSizeKB":"80181025","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Differentiation;Muscle;DIA;ProTrap;LFQ;Cell differentiation;Muscle development","pi":[{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"09d56af111934b7d85a7a3ff404ce526","id":"2589"}, {"dataset":"MSV000094655","datasetNum":"94655","title":"PRMT1 is a critical dependency in clear cell renal cell carcinoma through its role in RNA metabolism and the DNA damage response","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714596651000","created":"May. 1, 2024, 1:50 PM","description":"Data deposited contain results from proximity-dependent biotinylation LC-MS (BioID) experiments in which 786-O and RCC243 cells expressed PRMT1 protein fused to miniTurbo biotin carboxylase.\n","fileCount":"35","fileSizeKB":"10463775","spectra":"0","psms":"362025","peptides":"40438","variants":"65158","proteins":"21033","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"PRMT1, FmT, BioID, biotin, streptavidin, 786-O, RCC243 ","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051931","task":"7a418b344a104d0f9c02d4aa56737661","id":"2590"}, {"dataset":"MSV000094652","datasetNum":"94652","title":"GNPS - Rhizosphere-associated metabolites of four wetland plant species","user":"khaviland","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714575090000","created":"May. 1, 2024, 7:51 AM","description":"This dataset contains raw files for metabolites collected from the soil and roots of four wetland plant species under non-sterile conditions, both in soil and hydroponically, during the day and night time periods.","fileCount":"253","fileSizeKB":"5632170","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Spartina alterniflora var. glabra (NCBITaxon:198030);Phragmites australis (NCBITaxon:29695);Schoenoplectus americanus (NCBITaxon:46335);Spartina patens NCBITaxon:180100","instrument":"6510 Quadrupole Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"wetland;plants;roots;soil","pi":[{"name":"Katherine Haviland","email":"havilandk@si.edu","institution":"Smithsonian Environmental Research Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"635c5a82c5174cd78f6c17090d106815","id":"2591"}, {"dataset":"MSV000094651","datasetNum":"94651","title":"GNPS-fenziwangluo-2024bishe-huzhang-20240501","user":"Liyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714564991000","created":"May. 1, 2024, 5:03 AM","description":"Polygonum cuspidatum,extractive,compound,anthraquinone compound,Stilbenes","fileCount":"2","fileSizeKB":"134372","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Polygonum cuspidatum","instrument":"UHPLC-Q-Orbitrap HRMS","modification":"No PTMs included in the dataset","keywords":"Polygonum cuspidatum","pi":[{"name":"Li Yu","email":"2664405424@qq.com","institution":"Yantai University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3035db1a711f4cfba50b813e34d02035","id":"2592"}, {"dataset":"MSV000094650","datasetNum":"94650","title":"Extraction Comparison of Cannabis sativa inflorescences","user":"kellogglab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714563289000","created":"May. 1, 2024, 4:34 AM","description":"Hemp inflorescences were extracted using three different approaches (solvent, SFE, distillation) for comparison of phytochemical and cannabinoid composition","fileCount":"7938","fileSizeKB":"15412167","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cannabis sativa (NCBITaxon:3483)","instrument":"Orbitrap Exploris 120;5975 Agilent GC-MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cannabis;metabolomics;extraction comparison","pi":[{"name":"Josh J Kellogg","email":"jjk6146@psu.edu","institution":"Pennsylvania State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d38a7ccf4c5a45fbbb3816b3d90f860f","id":"2593"}, {"dataset":"MSV000094648","datasetNum":"94648","title":"Cheng Zhuo raw data for ACyPs manuscript","user":"bioczz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714537832000","created":"Apr. 30, 2024, 9:30 PM","description":"the raw data for the manuscript\"Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates\"","fileCount":"449","fileSizeKB":"925280","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"streptomyces","instrument":"Bruker impact Mass Spectrometer, high resolution QTOF MS","modification":"MOD:00190 - \\\"A protein modification that effectively converts an L-threonine residue to dehydrobutyrine.\\\";UNIMOD:23 - \\\"Dehydration.\\\";double bond reduction;UNIMOD:36 - \\\"Di-Methylation.\\\";MOD:00258 - \\\"A protein modification that effectively cross-links an L-cysteine residue and an L-threonine residue by a thioether bond to form S-(2-aminovinyl)-3-methyl-D-cysteine.\\\";thioether (Cys-Thr or Cys-Ser)","keywords":"Genome mining, RiPPs, Cyclic peptides, ACyPs, Antibiotics","pi":[{"name":"Philip Yong-Xin Li","email":"yxpli@hku.hk","institution":"The University of Hong Kong","country":"Hong Kong"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"39c23354d92d4d9b8aa82a42f24dbeca","id":"2594"}, {"dataset":"MSV000094647","datasetNum":"94647","title":"GNPS - spermine and spermidine standards","user":"mccall_lab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714521414000","created":"Apr. 30, 2024, 4:56 PM","description":"Spermine and spermidine pure standards for level 1 annotation confidence.","fileCount":"7","fileSizeKB":"243392","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - 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Pope","email":"sabina.leantilarosa@nmbu.no","institution":"Norwegian University of Life Sciences","country":"Norway"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f2a2a6b6a3354eb08e09fdc545438453","id":"2613"}, {"dataset":"MSV000094615","datasetNum":"94615","title":"Identification of base excision repair protein complexes","user":"xuzst11","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1714015095000","created":"Apr. 24, 2024, 8:18 PM","description":"We recapitulated two main, cellular base excision repair (BER) complexes (herein termed Complex A, comprised of POLB and XRCC1 and Complex B, XRCC1-devoid complexes) by exploiting a separation-of-function mutant of POLB that does not bind to XRCC1, the V303-loop mutant POLB(TM). Cell lines were developed that expressed Flag-tagged-POLB(WT) and Flag-tagged-POLB(TM). To screen for binding partners of POLB or the POLB\/XRCC1 complex, anti-Flag M2 affinity gel was used to immunoprecipitate proteins from cell lysates of LN428\/Flag-POLB(WT), LN428\/Flag-POLB(TM) or LN428\/EGFP cells. The immunoprecipitates were loaded on SDS-PAGE gels and proteins were separated from low molecular weight reagents using short gel (~1cm) fractionation. The gels were stained by Coomassie blue. Gel regions were excised as indicated and processed for tryptic digestion. Liquid-chromatography Fourier transform mass spectrometry was used to measure the mass-to-charge (m\/z) ratio, retention time, and intensity of more than 100,000 peptide signals that are detected in high-resolution full-scan mass spectra.","fileCount":"30","fileSizeKB":"6906795","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"TRIP12;POLB;Base Excision Repair;DNA Damage Response;Repair pathway choice","pi":[{"name":"Robert W. Sobol","email":"rwsobol@brown.edu","institution":"Brown University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD051729","task":"6e75db84d37142b08b6d38b91c34c256","id":"2614"}, {"dataset":"MSV000094614","datasetNum":"94614","title":"Cleavage of Stemloop RNA by SARS-CoV-2 Nsp15","user":"willia56","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713997663000","created":"Apr. 24, 2024, 3:27 PM","description":"Coronaviruses, such as SARS-CoV-2, use the endoribonuclease Nsp15 to evade the host immune system by cleaving double-stranded RNA (dsRNA) at uridine (U), thus regulating viral RNA levels. Although structural data shows that Nsp15 flips the target U out of the dsRNA helix to cleave it, the exact mechanism for this is unclear. Our study addresses this uncertainty by creating fluorinated dsRNA substrates to explore how a U's sequence context affects its tendency to flip and its susceptibility to Nsp15. Using a combination of nuclease assays, 19F NMR spectroscopy, mass spectrometry, and single-particle cryo-EM, we found that Nsp15 cleaves more effectively when U is unpaired and already flipped. Our results suggest that Nsp15's cleavage efficiency correlates with U's tendency to spontaneously flip, indicating that Nsp15's activity during infection may target bulged or accessible Us in the coronaviral genomic RNA, providing insights into Nsp15's role in immune evasion.","fileCount":"5","fileSizeKB":"409109","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"SARS-CoV-2","instrument":"Q Exactive Plus","modification":"NA","keywords":"RNA, Nsp15, uridine-specific endonuclease","pi":[{"name":"Robin E. Stanley","email":"robin.stanley@nih.gov","institution":"National Institute of Environmental Health Sciences","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7cb7509f99544784b373599974a312e0","id":"2615"}, {"dataset":"MSV000094613","datasetNum":"94613","title":"GNPS - 2024-Mobley-collaborative-project_2-99_neg","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713989677000","created":"Apr. 24, 2024, 1:14 PM","description":"Proteus mirabilis WGLW4 were cultured, supernatant was extracted using HLB-SPE and 80% MeOH\/water and metabolome was analyzed with QExactive HF. 2-99%, 500uL, negative mode ","fileCount":"133","fileSizeKB":"12051057","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteus mirabilis WGLW4 (NCBITaxon:1125693) ","instrument":"Q Exactive HF ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metal binding","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"37ae6a914e0b4b41aeb9f06f75193b94","id":"2616"}, {"dataset":"MSV000094612","datasetNum":"94612","title":"GNPS - The Campylobacter jejuni cell membrane protects against the bactericidal activity of human breastmilk","user":"kmhines5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713984458000","created":"Apr. 24, 2024, 11:47 AM","description":"Campylobacter jejuni is a common foodborne pathogen worldwide that is associated with high rates of morbidity and mortality among infants in low-to-middle income countries (LMICs). Human milk provides infants with an important source of nutrients and also contains antimicrobial components for protection against infection. However, recent studies, including our own, have found significantly higher levels of Campylobacter in diarrheal stool samples collected from breastfed infants from LMICs compared to non-breastfed infants. We hypothesized that C. jejuni may have unique strategies to resist the antimicrobial properties of human milk. In this study, RNAseq comparisons indicated that exposure of C. jejuni strains 81-176 and 11168 to human milk results in increased expression of ribosomal proteins, iron receptors and transporters, and proteins for amino acid utilization. However, unidentified proteinaceous components of human milk prevent bacterial growth. After evolving both C. jejuni isolates in increasing concentrations of human milk, followed by genomic sequence comparisons, we identified mutations in genes encoding the acyl carrier protein, AcpP, and major outer membrane porin, PorA, in addition to strain specific changes. Introduction of the observed PorA and AcpP amino acid changes back into the parental backgrounds followed by transmission electron microscopy indicated that changes in both proteins lead to distinctly altered cell membrane architectures. However, only the C. jejuni AcpP changes significantly improved growth in human milk presumably through the formation of a continuous layer of outer membrane vesicles. Analyses of the phospholipid and lipooligosaccharide lipid A composition demonstrated that these vesicles likely form due to an imbalance in acyl chain distribution. In the case of strain 11168, this added layer of vesicles protected both evolved and acpP mutated strains from bacteriophage infection and polymyxin killing. Taken together, this study provides insights into how C. jejuni strains may evolve to resist the bactericidal activity of human milk and flourish in the hostile environment of the gastrointestinal tract.","fileCount":"787","fileSizeKB":"23082819","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Campylobacter jejuni (NCBITaxon:197)","instrument":"Synapt XS;ACQUITY UPLC I-Class","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipids;phospholipids;membrane lipids","pi":[{"name":"Christine Szymanski","email":"cszymans@uga.edu","institution":"University of Georgia","country":"USA"},{"name":"Kelly M. Hines","email":"kelly.hines@uga.edu","institution":"University of Georgia","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"44438a98ea63402387f773fd97e13683","id":"2617"}, {"dataset":"MSV000094611","datasetNum":"94611","title":"Regulation of stochastic gene bursting by chromatin-independent acetylation","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713976676000","created":"Apr. 24, 2024, 9:37 AM","description":"Stochastic transcriptional bursting is a universal property of gene expression. Different genes exhibit distinct bursting patterns, but the molecular mechanisms that determine bursting kinetics are largely unknown. We have developed and applied a high-throughput-imaging based screening strategy to identify cellular factors and mechanisms that determine the bursting behavior of human genes. Focusing on epigenetic regulators, we find that protein acetylation is a strong acute modulator of burst frequency, burst size and heterogeneity of bursting. Acetylation globally affected the Off-time of genes, but had gene-specific effects on the On-time. Yet, these effects were not linked to promoter acetylation, which did not correlate with bursting properties, and forced promoter acetylation had variable effects on bursting. Instead, we identified acetylation of the Integrator complex as a key determinant of gene bursting. Specifically, we find that elevated Integrator acetylation increases bursting. Taken together our results suggest a prominent role of non-histone proteins in determining gene bursting properties, and they point towards histone-independent acetylation of a transcription cofactor as an allosteric modulator of bursting via a pause-release related bursting checkpoint.","fileCount":"31","fileSizeKB":"29057382","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Stochastic gene bursting, acetylation, Integrator complex, high-throughput imaging screen","pi":[{"name":"Tom Misteli","email":"mistelit@mail.nih.gov","institution":"NCI\/NIH","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ea5c1ada69914a4a85c79556ba821db2","id":"2618"}, {"dataset":"MSV000094610","datasetNum":"94610","title":"Alcoholic Hepatitis Stool Proteomics Comparison","user":"gonzolabucsd","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713973452000","created":"Apr. 24, 2024, 8:44 AM","description":"Data from study profiling the effects on the microbiome of alcohol users who have progressed to liver issues.","fileCount":"347","fileSizeKB":"412732945","spectra":"64334891","psms":"126928","peptides":"7837","variants":"11548","proteins":"1773","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);host stool (microbiome)","instrument":"Orbitrap Fusion","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"gut microbiome, human, hepatitis","pi":[{"name":"Bernd Schnabl","email":"beschnabl@health.ucsd.edu","institution":"University of California San Diego","country":"United States"},{"name":"David Gonzalez","email":"djgonzalez@health.ucsd.edu","institution":"University of California San Diego","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"","task":"7d0fde27c8c74018b3828f4fe7f5b459","id":"2619"}, {"dataset":"MSV000094609","datasetNum":"94609","title":"GNPS - koolengroup_microorganisms","user":"moyses","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713966524000","created":"Apr. 24, 2024, 6:48 AM","description":"LC-MS\/MS of fungi studied in the metabolomics and mass spectrometry research group (MMSRG) at the State University of Amazonas, Brazil.","fileCount":"325","fileSizeKB":"3722662","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Talaromyces (NCBITaxon:5094);Penicillium (NCBITaxon:5073);Pestalotiopsis (NCBITaxon:37840);Trichoderma (NCBITaxon:5543);Fusarium (NCBITaxon:5506)","instrument":"6550 iFunnel Q-TOF LC\\\/MS;micrOTOF-Q","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fungi;Fungus;Natural Products","pi":[{"name":"Hector Koolen","email":"hectorkoolen@gmail.com","institution":"University of the State of Amazonas","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ea027b0dc7e843cd8c26b376fb3a78d8","id":"2620"}, {"dataset":"MSV000094607","datasetNum":"94607","title":"Proteomic insights into the impact of COVID-19 on peripheral blood mononuclear cells in kidney transplant recipients","user":"ggfleite","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713961641000","created":"Apr. 24, 2024, 5:27 AM","description":"Background\nThe emergence of the Coronavirus disease 2019 (COVID-19) pandemic in 2020 has profoundly impacted global health systems, particularly affecting vulnerable populations like kidney transplant recipients (KTRs).\nMethods\nWe prospectively collected blood samples from 17 PCR-confirmed COVID-19 KTR patients and 10 non-COVID-19 KTRs between May and September 2020. Using tandem mass tag based quantitative proteomics, we characterized peripheral blood mononuclear cells (PBMCs) from KTRs alongside plasma protein biomarkers and lymphocyte counts, followed by bioinformatics analyses.\n","fileCount":"11","fileSizeKB":"5336841","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"COVID-19;kidney transplant recipient;KTRs;peripheral blood mononuclear cell;PBMC","pi":[{"name":"Giuseppe Leite","email":"giuseppe.gianini@unifesp.br","institution":"Escola Paulista de Medicina\/UNIFESP","country":"Brazil"},{"name":"Reinaldo Salomao","email":"rsalomao@unifesp.br","institution":"Escola Paulista de Medicina\/UNIFESP","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051702","task":"561e26fa45fa4965a865f0f884d4f050","id":"2621"}, {"dataset":"MSV000094605","datasetNum":"94605","title":"GNPS - 2024-Mobley-collaborative-project_2-99_pos","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713916799000","created":"Apr. 23, 2024, 4:59 PM","description":"Proteus mirabilis WGLW4 were cultured, supernatant was extracted using HLB-SPE and 80% MeOH\/water and metabolome was analyzed with QExactive HF. 2-99%, 500uL, positive mode","fileCount":"135","fileSizeKB":"11423479","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteus mirabilis WGLW4 (NCBITaxon:1125693)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metal binding","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"99dd4ffd6a8441d9ac97aa73d6d267c1","id":"2622"}, {"dataset":"MSV000094604","datasetNum":"94604","title":"Comparison of affinity enrichment methods for O-GlcNAc proteomics","user":"Chunyan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713905100000","created":"Apr. 23, 2024, 1:45 PM","description":"In this work, by using the lysates of PANC-1 (a pancreatic cancer cell line), we provided a head-to-head comparison of three affinity enrichment methods\/materials (i.e., antibody, lectin AANL6, and an OGA mutant) for O-GlcNAc proteomics. The enrichment was performed before or after high-pH HPLC fractionation. The enriched peptides were analyzed by EThcD or HCD-product dependent-EThcD (i.e., HCD-pd-EThcD) mass spectrometry. The resulting data files were processed by using three different data analysis packages (i.e. Sequest HT, Byonic, and FragPipe).","fileCount":"79","fileSizeKB":"39307907","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Fusion Lumos","modification":"O-GlcNAc","keywords":"O-GlcNAc;proteomics;antibody;AANL6;OGA;mutant;HCD-pd-EThcD;Sequest HT;Byonic;FragPipe","pi":[{"name":"Junfeng Ma","email":"Junfeng.Ma@georgetown.edu","institution":"Georgetown Univeristy","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"778ae0cdd5514e0d9b469eb50ec46d09","id":"2623"}, {"dataset":"MSV000094602","datasetNum":"94602","title":"Fish species authentication in commercial fish products using mass spectrometry and spectra library approach ","user":"madhu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713887730000","created":"Apr. 23, 2024, 8:55 AM","description":"Seafood fraud has become a global emerging issue, threatening food security and safety. Adulteration, substitution, dilution, and incorrect labeling of seafood products are fraudulent practices that violate consumer safety. In this context, developing sensitive, robust, and high-throughput molecular tools for food and feed authentication is becoming crucial for regulatory purposes. Analytical approaches such as proteomics mass spectrometry have shown promise in detecting incorrectly labeled products. For the application of these tools, genome information is crucial, but currently, for marine species of commercial importance, such information is unavailable. However, when combining proteomic analysis with spectra library matching, commercially important fish species were successfully identified, differentiated, and quantified in pure muscle samples and mixtures, even when genome information was scarce. This study further tested the previously developed proteomic-based spectra library-based approach was further tested to differentiate 29 fish species from the North Sea in individual samples, laboratory-prepared mixtures, and commercial samples. For authenticating libraries generated from 29 fish species, fresh muscle samples from the fish samples were matched against the reference libraries. Species of the fresh fish samples were correctly authenticated using the spectra libraries generated from the 29 fish species. Furthermore, processed commercial products containing mixtures of two or three fish species were matched against these spectra libraries to test the accuracy and robustness of this method for authentication of fish species. The results indicated that the method is suitable for the authentication of fish species from highly processed samples such as fish cakes and burgers. Spectra libraries built from 29 fish species in the North Sea can efficiently tackle current and future challenges in feed and food authentication analyses when prospecting new resources in the Arctic. ","fileCount":"338","fileSizeKB":"108687377","spectra":"0","psms":"5115360","peptides":"1946151","variants":"2580090","proteins":"83586","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gadus morhua (NCBITaxon:8049);Merluccius merluccius (NCBITaxon:8063);Pollachius virens (NCBITaxon:8060);Melanogrammus aeglefinus (NCBITaxon:8056);Pollachius pollachius (NCBITaxon:185739);Molva molva (NCBITaxon:163112);Trisopterus minutus (NCBITaxon:80722);Trisopterus esmarkii (NCBITaxon:80723);Micromesistius poutassou (NCBITaxon:81636);Gadiculus argenteus (NCBITaxon:185737);Clupea harengus (NCBITaxon:7950);Scomber scombrus (NCBITaxon:13677);Trachurus trachurus (NCBITaxon:36212);Microstomus kitt (NCBITaxon:106175);Pleuronectes platessa (NCBITaxon:8262);Limanda limanda (NCBITaxon:27771);Lepidorhombus whiffiagonis (NCBITaxon:154550);Scophthalmus maximus (NCBITaxon:52904);Cyclopterus lumpus (NCBITaxon:8103);Maurolicus muelleri (NCBITaxon:68502);Ammodytes marinus (NCBITaxon:146480);Anarhichas lupus (NCBITaxon:8204);Squalus acanthias (NCBITaxon:7797);Amblyraja radiata (NCBITaxon:386614);Argentina sphyraena (NCBITaxon:442169);Callionymus lyra (NCBITaxon:34785);Argentina silus (NCBITaxon:446415);Merlangius merlangus (NCBITaxon:8058);Eutrigla gurnardus (NCBITaxon:426098)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:903 - \\\"Lys->Cys substitution and carbamidomethylation.\\\";MOD:00768 - \\\"Oxidation of methionine to methionine sulfone with neutral loss of CH3SO2H.\\\"","keywords":"authentication;seafood;proteomics;tandem mass spectra;spectral libraries","pi":[{"name":"Madhushri Shrikant Varunjikar","email":"madhushri.shrikant.varunjikar@hi.no","institution":"INSTITUTE OF MARINE RESEARCH","country":"Norway"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD051671","task":"28bdb695c2ea4b72916614974a567259","id":"2624"}, {"dataset":"MSV000094600","datasetNum":"94600","title":"Untargeted metabolomic (LC-MS-MS) analysis of the spermosphere of eight common bean genotypes (Phaseolus vulgaris L)","user":"c_saccaram6354","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713883195000","created":"Apr. 23, 2024, 7:39 AM","description":"Seeds are crucial for plant reproduction, dispersal, and agriculture. Seed quality and vigour greatly impact crop production, referring to their ability to germinate rapidly and uniformly under varying environmental conditions, producing healthy seedlings that can withstand biotic and abiotic stress accentuated by global climate change. During germination, seeds release exudates, complex mixtures of organic and inorganic molecules, into the micro-environment surrounding them, known as the spermosphere. These exudates play a pivotal role in seedling development and overall plant fitness by influencing microbial selection, growth, and interactions in the spermosphere, ultimately shaping the plant's microbiome. To understand the composition and functional properties of germinating seed exudates, we conducted our study using different common bean (Phaseolus vulgaris L.) genotypes. Seeds were harvested in the year 2020 from eight different common bean genotypes (French commercial cultivars of Phaseolus vulgaris) cultivated in two different locations from the FNAMS field experimental stations: Gers in South-west of France (43.956991, 0.392127) and Maine et Loire (47.470532, -0.394526) in the Loire Valley. The common bean genotypes namely, VEZ, CON, CAP, FAC, FLA, LIN, DEE and VAN were chosen to represent the highest diversity among breeding programmes and qualitative seed traits in France by the seed company Vilmorin-Mikado SAS (Limagrain group). One seed lot corresponds to seeds from one genotype produced in one location. Independent biological replicates were conducted for each seed lot. Thus, 48 samples were analyzed, corresponding to three replicates of eight genotypes produced in two locations. Spermosphere collection of germinating seeds involved the imbibition of 30 seeds for each sample at four distinct time intervals: 2, 8, 16, and 24 hours. The collected spermosphere, consisting of the water surrounding germinating seeds, was gathered for each time interval and subsequently pooled. Subsequently we investigated the diversity of metabolites of each pooled spermosphere using untargetted metabolomic (LC-MS\/MS) analysis. ","fileCount":"107","fileSizeKB":"37777251","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phaseolus vulgaris (NCBITaxon:3885)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Common Bean;Seeds;Spermosphere;Specialised metabolites;Biotic interactions","pi":[{"name":"Chandrodhay Saccaram","email":"chandrodhay.saccaram@inrae.fr","institution":"Paris-Saclay University, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB)","country":"France"},{"name":"Loic Rajjou","email":"Loic.rajjou@inrae.fr","institution":"Paris-Saclay University, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB)","country":"France"},{"name":"Massimiliano CORSO","email":"massimiliano.corso@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"},{"name":"Stephanie Boutet","email":"stephanie.boutet@inrae.fr","institution":"Institut Jean-Pierre Bourgin (INRAE)","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"5fc6b660e0cc4abd99def61b38a9aa4a","id":"2625"}, {"dataset":"MSV000094599","datasetNum":"94599","title":"Redox control of the deubiquitinating enzyme Ubp2 regulates translation during stress ","user":"Gustavo_Silva_2024","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713882880000","created":"Apr. 23, 2024, 7:34 AM","description":"Protein ubiquitination is essential to govern cells ability to cope with harmful environments by regulating many aspects of protein dynamics from synthesis to degradation. As important as the ubiquitination process, the reversal of ubiquitin chains mediated by deubiquitinating enzymes (DUBs) is critical for proper recovery from stress and re-establishment of proteostasis. Although it is known that ribosomes are decorated with K63-linked polyubiquitin (K63-ub) chains that control protein synthesis under stress, the mechanisms by which these ubiquitin chains are reversed and regulate proteostasis during stress recovery are still illusive. Here, we showed in budding yeast that the DUB Ubp2 is redox regulated during oxidative stress in a reversible manner, which determines the levels of K63-ub chains present on ribosomes. We also demonstrate that Ubp2 is a processive enzyme whose activity is modulated by a series of repeated domains and the formation of important disulfide bonds. By combining, cellular, biochemical, and proteomics analyses, we showed that Ubp2 is crucial for restoring translation after stress cessation, indicating an important role in determining cellular response to oxidative stress. Our work demonstrates a novel role for Ubp2, revealing that a range of signaling pathways can be controlled by redox regulation of DUB activity in eukaryotes, which in turn will define cellular states of health and diseases. ","fileCount":"33","fileSizeKB":"169146220","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Astral","modification":"Fixed carbamidomethyl (Cys), oxidation (Met) and acetylation (protein N-terminus)","keywords":"yeast, DUBs, ubiquitination, oxidative stress, recovery","pi":[{"name":"Gustavo Monteiro Silva","email":"gustavo.silva@duke.edu","institution":"Duke University","country":"United States"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD051667","task":"7b8961d27dec4dcb8b98999bdaaa978c","id":"2626"}, {"dataset":"MSV000094598","datasetNum":"94598","title":"Comprehensive two-dimensional liquid chromatography high-resolution mass spectrometry for complex protein digest analysis using parallel gradients","user":"agargan1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713856496000","created":"Apr. 23, 2024, 12:14 AM","description":"The dataset summarizes results from the use of shifted and parallel 2DLC gradient programs for the analysis of complex protein digests","fileCount":"727","fileSizeKB":"21067354","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"orbitrap QExactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"2DLC HRMS;parallel gradients;RPLCxRPLC HRMS","pi":[{"name":"Andrea Gargano","email":"a.gargano@uva.nl","institution":"University of Amsterdam","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c0dfcffe535e46d9bddec4eefd208a6a","id":"2627"}, {"dataset":"MSV000094596","datasetNum":"94596","title":"Direct Evidence for Intact 20S Proteasomes in Nondiabetic and Diabetic Wound Repair by Charge Detection Mass Spectrometry","user":"adam_anthony","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713832437000","created":"Apr. 22, 2024, 5:33 PM","description":"Nondiabetic and diabetic murine skin tissue was analyzed during the course of wound repair. The samples were fractionated by density gradient ultracentrifugation. Proteasomes were found to be enriched in the lightest density fraction and analyses over time were done at this density.","fileCount":"134","fileSizeKB":"65498426","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Proteasome","pi":[{"name":"David Clemmer","email":"clemmer@indiana.edu","institution":"IU Bloomington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d26cf799eb7d42509833d043c9e01db7","id":"2628"}, {"dataset":"MSV000094594","datasetNum":"94594","title":"MHC-II peptides from monoallelic B cell platform","user":"mlannan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713811945000","created":"Apr. 22, 2024, 11:52 AM","description":"MHC-II peptides from monoallelic B cell platform (endogenous and test compound)","fileCount":"152","fileSizeKB":"27210769","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:366 - \\\"Deamidation in presence of O18.\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:351 - \\\"Tryptophan oxidation to kynurenin.\\\";UNIMOD:350 - \\\"Tryptophan oxidation to hydroxykynurenin.\\\";UNIMOD:345 - \\\"Cysteine oxidation to cysteic acid.\\\";UNIMOD:425 - \\\"Dihydroxy.\\\";UNIMOD:312 - \\\"Cysteinylation.\\\";UNIMOD:55 - \\\"Glutathione disulfide.\\\";UNIMOD:374 - \\\"Half of a disulfide bridge.\\\"","keywords":"immunopeptidomics;MAPPs;MHC;HLA","pi":[{"name":"Robert Siegel","email":"siegel_robert@lilly.com","institution":"Eli Lilly and Co.","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b0e6e0ee22674a0aa88244a3a125f3f5","id":"2629"}, {"dataset":"MSV000094591","datasetNum":"94591","title":"GNPS - SARS-CoV-2 infection unevenly impacts metabolism in the coronal periphery of the lungs","user":"jarrodroach","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713799868000","created":"Apr. 22, 2024, 8:31 AM","description":"This project was performed on a cohort of mice that were either infected on day 5 with 1000 or 5000 pfu (D5_1000 or D5_5000), uninfected on day 5 (D5_MOCK), infected on day 20 (D20) or uninfected on day 20 (D20_MOCK). Lungs were removed and broken into 12 pieces. See \"SARS-CoV-2 infection unevenly impacts metabolism in the coronal periphery of the lungs\" for more information on this study","fileCount":"824","fileSizeKB":"66233896","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"COVID-19;SARS-CoV-2;Metabolomics;Spatial Metabolomics;Coronavirus;Mouse;Lungs","pi":[{"name":"Laura-Isobel McCall","email":"lmccall@sdsu.edu","institution":"San Diego State University","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0934d537663042a9bd63d513c1c28fe3","id":"2630"}, {"dataset":"MSV000094589","datasetNum":"94589","title":"GNPS - Atlantic salmon gut metabolites","user":"sale","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713778096000","created":"Apr. 22, 2024, 2:28 AM","description":"Untargeted metabolomics data obtained from gut samples from adult Atlantic salmon. Sample (about 200 mg) was transferred into a 1.5 ml tube and eluted with 4x wt\/vol of ultra-pure water. After homogenization with a Vortex for 1-2 min the sample was centrifuged at 16.000 g for 10 min. The supernatant was transferred into a spinX centrifuge filter, and centrifuged again (15.000 g\/4 C\/5 min). The filtrate was collected for LC-MS\/MS analysis.","fileCount":"2","fileSizeKB":"57505","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Salmon gut microbiome","instrument":"UPLC system (Vanquish, Thermo Fisher Scientific) coupled with a high-resolution quadrupole-orbitrap mass spectrometer Orbitrap Exploris 240 MS, Thermo Fisher Scientific.","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"untargeted metabolomics;Atlantic salmon gut microbiota;gut microbiota","pi":[{"name":"Sabina Leanti La Rosa\/Phil B. Pope","email":"sabina.leantilarosa@nmbu.no","institution":"Norwegian University of Life Sciences","country":"Norway"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"eaa10b0bd96649d8aa636006a4f2d9fa","id":"2631"}, {"dataset":"MSV000094587","datasetNum":"94587","title":"Raw data for : \"Genetic and pharmacological targeting of hepatic oxalate overproduction ameliorates metabolic dysfunction-associated steatohepatitis\"","user":"aliagh81","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713757232000","created":"Apr. 21, 2024, 8:40 PM","description":"Metabolic dysfunction-associated steatohepatitis (MASH) is on the rise, and with limited pharmacological therapy available, identification of new metabolic targets is urgently needed. Oxalate is a terminal metabolite produced from glyoxylate by lactate dehydrogenase (LDHA). The liver-specific alanine-glyoxylate aminotransferase (AGXT) detoxifies glyoxylate, preventing oxalate accumulation. We report that AGXT is suppressed and LDHA is activated in livers from patients and mice with MASH, leading to oxalate overproduction. In turn, oxalate promotes steatosis in hepatocytes by inhibiting peroxisome proliferator activated receptor-alpha (PPARa) transcription and fatty acid b-oxidation (FAO), and induces monocyte chemotaxis via C-C motif chemokine ligand 2. In male mice with diet-induced MASH, blocking oxalate overproduction through hepatocyte-specific AGXT overexpression or pharmacological inhibition of LDHA potently lower steatosis, inflammation, and fibrosis by inducing PPARa-driven FAO, and suppressing monocyte chemotaxis, nuclear factor-kappa B and transforming growth factor-beta targets. These findings highlight hepatic oxalate overproduction as a new target for the treatment of MASH.","fileCount":"21","fileSizeKB":"7397201","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Alanine-glyoxylate aminotransferase;Lactate dehydrogenase;Metabolic dysfunction-associated steatohepatitis;Oxalate;Peroxisome proliferator activated receptor-alpha","pi":[{"name":"Oren Rom ","email":"oren.rom@lsuhs.edu","institution":"LSU Health Shreveport ","country":"LA, United States "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"652cda10ee074456a20448ca2db3a8d0","id":"2632"}, {"dataset":"MSV000094586","datasetNum":"94586","title":"Label-free quantitative data dependent (DDA) nano-LC-MS\/MS proteomic profiling of mouse lymph harvested from mesenteric and cervical anatomical districts","user":"oriongalaxy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713745267000","created":"Apr. 21, 2024, 5:21 PM","description":"To fully quantify differences in the lymph composition and associated dendritic cells antigenic load, from different anatomical districts and in physiological and pathological conditions, we collected the afferent lymph draining to the cervical and mesenteric lymph nodes in healthy mice. Most of the proteome present in the mesenteric afferent lymph, showed a profile of proteins involved in different metabolic pathways associated with lipoproteintransport, and lipid metabolism, such as adipocyte-type fatty acid binding protein, Apolipoproteins A, B, C and E, and phospholipid transfer proteins, consistent with the known role of the mesenteric lymph in chylomicron transport. Network analysis on the mesenteric afferent lymph unique\/enriched proteome highlighted pathways associated with lipase and hydrolase activity, lipoproteins remodeling, fat digestion and absorption, triglyceride catabolism and gut-associated immune cells and cytokines responses. Among the proteome shared across tissue a brain-specific or highly enriched proteome including glia maturation factor, nerve growth factor, mesencephalic astrocyte-derived neurotrophic factor, alpha-crystallin, brain-specific isoform of glycogen phosphorylase, and proteins associated with voltage-dependent channels, were uniquely observed in the lymph harvested from the afferent lymphatics entering the deep cervical nodes. Network analysis on the afferent cervical unique\/enriched proteome highlighted pathways associated with neurotransmitter release cycle, synaptic transmission, neuronal development, mitochondrial activity, and an overall CNS proteome.","fileCount":"132","fileSizeKB":"44126370","spectra":"0","psms":"134651","peptides":"14721","variants":"27051","proteins":"1866","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\"","keywords":"mouse; mesenteric and cervical lymph; label free quantitative proteomics profiling on QEHF mass spectrometer","pi":[{"name":"Cristina C Clement","email":"ccc4002@med.cornell.edu","institution":"Weill Cornell Medicine College","country":"United States"},{"name":"Laura Santambrogio","email":"las4011@med.cornell.edu","institution":"Weill Cornell Medicine College","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051618","task":"893be71ae85d42428a409e77337e358e","id":"2633"}, {"dataset":"MSV000094585","datasetNum":"94585","title":"Comparative label free proteomics analysis of MCF-7 and K562 cancer cells treated with mitomycin C and dicarbamoyl mitomycin C ","user":"oriongalaxy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713737298000","created":"Apr. 21, 2024, 3:08 PM","description":"Mitomycin C (MC) is an anti-cancer drug which functions by forming interstrand crosslinks between opposing DNA strands. MC analog, 10-decarbamoyl mitomycin C (DMC), unlike MC, has stronger cytotoxic effects on cancer with TP53 mutation. We previously demonstrated that MC\/DMC could activate p21WAF1\/CIP1 in MCF-7 (TP53-proficient) and K562 (TP53 mutant) cells in a TP53-independent mode. We also found that MC\/DMC regulate Akt activation in a TP53-dependent manner and that the Akt deactivation is not associated with the activation of p21WAF1\/CIP1 in response to MC\/DMC treatment. RAS proteins are known players in the upstream mediated signaling of p21WAF1\/CIP1 activation that leads to control of cell proliferation and cell death. Thus, this prompted us to investigate the effect of both drugs on the expression of RAS proteins and regulation of the MAPK\/ERK signaling pathways in MCF-7 and K562 cancer cells. To accomplish this goal, we employed comparative label free proteomics profiling coupled to bioinformatics and complementary phosphoprotein arrays and western blot validations of key signaling molecules. The MAPK\/ERK pathway exhibited an overall downregulation upon MC\/DMC treatment in MCF-7 cells but only DMC exhibited a mild downregulation of that same pathway in TP53 mutant K562 cells. Furthermore, treatment of MCF-7 and K562 cell lines with oligonucleotides containing the interstrand crosslinks (ICLs) formed by MC or DMC shows that both ICLs had a stronger effect on the downregulation of RAS protein expression in mutant TP53 K562 cells. \n\n\n","fileCount":"75","fileSizeKB":"26325660","spectra":"0","psms":"230129","peptides":"29835","variants":"61109","proteins":"3789","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";MOD:00420 - \\\"A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid.\\\"","keywords":"bottom-up proteomics, mitomycin C and decarbamoyl mitomycin C treated MCF-7 and K-562 cancer cells","pi":[{"name":"Cristina C Clement","email":"ccc4002@med.cornell.edu","institution":"Weill Cornell Medicine College","country":"United States"},{"name":"Elise Champeil","email":"echampeil@jjay.cuny.edu","institution":"John Jay College of Criminal Justice, the City University of New York (CUNY)","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051617","task":"150800232b874008a165e0dbdacc9708","id":"2634"}, {"dataset":"MSV000094584","datasetNum":"94584","title":"GNPS - Synechococcus elongatus PCC 7942","user":"Nike","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713731374000","created":"Apr. 21, 2024, 1:29 PM","description":"Purified Pteridines from Synechococcus elongatus PCC 7942 extratcs","fileCount":"19","fileSizeKB":"225","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Synechocccus elongatus;Pteridines;Pterines;Lumazines;Cyanobacteria","pi":[{"name":"Daniel Petras","email":"Daniel.Petras@uni-tuebingen.de","institution":"Univeristy of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da1dcdfd22284cf3982ebbf4bd20789d","id":"2635"}, {"dataset":"MSV000094583","datasetNum":"94583","title":"The Ubiquitin Ligase RBX2\/SAG Regulates Mitochondrial Ubiquitination and Mitophagy","user":"WW_1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713719092000","created":"Apr. 21, 2024, 10:04 AM","description":"The goal of this experiment is to identify differentially expressed proteins in RBX2-deficient cardiomyocytes. Neonatal rat ventricular cardiomyocytes were transfected with indicated siRNAs and treated with or without CCCP for 6 hours. The collected cell lysates were processed for tandem mass tag labeling and quantitative proteomics analysis.","fileCount":"5","fileSizeKB":"5033754","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RBX2, mitophagy","pi":[{"name":"Huabo Su","email":"hsu@augusta.edu","institution":"Augusta University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"2e04226fe89645b29fcb89bb8287a15c","id":"2636"}, {"dataset":"MSV000094580","datasetNum":"94580","title":"Primary human fibroblast cell siRNA anti-fibrosis treatment and proteome remodelling","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713712427000","created":"Apr. 21, 2024, 8:13 AM","description":"Primary human fibroblast (ventricle and atrial source) cells were treated with a regime of TGF-b, and various siRNA targets from single cell analysis, to identify impact as anti-fibrosis targets. Label free proteome remodeling analysis was performed","fileCount":"105","fileSizeKB":"77539804","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"fibrosis;sirna;primary human fibroblasts;atrial;ventricle","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1123a5f6053e48d6a4e8a1103dda8db1","id":"2637"}, {"dataset":"MSV000094579","datasetNum":"94579","title":"A proteomic map of the life cycle stages of the spotted lanterfly (Lycorma Delicatula)","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713707126000","created":"Apr. 21, 2024, 6:45 AM","description":"Proteomic samples were harvested from different life cycle stages of the invasive pest Lycorma Delicatula, or the Spotted Lanternfly. Adults were captured in the wild while egg and early instar samples were obtained by hatching insects in captivity. Samples were homogenized by bead disruption after percussive homogenization of samples frozen at -80C. Homogenization in 1x S-trap lysis buffer (Protifi, Long Island, NY) was performed in 30s pulses until homogenization appeared complete by visual inspection. The resulting lysate was reduced in DTT and alkylated with iodoacetamide prior to S-Trap mini digestion following vendor protocols. The resulting peptides were analyzed by diaPASEF based proteomics using the default workflow for \"short gradient diaPASEF\" in TimsControl 4.0. Raw files were processed with a 6 frame translation of the L. delicatula genome sequence and annotated with EggNog Mapper V2 with peptide match and quantification performed with SpectroNaut 18. Please see the associated metadata excel sheet for sample identities. 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These synthetic strains were cultures in BHI media with bile acids spiked in. 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Samples were extracted in a solution of 60% methanol at a 1:20 to 1:100 ratio based on pilot tests on solubilization of material. Extracts were clarified by high speed centrifugation, dried by speedvac and diluted to a 1:100 to 1:500 g\/g ratio of the original material in 5% acetonitrile in LCMS grade water. Samples were analyzed on a Q Exactive Classic system coupled to a Dionex UHPLC using a 15cm x 2.1mm HyperSil gold column with 1.5um particles (Thermo, all). A 20 minute method with a data dependent top 3 method was used with each sample analyzed in triplicate, separately in each polarity. The output files were analyzed in Compound Discoverer 3.3 SP2 using a combination of libraries as described in the manuscript. Standards were obtained from MilliPore Sigma for Nicotinamide and derivatives for retention time matching and concentation estimations. 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Despite attempts to harvest proteins from the surface of an aluminum baseball bat, proteomic coverage was quite poor. In 2023, a mature female was temporarily stunned by the shockwave of an aluminum ballbat on concrete in a blow that altered the shape of both objects. This example of Latrodectus was transferred into a 15 mL falcon tube by a mass spectrometrist who made very undignified noises while making this transfer. The tube was rapidly sealed and the tube was placed at -20C before being transferred to -80C for storage. After the project was declined by multiple people in the laboratory a new student in the lab accepted this as his first proteomics project. The spider was carefully removed from the tube but the freeze\/thaw process only allowed the separation of 2 distinct sections, titled \"body\" and \"legs\". These were homogenized in 4 fractions per section in a bead mill using 30 second pulses in 1x S-Trap lysis buffer. The resulting lysate was clarified by brief centrifugation and the lysates were digested using the S-Trap Mini spin columns following vendor protocols including the reduction and alkylation of cysteines with DTT and iodoacetamide. Peptides concentrations were determined by colorimetric assay (Pierce) and 400 nanograms of each were loaded onto EvoTips for analysis using a 30SPD method. A diaPASEF method on a TIMSTOF Flex instrument was used for analysis. Resulting samples were processed in SpectroNaut 18 using a combination of Latrodectus and Spider fastas from UniProt, as described in the manuscript. 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Cells were grown according to vendor protocols and treated with DMSO control or acetaminophen at the IC50 dose previously determined by R. Bruderer et al., 2015. Single cells were isolated using a Tecan UNO system using vendor protocols. 400 nanogram of bulk cell lysates from each condition were analyzed using diaPASEF using a TIMSTOF Flex system coupled to an EvoSep One system and using a 44 minute total gradient (30SPD). Single isolated cells were ran with a method with a compable run to run time and diaPASEF method using an EasyNLC 1200 system coupled to a TIMSTOF SCP system. In the case of the latter, cells were separated on a PepSep C-18 75 um column operating at 200 nL\/min. Bulk cell lysates were used to create a library in SpectroNaut 18 from which was used for the analysis of all single cells. 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Stems and leaves were frozen in a dry ice bath and homogenized by beadmill in a solution of methanol, acetonitrile and water (35\/35\/30). The supernatants were clarified by centrifugation at 13,000 x g for 5 minutes at 4C. The supernatant was removed and dried for metabolomic analysis while the precipitate was dried by speedvac and resuspended in 1x S-Trap lysis buffer. Samples were prepared following vendor instructions using the S-Trap 96-well plate format with the exception that cysteines were not reduced and alkylated. Samples were digested for 2 hours at 47C with a 20 nanograms of trypsin in 100mM TEAB solution. Eluted peptides were dried by SpeedVac and quantified using a colorimetric peptide kit. 400 nanograms of peptides were loaded onto EvoTips and were analyzed using ddaPASEF on a TIMSTOF Flex insturment using a 15cm x 75 um column and the 15SPD and 30SPD methods. Metabolomics was performed on a Q Exactive \"Classic\" system coupled to an RSLCnano with a 15cm x 2.1mm HyperSil Gold column using a 20min method. Separate runs were performed in triplicate in positive and negative polarities. Proteomic samples were analyzed with FragPipe 21.1 and Metabolomic samples were analyzed in Compound Discoverer 3.3 SP3. 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However, prolonged cold storage (CS) of kidneys results in poor long-term outcomes after transplantation. We reported previously that CS of rat kidneys for 18 h prior to transplant impaired proteasome function, disrupted protein homeostasis, and reduced graft function. The goal of the present study was to identify the renal proteins that are dysregulated by this CS-induced injury. Isolated donor Lewis rat kidneys were subject to 18-h CS and transplanted into recipient Lewis rats (CS+Tx). Autotransplantation (ATx: transplant with 0-h CS) or Sham (right nephrectomy) surgeries served as controls. The proteome of kidney homogenates was analyzed with tandem mass-tag mass spectrometry to identify CS-induced abnormalities in kidney grafts. CS injury disrupted the renal phosphoproteome in kidney grafts and dysregulated numerous signaling pathways. Integrated analysis of global proteomes and phosphoproteomes identified 15 proteins that were significantly regulated in a CS-specific manner. In particular, proteins and pathways such as complement and coagulation cascades were upregulated, while antioxidant pathways, such as glutathione, were suppressed in CS+Tx groups compared to ATx and Sham controls. This study, for the first time, provides deeper insight into the disruption of the renal graft proteome caused by CS injury and provides a novel set of pathways and molecules that can be investigated to delineate their specific role in renal transplant outcomes, ultimately improving outcomes for patients with end-stage kidney disease.","fileCount":"171","fileSizeKB":"86710189","spectra":"0","psms":"239964","peptides":"60844","variants":"86644","proteins":"8560","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Kidney transplant;cold storage","pi":[{"name":"Nirmala Parajuli","email":"nparajuli@uams.edu","institution":"University of Arkansas for Medical Sciences","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD051567","task":"14aa21ed1edc4af2b4a96108c20d198a","id":"2646"}, {"dataset":"MSV000094565","datasetNum":"94565","title":"A comparison of acetic and formic acid in single H358 cells analyzed by diaPASEF","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713456043000","created":"Apr. 18, 2024, 9:00 AM","description":"Single human H358 cancer cells were isolated by flow cytometry into 96 well plates containing 1 uL of LCMS grade acetonitrile. The cells were placed immediately on dry ice and transported to the lab where they were stored at minus 80C. Dried cell lysate was digested using a solution of 5 nanogram\/microliter LCMS grade trypsin (Pierce) in 0.1percent n-Dodecyl-beta-Maltoside Detergent (DDM, Thermo Fisher, 89902) and 50mM TEAB. Two microliters of trypsin solution were used for each cell prior to the plate being tightly sealed with adhesive plate tape (Fisher, 60180-M143) and room temperature overnight digestion. Following digestion, the peptide digest was briefly centrifuged to condense evaporation and the plates were completely dried with vacuum centrifugation. The peptides were resuspended in 3.5 uL of 0.1 percent formic acid, vortexed and centrifuged prior to loading on the autosampler. ","fileCount":"2163","fileSizeKB":"142375812","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Single cell proteomics;diaPASEF;Buffer modifiers","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051562","task":"fdf0266fb8014d58a4e6860e7b573bf0","id":"2647"}, {"dataset":"MSV000094564","datasetNum":"94564","title":"High-density CRISPRi screens reveal adaptive transcriptional gradients in cyanobacteria","user":"dlcarper","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713452474000","created":"Apr. 18, 2024, 8:01 AM","description":"Cyanobacteria are the oldest form of photosynthetic life and contribute to primary production in nearly every habitat, from permafrost to hot springs. Despite longstanding interest in the biochemical basis of environmental adaptation in these microbes, it remains poorly understood. Here we used a high-density, genome-wide CRISPRi screen to examine the influence of gene-specific transcriptional variation on the growth of Synechococcus sp. PCC 7002 under environmental extrema. Surprisingly, many partial knockdowns enhanced fitness under cold monochromatic conditions. Notably, transcriptional repression of a gene for a core subunit of the NDH-1 complex, which is important for photosynthesis and carbon uptake, improved growth rates under both red and blue light but at distinct, color-specific optima. Multi-target transcriptional repression produced nonadditive effects. Findings reveal diverse mechanisms of environmental adaptation in cyanobacteria and provide a new approach for using gradients in sgRNA activity to pinpoint biochemically influential transcriptional changes in cells.","fileCount":"98","fileSizeKB":"170044845","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus sp. 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The set was used to corroborate the presence of piperlongumine in other plants aside the Piper genus, according to PlantMasst.","fileCount":"42","fileSizeKB":"5366726","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Several","instrument":"Orbitrap Exploris 120","modification":"PRIDE:0000398","keywords":"Natural Products;Natural Extracts;Piperales;Ranunculales","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5a23583ee73146c187631dbde6e6bde5","id":"2650"}, {"dataset":"MSV000094561","datasetNum":"94561","title":"GNPS - CMMC_bile_acid_amino_acid_conjugates","user":"ipmohanty","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713406636000","created":"Apr. 17, 2024, 7:17 PM","description":"MS\/MS fragmentation data of 23 different bile acid steroid core conjugated with amino acids acquired on Q Exactive (positive ionization mode)-with chromatographic separation on a Phenomenex polar C18 column. 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We mutated a series of acetylation sites on Ydj1s J domain to either arginine to block acetylation or glutamine to mimic constitutive acetylation.","fileCount":"52","fileSizeKB":"13062356","spectra":"0","psms":"31024","peptides":"2020","variants":"2411","proteins":"516","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\"","keywords":"Ydj;Translation;Acetylation","pi":[{"name":"Andrew W Truman","email":"A.Truman@uncc.edu","institution":"University of North Carolina at Charlotte","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051428","task":"2366c9eaea68417e94c2b445292ee7a8","id":"2669"}, {"dataset":"MSV000094534","datasetNum":"94534","title":"Broad proteomics analysis of seeding-induced aggregation of a-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinsons disease pathogenesis","user":"pottsgr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713066053000","created":"Apr. 13, 2024, 8:40 PM","description":"Quantitative total proteomics and phospho-proteomics were used to extensively characterize temporal changes in the total and detergent-insoluble protein fractions isolated from neurons from M83 transgenic mice treated with recombinant a-syn PFF. Protein-protein interaction-based network analysis was utilized to define the biological mechanisms altered due to a-syn aggregation to get a comprehensive understanding of specific mechanisms that can be targeted for rational drug design. Analysis results showed broad changes in several key biological processes such as mechanisms regulating cellular proteostasis including changes in several RNA binding proteins.","fileCount":"111","fileSizeKB":"88447934","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Parkinsons Disease, M83 mouse model, total and phosphoproteomics","pi":[{"name":"Brinda Ravikumar","email":"brinda.ravikumar@abbvie.com","institution":"AbbVie","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051424","task":"c5d441297ec945bba6ffb7fa25025016","id":"2670"}, {"dataset":"MSV000094533","datasetNum":"94533","title":"Proteomics identify bowhead whale baleen and muscle tissue in cinder residues at a 16th c. Basque whaling site","user":"solazzoc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713032511000","created":"Apr. 13, 2024, 11:21 AM","description":"Basque whalers were active in the North Atlantic between the 11th and 18th. In the 16th and 17th c., they focused their attention to the coasts of Labrador and the Gulf of St. Lawrence, establishing shore stations from where they launched boats for chasing whales. On shore, they proceeded to render the blubber into oil by boiling it in large trypots. The residual blubber and remaining tissues were then used as fuel to boil more blubber. When the fire pit was full, the cinders were shoveled out, and the process began anew with new materials. Fist-sized lumps of cinder found at Bonne Espérance-4 (EiBk-61), a 16th Basque whaling site on the Quebec Lower North Shore, were sampled for proteomics analysis, to detect potential remains of whale tissues in the cinder. A simple protocol was employed for rapidly processing samples for nanoLC-MS\/MS analysis. Out of 10 spots sampled on two lumps, materials recovered from one successfully yielded whale proteins. The study confirmed the presence of blubber and muscle remains (42 protein groups, including proteins such as myosin, myoglobin and hemoglobin) as well as baleen remains identified by cuticular keratins (12 protein groups, and up to 46 % protein coverage on type I keratin). Baleen, abundantly found at the site, was likely also used as fuel; based on keratin markers, the baleen belonged to a Balaenidae species. The processing of bowhead whale tissue was substantiated by specific peptides from myoglobin and obscurin, a result consistent with the targeting of bowhead whale by Basque whalers.","fileCount":"82","fileSizeKB":"12964783","spectra":"69978","psms":"2337","peptides":"601","variants":"859","proteins":"1464","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mysticeti (NCBITaxon:9761)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"baleen;blubber","pi":[{"name":"Caroline Solazzo","email":"solazzo.c@gmail.com","institution":"Independent","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051422","task":"ef86e7bf96fc4538973179806a503c62","id":"2671"}, {"dataset":"MSV000094531","datasetNum":"94531","title":"GNPS 2404_Workshop_Dysidea_avaria_and_Olea_europa","user":"lfxnothias","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1713010887000","created":"Apr. 13, 2024, 5:21 AM","description":"Mass spectrometry method: the extracts were analyzed by high-performance liquid chromatography (LC) coupled to a high-resolution tandem mass spectrometer (HRMS, q-Exactive, Orbitrap) fitted with a heated ElectroSpray Ionization (ESI) and operating in positive ionization mode. Fragmentation spectra (MS\/MS) were collected in data-dependent mode.\nThe chromatography conditions were as follow: reverse-phase column (2 um C18 particles, 150 x 2.1 mm) and the mobile phase consisted of acetonitrile-water + 0.1% formic acid (gradient mode starting from 10% acetonitrile to 100% in 30 min). ","fileCount":"9","fileSizeKB":"905821","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Olea europaea subsp. europaea (NCBITaxon:158383);Dysidea avara","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sponge;Plant;Annotation;Workshop","pi":[{"name":"Mohamed MEHIRI","email":"Mohamed.MEHIRI@univ-cotedazur.fr","institution":"University Cote d Azur","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2cae78df549147e1bfb64c61c5d1c415","id":"2672"}, {"dataset":"MSV000094528","datasetNum":"94528","title":"GNPS - MSnLib - Multi-stage fragmentation mass spectral library","user":"corinnabrungs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712946743000","created":"Apr. 12, 2024, 11:32 AM","description":"MSnLib - Multi-stage fragmentation mass spectral library of different compound libraries","fileCount":"18281","fileSizeKB":"266512568","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Spectral Library (multi-stage fragmentation)","pi":[{"name":"Corinna Brungs","email":"corinna.brungs@uochb.cas.cz","institution":"Institute of Organic Chemistry and Biochemistry of the CAS","country":"Czech Republic"},{"name":"Robin Schmid","email":"rschmid1789@gmail.com","institution":"Institute of Organic Chemistry and Biochemistry of the CAS","country":"Czech Republic"},{"name":"Tomas Pluskal","email":"tomas.pluskal@uochb.cas.cz","institution":"Institute of Organic Chemistry and Biochemistry of the CAS","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"676a38e2dd574a15905e807d78cf1e57","id":"2673"}, {"dataset":"MSV000094525","datasetNum":"94525","title":"Butcher et al. 2025 metabolomics raw data","user":"cvillette","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712927528000","created":"Apr. 12, 2024, 6:12 AM","description":"Raw data of the non-targeted metabolomics analysis from Butcher et al. 2025\r\nSample G: nettle plant\r\nSample H: reed plant\r\nSample K: nettle fertilizer\r\nSample L: reed fertilizer","fileCount":"13","fileSizeKB":"502524","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Urtica dioica (NCBITaxon:3501);Phragmites australis (NCBITaxon:29695)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Nettle;nettle fertilizer;reed;reed fertilizer;metabolomics","pi":[{"name":"Heintz Dimitri","email":"dimitri.heintz@ibmp-cnrs.unistra.fr","institution":"CNRS","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3db0efb227254dbe9baecdb31d2afaf7","id":"2674"}, {"dataset":"MSV000094521","datasetNum":"94521","title":"Characterization of Monoclonal Antibody Charge Variants under Near-Native Separation Conditions using Nanoflow Sheath Liquid Capillary Electrophoresis-Mass Spectrometry","user":"AZON","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712912421000","created":"Apr. 12, 2024, 2:00 AM","description":"Monoclonal antibodies (mAbs) can undergo post-translational modifications (PTMs) in the production process, these are part of the critical quality attributes (CQA) to ensure protein safety. Charge variants are important PTMs in mAbs and can be separated by using capillary zone electrophoresis (CZE). The EACA method, developed by He et al. (2011), is a popular method for analyzing charge variants in pharmaceutical industries. However, it requires optical detection (e.g., UV) due to non-volatile buffers and does not allow for MS coupling and the identification of the separated charge variants.\r\n\r\nThis study presents a CZE-UV\/MS method that uses a coated neutral static hydroxypropyl methylcellulose (HPMC) with a background electrolyte (BGE) at pH 5 using a nanoflow sheath liquid MS interface (nanoCEasy). Here we describe the effect of several parameters, including pH of BGE, ionic strength, applied voltage, and concentration of mAb in terms of separation performance. Our final method was tested with mAbs of different pIs (7.4-9.2), IgG subclasses (IgG1 and IgG4), and degrees of heterogeneity. Basic and acidic variants were separated from the main variant using 50 mM acetic acid at pH 5, which was adjusted using ammonium hydroxide to the appropriate pH. A linear correlation was obtained in relative abundance of charge variants between our method and the EACA method of He et al. (2011). Coupling the method with the low-flow sheath liquid nanoCEasy interface allowed the identification of low-abundance species (< 10 % relative abundance with respect to the main variant). \r\n\r\nThis method uses volatile buffers and operates at pH closer to non-denaturing conditions (pH 5), allowing for flexibility in hyphenation with MS. It is an open platform method in which no commercial capillaries and interfaces are required. This method can be a useful tool for in-depth charge variants characterization of mAbs. \r\n","fileCount":"9","fileSizeKB":"356802","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Monoclonal antibodies","instrument":"QExtactive Plus","modification":"Charge variants","keywords":"mAbs, charge variants, CZE-MS","pi":[{"name":"Annika van der Zon","email":"a.a.m.vanderzon@uva.nl","institution":"University of Amsterdam","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e37c3bb2838e4972ac112991a8cf8826","id":"2675"}, {"dataset":"MSV000094520","datasetNum":"94520","title":"Molecular Mechanisms of Stress Granule Disassembly Revealed by Chemogenetic Microenvironment Mapping (MicroMap) in Living Cells","user":"RoderickPan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712871958000","created":"Apr. 11, 2024, 2:45 PM","description":"Phase-separated condensates are membrane-less intracellular structures comprised of dynamic protein interactions that organize essential biological processes. Understanding the composition and dynamics of these organelles advances our knowledge of cellular behaviors and disease pathologies related to granule dysregulation. In this study, we apply microenvironment mapping (MicroMap) with a novel HaloTag-based platform (HaloMap) to characterize intracellular stress granule dynamics in living cells. After validating the robustness and sensitivity of this approach, we then profile the stress granule proteome throughout the formation and disassembly, and under pharmacological perturbation. These experiments reveal several novel ubiquitin-related modulators, including the HECT-type E3 ligases ITCH and NEDD4L, as well as the ubiquitin receptor TOLLIP, as key mediators of granule disassembly. In addition, we identify an autophagy-related pathway that promotes granule clearance. Collectively, this work establishes a general photoproximity labeling approach for unraveling intracellular protein interactomes and uncovers previously unexplored regulatory mechanisms of stress granule dynamics.","fileCount":"4931","fileSizeKB":"169546153","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:894 - \\\"Carboxymethylated DTT modification of cysteine.\\\"","keywords":"Stress granules;Proximity labeling;Granule disassembly;MicroMap","pi":[{"name":"David MacMillan","email":"dmacmill@princeton.edu","institution":"Princeton","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d03bd8e2e0304111a217cb10f0360ac7","id":"2676"}, {"dataset":"MSV000094519","datasetNum":"94519","title":"GNPS - Metabolomics of Ilex guayusa leaves focused on methylxanthine","user":"LPN_IKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712870283000","created":"Apr. 11, 2024, 2:18 PM","description":"This study evaluated the variability of methylxanthine content of Ilex guayusa under different geographical, light, and age conditions, as an opportunity to emphasize the value of the chakra agroforestry system in the search for sustainable use of natural products with potential industrial applications.","fileCount":"524","fileSizeKB":"3319165","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ilex guayusa","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS;Guayusa;Methylxanthine","pi":[{"name":"Mateo Andrei Fernandez Valverde","email":"mateo.fernandez@est.ikiam.edu.ec","institution":"Universidad Regional Amazonica Ikiam","country":"Ecuador"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f4b7b5bdb6ee44b5ae5546fa84341fbb","id":"2677"}, {"dataset":"MSV000094518","datasetNum":"94518","title":"Proteomic analysis of unicellular cyanobacterium Crocosphaera subtropica ATCC 51142 under extended light or dark growth","user":"uma_aryal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712863771000","created":"Apr. 11, 2024, 12:29 PM","description":"The daily light-dark cycle is a recurrent and predictable environmental phenomenon to which many organisms, including cyanobacteria, have evolved to adapt. Understanding how cyanobacteria alter their metabolic attributes in response to subjective light or dark growth may provide key features for developing strains with an improved photosynthetic efficiency as well as for applications in enhanced carbon sequestration and renewable energy. Here, we undertook a label free proteomic approach to investigate the effect of extended light (LL) or extended dark (DD) conditions on the unicellular cyanobacterium Crocosphaera subtropica ATCC 51142. We quantified 2287 proteins, of which 603 proteins were significantly different between the two growth conditions. These proteins represent several biological processes, including photosynthetic electron transport, carbon fixation, stress responses, translation, and protein degradation. Results highlight the regulation of proteases including ATP dependent Clp-proteases (endopeptidases) and metalloproteases and may suggest dynamic responses of proteases to extended light or dark exposure to regulate protein turnover or protein quality control mechanisms. The results enhance our understanding of how Crocosphaera subtropica ATCC51142 adjusts its molecular machinery in response to extended light or dark growth conditions. ","fileCount":"33","fileSizeKB":"66680070","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crocosphaera subtropica (NCBITaxon:2546360)","instrument":"Q Exactive HF","modification":"Methionine Oxidation 9M)","keywords":"Crocosphaera subtropica, photosynthesis, nitrogen fixation, light-dark cycle, peptidases","pi":[{"name":"Uma Aryal","email":"uaryal@purdue.edu","institution":"Purdue University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b083ff215be44d3aaa9defabb7b6aba7","id":"2678"}, {"dataset":"MSV000094516","datasetNum":"94516","title":"GNPS - Fasting in Female retina RPE with C13 glucose tracing","user":"jianhaidulab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712858777000","created":"Apr. 11, 2024, 11:06 AM","description":"22 week old female Tfamfl\/fl (aka WT), BEST1Cre;Tfamfl\/fl, BEST1Cre;Tfamfl\/fl;AN\/+ mice were fasted for 6 hrs (8am-2pm), then were retro-orbital injected with 13C6-glucose (Cambridge Isotopes Laboratories): 250mg\/kg in 100-135ul saline and 0.2 um sterile filtered. Tissues were processed 30min after injection. A cryolysis method was used to extract RPE metabolites. NR metabolites were extracted as usual.","fileCount":"2","fileSizeKB":"20083","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus sp. (NCBITaxon:10095)","instrument":"Agilent 7890B\\\/5977B GC MS system","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"metabolism;fasting","pi":[{"name":"Jianhai Du","email":"jianhai.du@wvumedicine.org","institution":"West Virginia University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c17dd5d6fa334a169f9b562386c7ca71","id":"2679"}, {"dataset":"MSV000094515","datasetNum":"94515","title":"GNPS - U19 ADRC NCRAD 42167 Stool","user":"jzemlin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712856391000","created":"Apr. 11, 2024, 10:26 AM","description":"Corrected U19 ADRC human stool samples dataset. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"2597","fileSizeKB":"86953983","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"\\tMS:1001911","modification":"\\tMS:1002864","keywords":"stool;fecal;U19;metabolomics","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b8d8f89d14094df7954b1966cf699025","id":"2680"}, {"dataset":"MSV000094513","datasetNum":"94513","title":"GNPS - Bacteroides thetaiotaomicron Lipidomics LC-MSMS","user":"MSF_MPI_Tue","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712839920000","created":"Apr. 11, 2024, 5:52 AM","description":"This dataset contains LC-MS-MS data for lipidomics of Bacteroides thetaiotaomicron. 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Consequently, how peptide properties and post-translational modifications influence exchange rates remain unknown. In this study, we sought to test the accuracy of predicted values by performing hydrogen exchange measurements on whole cell digests to generate an unbiased dataset of approximately 1100 peptides derived from naturally-occurring protein sequences. A remarkable 97% of observed exchange rates of peptides are within two-fold of predicted values. Using fully deuterated controls, we found that for approximately 50% of the peptides, the amino acid sequence and, consequently, the intrinsic exchange rate, are the primary contributors to back exchange. A meta-analysis of the remaining peptides physicochemical properties revealed multiple features that contribute either positively or negatively to back exchange discrepancies. Employing our workflow for comparable measurements on synthetic peptide mixtures containing post-translational modifications, and their unmodified counterparts, we show that lysine acetylation has a strong effect on the observed exchange rate, whereas serine\/threonine phosphorylation does not. Our automated workflow enables high-throughput determination of exchange rates in peptide mixtures with diverse properties.","fileCount":"137","fileSizeKB":"30693702","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend;Q Exactive HF","modification":"C-carbamidomethylation, ST-phosphorylation, K-acetylation","keywords":"hydrogen exchange, mass spectrometry, cell digest, exchange rates, acetylation, phosphorylation","pi":[{"name":"Steven A. 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The expression of mHTT causes selective degeneration, mainly in the striatum and cortex brain regions. Yet, the molecular signatures that underlie their selective sensitization remain incompletely characterized. In HD mouse models, we systematically employed immunopurification-mass spectrometry using HTT antibodies targeting non-overlapping epitopes to capture distinct sub-cellular pools of HTT complexes and postulate domain-specific interactions. We also identified mHTT- and tissue-dependent interactions at different disease stages, which were validated using targeted mass spectrometry and computational analysis of HD genetic modifiers. Among the polyQ-dependent, striatum-enriched interactions, we identified interaction with the mediator complex that results in its altered nuclear-cytoplasmic distribution. Integrating IP-MS data with thermal profiling of the mediator complex in HTT deficient cells supports an interaction interface with the mediator tail domain. Broadly, striatum-enriched HTT interactions highlight calcium homeostasis and ion transport at the synapse as sensitizing molecular signatures.","fileCount":"4926","fileSizeKB":"979467209","spectra":"11771840","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF;timsTOF Ultra","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"IP-MS;protein interactions;thermal profiling;DIA;pasef;FragPipe;DIANN","pi":[{"name":"Ileana M Cristea","email":"icristea@princeton.edu","institution":"Department of Molecular Biology, Princeton University, USA","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD051339","task":"2a89f97ea8a24bbb93bee9c56f9ea019","id":"2685"}, {"dataset":"MSV000094508","datasetNum":"94508","title":"EVs enriched from plasma by placental proteins ","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712749427000","created":"Apr. 10, 2024, 4:43 AM","description":"Plasma EVs were enriched using placental protein markers. The proteins were extracted in 5% SDS and processed with S-Trap 96 well plates without reduction and alkylation to preserve potential labile PTMs. Digestion was performed with trypsin. Eluted peptides were loaded onto EvoTips and peptides were analyzed using an EvoSep one with a 30SPD method (15cm column and approximately 44 minutes of run time) coupled to a TIMSTOF Flex mass spectrometer with 20um CaptiveSpray emitter. A default diaPASEF method in TIMSControl 5.0 was used \"Short gradient diaPASEF\" with the exception that the upper 1\/k0 limit was increased to 1.45 for MS1 to allow the monitoring of the 1222 internal calibrant during run times. This is essential as the Johns Hopkins University does not have buildings with functional HVAC and calibrations can drift considerably during all run times. Monitoring the 1222 ion mass and ion mobility every 4 hours is required to identify when instrument calibrations are required, on average every 8-12 hours. 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We complemented the analysis with HNSC and normal oral epithelial cell lines.","fileCount":"205","fileSizeKB":"496016106","spectra":"12790211","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\"","keywords":"hnscc","pi":[{"name":"Dr. Thomas Kislinger","email":"thomas.kislinger@utoronto.ca","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8569c45d043645d2b36ef771464d1447","id":"2687"}, {"dataset":"MSV000094506","datasetNum":"94506","title":"Targeting the autophagy-NAD axis protects against cell death in Niemann-Pick type C1 disease models","user":"alejandro_metabo10","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712698254000","created":"Apr. 9, 2024, 2:30 PM","description":"Impairment of autophagy leads to an accumulation of misfolded proteins and damaged organelles and has been implicated in plethora of human diseases. Loss of autophagy in actively respiring cells has also been shown to trigger metabolic collapse mediated by the depletion of nicotinamide adenine dinucleotide (NAD) pools, resulting in cell death. Here we found that the deficit in the autophagy-NAD axis underpins the loss of viability in cell models of a neurodegenerative lysosomal storage disorder, Niemann-Pick type C1 (NPC1) disease. Defective autophagic flux in NPC1 cells resulted in mitochondrial dysfunction due to impairment of mitophagy, leading to the depletion of both the reduced and oxidised forms of NAD as identified via metabolic profiling. Consequently, exhaustion of the NAD pools triggered mitochondrial depolarisation and apoptotic cell death. Our chemical screening identified two FDA-approved drugs, celecoxib and memantine, as autophagy activators which effectively restored autophagic flux, NAD levels, and cell viability of NPC1 cells. Of biomedical relevance, either pharmacological rescue of the autophagy deficiency or NAD precursor supplementation restored NAD levels and improved the viability of NPC1 disease patient-derived primary fibroblasts and cortical neurons differentiated from induced pluripotent stem cells (iPSCs). Together, our findings identify the autophagy-NAD axis as a mechanism of cell death and a target for therapeutic interventions in NPC1 disease, with a potential relevance to other neurodegenerative disorders.","fileCount":"59","fileSizeKB":"1566618","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Autophagy, fibroblasts, lysosomal storage disorders, NAD, neurodegeneration, NPC1","pi":[{"name":"Viktor I. 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Endogenous tracing of glucose metabolism highlighted the gamma-glutamyl cycle as a downstream pathway implicated in lung cancer, driven by an imbalance in glutathione metabolism due to reactive oxygen species (ROS) accumulation. Notably, our study unveiled unique volatile changes associated with gemcitabine and cisplatin treatment, which significantly abrogated tumor growth in vivo. ","fileCount":"306","fileSizeKB":"8442127","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cancer;VOC;metabolism;oxidative stress","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ae706b3e8b9e43588686075e2deb3b82","id":"2689"}, {"dataset":"MSV000094501","datasetNum":"94501","title":"Immunoprecipitation and LC-MS\/MS to identify protein partners of the Brain tumor (BRAT) RNA-binding protein during the Drosophila maternal-to-zygotic transition","user":"Sichun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712683018000","created":"Apr. 9, 2024, 10:16 AM","description":"The RNA-binding protein, Brain tumor (BRAT), binds to mRNAs through its NHL domain and targets them for degradation and\/r translational repression. During early embryogensis of all animals, a subset of maternal mRNAs is degraded during a process know as the maternal-to-zygotic transition (MZT). BRAT has been shown to bind and destabilize a subset of maternal mRNAs. The goal of this study was to identify possible partner proteins of BRAT in post-transcriptional regulation. To do so, BRAT was immunoprecipitated from 0-3 hour old Drosophila embryos with a phage-displayed synthetic antibody and the co-purified proteins identified by LC-MS\/MS relative to IP with a control antibody.","fileCount":"52","fileSizeKB":"15867650","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"QE-HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Brain tumor, BRAT, NHL domain, RNA-binding protein, Drosophila, embryo, maternal-to-zygotic transition, immunoprecipitation, mass spectrometry","pi":[{"name":"Howard Lipshitz","email":"howard.lipshitz@utoronto.ca","institution":" University of Toronto","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"907bb627d5e149338d258af78209b098","id":"2690"}, {"dataset":"MSV000094498","datasetNum":"94498","title":"Phospho-proteome of meiotic maturation","user":"peshkin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712618456000","created":"Apr. 8, 2024, 4:20 PM","description":"we analyze quantitatively the abundance of the proteins and their phosphorylation state in the full-grown Stage VI oocyte of Xenopus during meiotic maturation","fileCount":"6","fileSizeKB":"21348750","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xenopus laevis (NCBITaxon:8355)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:21 - 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Amino Acids;N-acyl lipids;Fatty ACids;Decarboxylated Amino Acids","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c9e2596086414e9588f1a902823bd30a","id":"2692"}, {"dataset":"MSV000094494","datasetNum":"94494","title":"Chikungunya virus glycoprotein targeting of host factors increases viral fitness in human macrophage","user":"jameswohl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712613496000","created":"Apr. 8, 2024, 2:58 PM","description":"Proteomic analysis of Chikungunya virus E1 and E2 interacting proteins during macrophage infection","fileCount":"13","fileSizeKB":"12868938","spectra":"824916","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - 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This study used an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS\/MS) approach and biochemical analysis to investigate substance changes in leaves at three different stages and elucidate the relationship between metabolites and antioxidant capacity. The findings showed that MpP leaves contained 957 metabolites, the majority of which were phenolic acids, lipids, and terpenoids. The metabolite profiling of Mp leaves was significantly influenced by their growth and development at different stages. A total of 317 differentially accumulated metabolites (DAMs) were screened, including 150 primary metabolites and 167 secondary metabolites, with 202 DAMs found in bud leaf vs. tender leaf, 54 DAMs in tender leaf vs. mature leaf, and 254 DAMs in bud leaf vs. mature leaf. Total phenolics, flavonoids, and anthocyanin concentrations decreased as Mp leaves grew and developed, whereas terpenoids increased significantly. The secondary metabolites also demonstrated a positive correlation with antioxidant activity. Phenolics, flavonoids, terpenoids, and anthocyanins were the primary factors influencing the antioxidant activity of leaves. These findings provide new insights into the metabolite formation mechanism, as well as the development and utilization of Mp tea.","fileCount":"63","fileSizeKB":"307409","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mussaenda pubescens (NCBITaxon:271247)","instrument":"UPLC-MS\\\/MS ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Mussaenda pubescens;antioxidant;Leave growth stages","pi":[{"name":"Caibi Zhou","email":"teasky@foxmail.com","institution":"Qiannan Normal University for Nationalities","country":"China"},{"name":"Teerayoot Girdthai","email":"teerayoot@sut.ac.th","institution":"Suranaree University of Technology","country":"Thailand"},{"name":"Xiaolu Zhou","email":"arainbowl@163.com","institution":"Qiannan Normal University for Nationalities","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051276","task":"563b15a7882c4c3b9099c381ae4f4f00","id":"2695"}, {"dataset":"MSV000094490","datasetNum":"94490","title":"Fungi isolated from ants, anthills, and the soil of Mexican cloud forest","user":"Stahgal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712592989000","created":"Apr. 8, 2024, 9:16 AM","description":"The database consists of 248 HPLC-QTOF-HRMS\/MS analyses of microscopic fungi isolated from soil samples collected in 2021, in the cloud forest of central Veracruz, Mexico. Soil samples were collected from around of 17 ant nests, from inside of 15 anthills, and from two transit areas. Also entomogenic fungi of ants. The two best represented ants were Solenopsis geminata and Atta mexicana, the others were Dorymyrmex bicolor, Nomamyrmex esenbeckii, Cheliomyrmex morosus, and Camponotus sericeiventris. Growth media and solvents analyses are available.\r\nDataset license: CC BY-NC-ND 4.0","fileCount":"268","fileSizeKB":"5688614","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"248 morphotypes","instrument":"Agilent 6530 Accurate-Mass Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"fungi;soil;anthill;ant;cloud forest;Solenopsis;Atta;Nomamyrmex;Cheliomyrmex;Dorymyrmex;Camponotus;Mexico","pi":[{"name":"Dr. Jose Alberto Rivera Chavez","email":"jrivera@iquimica.unam.mx","institution":"Universidad Nacional Autonoma de Mexico","country":"Mexico"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fc42ad477f5045a2ad74e90ae22148d6","id":"2696"}, {"dataset":"MSV000094489","datasetNum":"94489","title":"Proteome of clothianidin exposed honey bees reveals a possible mechanism behind impairment of sucrose responsiveness","user":"NadiaTs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712592649000","created":"Apr. 8, 2024, 9:10 AM","description":"Honey bee workers were exposed to Clothianidin for 7 days. After exposure, they were subject to sucrose responsiveness test and a discrimination learning and memory test using the proboscis extension paradigm. After the 24-hour memory test, the bees were frozen on dry ice. Their brains were extracted with hypopharyngeal gland removed. 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Database files contain the predicted Lymnaea stagnalis proteome used for searches as well as the reference mouse proteome used for annotation of Lymnaea stagnalis sequences. 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Currently, the heterogeneity of sepsis makes it challenging to determine the molecular mechanisms that define the syndrome. Here, we leverage population scale proteomics to analyze a well-defined cohort of 1364 blood samples taken at time-of-admission to the emergency department from patients suspected of sepsis. We identified panels of proteins using explainable artificial intelligence that predict clinical outcomes and applied these panels to reduce high-dimensional proteomics data to a low-dimensional interpretable latent space (ILS). Using the ILS, we constructed an adaptive digital twin model that accurately predicted organ dysfunction, mortality, and early-mortality-risk patients using only data available at time-of-admission. In addition to being highly effective for investigating sepsis, this approach supports the flexible incorporation of new data and can generalize to other diseases to aid in translational research and the development of precision medicine.","fileCount":"30071","fileSizeKB":"938236134","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sepsis;DIA;diaPASEF;plasma","pi":[{"name":"Adam Linder","email":"adam.linder@med.lu.se","institution":"Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University","country":"Sweden"},{"name":"Johan Malmstrom","email":"johan.malmstrom@med.lu.se","institution":"Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University","country":"Sweden"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051271","task":"9cf5069e60f24857a4fedbb26894853a","id":"2699"}, {"dataset":"MSV000094483","datasetNum":"94483","title":"Liver and Pancreatic-Targeted Interleukin-22 as a Therapeutic for Metabolic Dysfunction-Associated Steatohepatitis","user":"hsajiir","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712555952000","created":"Apr. 7, 2024, 10:59 PM","description":"Metabolic dysfunction-associated steatohepatitis (MASH) is the most prevalent cause of liver disease worldwide, with a single approved therapeutics. Previous research has shown that interleukin-22 (IL-22) can suppress beta-cell stress, reduce local islet inflammation, restore appropriate insulin production, reverse hyperglycemia, and ameliorate insulin resistance in preclinical models of diabetes. In clinical trials long-acting forms of IL-22 have led to increased proliferation in the skin and intestine, where the IL-22RA1 receptor is highly expressed. To maximise beneficial effects whilst reducing the risk of epithelial proliferation and cancer, we designed short-acting IL-22-bispecific biologic drugs that successfully targeted the liver and pancreas. 10-fold lower doses of these bispecific biologics exceeded the beneficial effects of native IL-22 in multiple preclinical models of MASH, without off-target effects. Treatment restored glycemic control, markedly reduced hepatic steatosis, inflammation, and fibrogenesis. These short-acting IL-22-bispecific targeted biologics are a promising new therapeutic approach for MASH.","fileCount":"50","fileSizeKB":"61606547","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"Static Modification: Carbamidomethyl (C); Unimod Accession # 4 ;Dynamic Modification: Oxidation (M); Unimod Accession # 35","keywords":"Liver;MASH;Steatosis;HepG2;IL-22","pi":[{"name":"Sumaira Zia Hasnain","email":"sumaira.hasnain@mater.uq.edu.au","institution":"Mater Research Institute - The University of Queensland","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051262","task":"b99393ba694b4201b0285a28fcf820be","id":"2700"}, {"dataset":"MSV000094482","datasetNum":"94482","title":"GNPS - Bacteria Endophyte Extract (Strain 191, 76)","user":"nolasuryani","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712549534000","created":"Apr. 7, 2024, 9:12 PM","description":"Bacteria endophyte strain 191, 76 isolated from ginseng plant","fileCount":"5","fileSizeKB":"360685","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"LCMS-8040","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"endophyte","pi":[{"name":"Nola Suryani Putri","email":"nolasuryani@yu.ac.kr","institution":"Yeungnam University","country":"South Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d55d0b7da91f488b882acf810be9ee64","id":"2701"}, {"dataset":"MSV000094479","datasetNum":"94479","title":"Comparative proteomic analysis of Arabidopsis plants treated with osmotic stress","user":"Liyongkang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712473096000","created":"Apr. 6, 2024, 11:58 PM","description":"To evaluate the differences in the acclimation of gcd1 gcd3 and WT plants to osmotic stress, we conducted an LC-MS\/MS-based label-free quantitative proteomics analysis of WT and gcd1 gcd3 seedlings grown under mock conditions or osmotic stress imposed by 300 mM mannitol treatment. Comparative proteomic analysis of plants treated with osmotic stress reveals the basis of the underlying acclimation mechanism.","fileCount":"14","fileSizeKB":"13415810","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis; glucosylceramides; osmotic stress; plasma membrane","pi":[{"name":"Nan Yao","email":"yaonan@mail.sysu.edu.cn","institution":"Sun Yat-sen University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f5b65f05a4bd450ca97330c4fc13c84f","id":"2702"}, {"dataset":"MSV000094478","datasetNum":"94478","title":"GNPS - proteomics and lipidomics of LAT1-4F2hc complex","user":"wudi1985","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712440696000","created":"Apr. 6, 2024, 2:58 PM","description":"proteomics and lipidomics analysis of recombinant LAT1-4F2hc complex purified from HEK293S cells","fileCount":"6","fileSizeKB":"1177082","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"LTQ Orbitrap XL","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"LAT1-4F2hc","pi":[{"name":"Prof. Carol v. 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The cells were cultured for an additional 2 hr and harvested. Proteins from the wild-type and delta prmA strains were extracted, digested with trypsin, and analyzed by LC-MS\/MS on a Q-Exactive HF-X. LC-MS\/MS data was processed with MaxQuant v2.2.0.0, identifying peptides by searching tandem mass spectra against the E. coli K12 sequences from Uniprot Knowledgebase downloaded on December 19, 2022. The search parameters included fully LysC digestion with 2 missed cleavage sites, oxidation of methionine as variable modifications, and precursor mass tolerances of 20 ppm and 4.5 ppm for the first and main searches, respectively. Multiplicity was set as 2 of a light channel, and a heavy channel with Lys8. The \"requantify\" function was enabled.","fileCount":"71","fileSizeKB":"79246453","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli BW25113 (NCBITaxon:679895)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"bacteria;methylation;ribosome;PrmA","pi":[{"name":"Ernesto Nakayasu","email":"ernesto.nakayasu@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"29025393ca0543008b38c298283701ba","id":"2705"}, {"dataset":"MSV000094474","datasetNum":"94474","title":"GNPS - CMMC_Stearic_Acid_with_QXX_Tripeptides","user":"kyvittali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712342838000","created":"Apr. 5, 2024, 11:47 AM","description":"Stearoyl Chloride conjugated with QXX tripeptide sequence for screening reaction","fileCount":"3","fileSizeKB":"446900","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Stearic Acid;QXX;Tripeptides;CMMC;Combinatorial Synthesis","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"522a00dbd44a47588b0de81318a22107","id":"2706"}, {"dataset":"MSV000094473","datasetNum":"94473","title":"GNPS - CMMC_Oleic_Acid_with_QXX_Tripeptides","user":"kyvittali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712342372000","created":"Apr. 5, 2024, 11:39 AM","description":"Oleic Acid conjugated with QXX tripeptides using EDC and DMAP","fileCount":"3","fileSizeKB":"430055","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Oleic Acid;QXX;Combinatorial Synthesis;Tripeptides;N-acyl lipids","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c6bd94dd9c2b4532a0a91da656d4d903","id":"2707"}, {"dataset":"MSV000094471","datasetNum":"94471","title":"Proteomic changes orchestrate metabolic acclimation of a unicellular diazotrophic cyanobacterium during light-dark cycle and nitrogen fixation states","user":"uma_aryal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712266980000","created":"Apr. 4, 2024, 2:43 PM","description":"Cyanobacteria have developed an impressive array of proteins and pathways, each tailored for specific metabolic attributes, to execute photosynthesis and biological nitrogen (N2)-fixation. An understanding of these biologically incompatible processes provides important insights into how they can be optimized for renewable energy. To expand upon our current knowledge, we performed label-free quantitative proteomic analysis of the unicellular diazotrophic cyanobacterium Crocosphaera subtropica ATCC 51142 grown with and without nitrate under 12-hour light-dark cycles. Results showed significant shift in metabolic activities including photosynthesis, respiration, biological nitrogen fixation (BNF), and proteostasis to different growth conditions. We identified more than 20 nitrogenase enzymes which were among the most highly expressed proteins in the dark under nitrogen-fixing conditions, emphasizing their importance in BNF. Nitrogenase enzymes were not expressed under non nitrogen fixing conditions, suggesting a regulatory mechanism based on nitrogen availability. The synthesis of key respiratory enzymes and uptake hydrogenase (HupSL) synchronized with the synthesis of nitrogenase indicating a coordinated regulation of processes involved in energy production and BNF. Data suggests alternative pathways that cells utilize, such as oxidative pentose phosphate (OPP) and 2-oxoglutarate (2-OG) pathways, to produce ATP and support bioenergetic BNF. Data also indicates the important role of uptake hydrogenase for the removal of O2 to support BNF. Overall, this study expands upon our knowledge regarding molecular responses of Crocosphaera 51142 to nitrogen and light-dark phases, shedding light on potential applications and optimization for renewable energy.","fileCount":"33","fileSizeKB":"87628763","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Crocosphaera subtropica (NCBITaxon:2546360)","instrument":"Orbitrap Fusion Lumos","modification":"Oxidation [M]","keywords":"Cyanobacteria, photosynthesis, nitrogen fixation, proteomics, mass spectrometry","pi":[{"name":"Uma Aryal","email":"uaryal@purdue.edu","institution":"Purdue University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"22cb559d25ee4be589d63b2db588581f","id":"2708"}, {"dataset":"MSV000094470","datasetNum":"94470","title":"Modification of human formin homology domain containing proteins (Fhod1 and Fhod3) by protein arginine methyltransferase 7 (PRMT7): Interplay between methylation and phosphorylation of a novel cytoplasmic target. ","user":"Tlowe6","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712259284000","created":"Apr. 4, 2024, 12:34 PM","description":"Enzymatic assay of the phosphorylation of Fhod3 peptides by ROCK1","fileCount":"62","fileSizeKB":"2247615","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6545 Q-TOF LC\\\/MS","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Enzymatic assay;ROCK1;Fhod1;Fhod3","pi":[{"name":"Steven G. 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","fileCount":"5","fileSizeKB":"288031","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile Salt Hydrolase;Cholic glycine;BSH Assay;CMMC","pi":[{"name":"Pieter C. 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In humans, multiple loss-of-function mutations in genes affecting plasmenyl-PE metabolism have been implicated in hereditary spastic paraplegia (HSP), including SELENOI. Herein, we developed a mouse model of nervous system-restricted SELENOI deficiency that circumvents embryonic lethality caused by constitutive deletion and recapitulates phenotypic features of HSP. Resulting mice exhibited pronounced alterations in brain lipid composition, which coincided with motor deficits and neuropathology including hypomyelination, elevated reactive gliosis, and microcephaly. Further studies revealed increased lipid peroxidation in oligodendrocyte lineage cells and disrupted oligodendrocyte maturation both in vivo and in vitro. Altogether, these findings detail a critical role for SELENOI-derived plasmenyl-PE in myelination that is of paramount importance for neurodevelopment.","fileCount":"71","fileSizeKB":"9982207","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lipidomics, Selenium, Selenoprotein I, Plasmenyl-PE, Myelin, Brain","pi":[{"name":"Ashley E Shay","email":"aes5254@psu.edu","institution":"The Pennsylvania State University","country":"United States of America"},{"name":"Matthew W Pitts","email":"mwpitts@hawaii.edu","institution":"John A Burns School of Medicine, University of Hawaii","country":"United States of America"},{"name":"Peter R Hoffman","email":"peterrh@hawaii.edu","institution":" John A Burns School of Medicine, University of Hawaii","country":"United States of America "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"d41f30e57ff14e50a556e0f02ff289cf","id":"2711"}, {"dataset":"MSV000094462","datasetNum":"94462","title":"GNPS Rhodococcus sp. 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AcOEt exctratcts were analysed through UPLC-MS\/MS and MS data was processed using NP3_MS_workflow.","fileCount":"31","fileSizeKB":"1979706","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rhodococcus (NCBITaxon:1827)","instrument":"ACQUITY UPLC H-Class;Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bacteria soil;Rhodococcus;metabolomics;NP3_MS_Workflow","pi":[{"name":"Daniela B. B. 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AcOEt exctratcts were analysed through UPLC-MS\/MS and MS data was processed using NP3_MS_workflow.","fileCount":"22","fileSizeKB":"1941319","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brevibacillus brevis (NCBITaxon:1393)","instrument":"ACQUITY UPLC;Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"soil bacteria;brevibacillus;metabolomics;NP3_MS_Workflow","pi":[{"name":"Daniela B. B. 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Macrophages represent a cell type of high relevance in the TME, but the impact of LPA on them remains obscure. Here, we uncovered distinct LPA-species-specific responses in human monocyte-derived macrophages through unbiased phosphoproteomics, with 87 and 161 phosphosites upregulated by 20:4 and 18:0 LPA, respectively, and only 24 shared sites. Specificity was even more pronounced for downregulated phosphosites (163 versus 5 sites). Considering the frequently high levels of 20:4 LPA in the TME and its association with poor survival, these findings are of relevance for further understanding of cancer promotion and maintenance. Pathway analysis pinpointed RHO\/RAC1 GTPase signaling as the predominantly impacted pathway, including AHRGEF and DOCK guanine exchange factors, ARHGAP GTPase activating proteins, and regulatory protein kinases. Consistent with these findings, exposure to 20:4 resulted in strong alterations to the actin filament network and a consequent enhancement of macrophage migration. Moreover, 20:4 LPA induced p38 phosphorylation, a response not mirrored by 20:4 LPA, whereas the pattern for AKT was reversed. Furthermore, RNA profiling identified genes involved in cholesterol\/lipid metabolism as selective targets of 20:4 LPA. These findings imply that the two LPA species cooperatively regulate different pathways to support functions essential for pro-tumorigenic macrophages within the TME. These include cellular survival via AKT activation and migration through RHO\/RAC1 and p38 signaling.","fileCount":"95","fileSizeKB":"60172645","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Exploris ;Phosphorylation;Orbitrap;macrophages;lysophosphatidic acid","pi":[{"name":"Prof. Dr. Rolf Mueller","email":"rmueller@imt.uni-marburg.de","institution":"Philipps-Universitaet Marburg, Zentrum fuer Tumorbiologie (Tumorbiologie) Institut fuer Molekularbiologie und Tumorforschung (IMT)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD051172","task":"35256dc81b4a4120b3743f67c041b21f","id":"2715"}, {"dataset":"MSV000094457","datasetNum":"94457","title":"Digestion of whey peptide induces bioactivity on glial cells","user":"lucilene","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712112198000","created":"Apr. 2, 2024, 7:43 PM","description":"Whey derived peptides have shown potential activity improving brain function in pathological condition. However, there is little information about their mechanism of action on glial cells, which have important immune functions in brain. Astrocytes and microglia are essential in inflammatory and oxidative defense that take place in neurodegenerative disease. In this work we evaluate antioxidant and anti-inflammatory bioactivity of whey peptide in glial cells. Peptides were formed during simulated gastrointestinal digestion (Infogest protocol), and low molecular weight (<5kDA) peptides (WPHf) attenuated reactive oxygen species (ROS) production induced by hydrogen peroxide stimulus in both cells in dose-dependent manner. WPHf induced an increase in the antioxidant glutathione (GSH) content and prevented GSH reduction induced by lipopolysaccharides (LPS) stimulus in astrocytes cells in a cell specific form. An increase in cytokine mRNA expression (TNFalpha and IL6) and nitric oxide secretion induced by LPS was attenuated by WPHf pre-treatment in both cells. The inflammatory pathway was dependent on NFkB activation. Bioactive peptide ranking analysis showed positive correlation with hydrophobicity and negative correlation with high molecular weights. The sequence identification revealed 19 peptides cross-referred with bioactive database for others functions in addition to anti-inflammatory and antioxidant. Bioactive peptides were reach in leucine, valine and tyrosine in the C-terminal region and lysine in the N-terminal region. These proteomics data bring important aspects regarding the mechanism of action in glial cells and the structural-activity relationship of whey peptides resistant to digestion.","fileCount":"5","fileSizeKB":"6792595","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913)","instrument":"Q-Exactive (Thermo Fisher)","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Mass spectrometry;peptide sequencing;Whey peptide;Glial cells","pi":[{"name":"Bruno Cesar Rossini","email":"bruno.rossini@unesp.br","institution":"Institute of Biotechnology, UNESP, Botucatu, SP","country":"Brazil"},{"name":"Eduarda Spagnol Sacilotto","email":"dudassacilotto@gmail.com","institution":"Institute of Food Technology (ITAL)","country":"Brazil"},{"name":"Fabiana Galland","email":"fabiana.pe@ital.sp.gov.br","institution":"Institute of Food Technology (ITAL)","country":"Brazil"},{"name":"Joseane Morari","email":"morarij@gmail.com","institution":"University of Campinas (UNICAMP)","country":"Brazil"},{"name":"Juliana Santos de Espindola","email":"juliana.s.espindola@gmail.com","institution":"Institute of Food Technology (ITAL)","country":"Brazil"},{"name":"Licio Augusto Velloso","email":"lavellos@unicamp.br","institution":"University of Campinas (UNICAMP)","country":"Brazil"},{"name":"Lilian Gabriely Almeida","email":"liliangvca@gmail.com","institution":"Institute of Food Technology (ITAL)","country":"Brazil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Institute of Biotechnology, UNESP, Botucatu, SP","country":"Brasil"},{"name":"Maria Teresa Bertoldo Pacheco","email":"amtb@ital.sp.gov.br","institution":"Institute of Food Technology (ITAL)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"17d8ae7132ef4158a504da15f2aee861","id":"2716"}, {"dataset":"MSV000094452","datasetNum":"94452","title":"ZBTB7A and KDM5 activity co-regulate NF-kB target gene expression and oxidative phosphorylation in triple negative breast cancer","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712070962000","created":"Apr. 2, 2024, 8:16 AM","description":"We previously described that the KDM5B histone H3 lysine 4 (H3K4) demethylase is an oncogene in estrogen receptor-positive breast cancer. Here we report that KDM5A is amplified and overexpressed in basal breast tumors and is associated with chemotherapy resistance. Using CRISPR knockout viability screens -\/+ KDM5 inhibition (KDM5i), we found that deletion of the ZBTB7A transcription factor and core SAGA complex sensitized to KDM5i, whereas knockout of RHO-GTPases led to resistance. ChIP-seq and RNA-seq analyses revealed colocalization of ZBTB7A and KDM5A\/B at promoters with high H3K4me3 and dependence of KDM5A binding on ZBTB7A. ZBTB7A knockout altered transcriptional response to KDM5i specifically at NF-kB target genes, oxidative phosphorylation, and E2F-driven proliferation pathways. Our work furthers understanding of KDM5-mediated gene regulation in breast cancer and identified key pathways mediating sensitivity to KDM5i.","fileCount":"27","fileSizeKB":"8059501","spectra":"337294","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"K-monomethylation, K-dimethylation, K-trimethylation, K-acetylation, K-propionylation, N-terminal propionylation, S-phosphorylation, K-ubiquitination","keywords":"global chromatin profiling","pi":[{"name":"Kornelia Polyak","email":"Kornelia_Polyak@dfci.harvard.edu","institution":"Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6cdb4a21a7394726bb5c4e8fa055ea9b","id":"2717"}, {"dataset":"MSV000094448","datasetNum":"94448","title":"Mass Spectrometry Imaging of the Extracellular Matrix of the Subchondral Bone in Osteoarthritis Provides Evidence of Tissue Remodeling on the Protein Level that May Precede Cartilage Loss","user":"cschurman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712016787000","created":"Apr. 1, 2024, 5:13 PM","description":"Osteoarthritis (OA) of the knee is a degenerative condition of the skeletal extracellular matrix (ECM) marked by the loss of articular cartilage and subchondral bone homeostasis that preferentially occurs in the medial side of the joint. Treatments for OA beyond full joint replacement are lacking primarily due to gaps in molecular knowledge of the biological drivers for disease progression. MALDI-Mass Spectrometry Imaging (MSI) allows molecular spatial mapping that is used to investigate the proteomic landscape of OA providing molecular details on the progression of joint degeneration. Entire histologic sections of human tibial plateaus from OA patients and cadaveric controls were treated with collagenase III to target ECM proteins prior to imaging using a timsTOF flex mass spectrometer (Bruker) for the first reported study of MALDI-MSI on bone protein. Data from healthy cadaveric joints and both lateral and medial sides of OA joints were automatically segmented identifying distinct areas of joint damage. Candidate ECM markers comparing either OA to cadaveric tissues or OA medial to OA lateral tissues resulted in 44 candidate peptides that emphasize the significant spatial difference between OA and healthy bone (AUROC >0.85). 31 of 44 peptide markers, resulting from ECM proteins such as COL1A1, COL3A1, and novel detection of COL6A1 and COL6A3 in bone, with significantly elevated abundance in our full OA cohort, indicate disease progression. Spatial maps of these markers revealed distinct tissue damage and disease pathologies in the subchondral bone that are related to protein structural changes in the ECM, changes that may precede overlying cartilage loss in OA.","fileCount":"134","fileSizeKB":"381935900","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX","modification":"MOD:00038 - \\\"A protein modification that effectively converts an L-proline residue to 3-hydroxy-L-proline.\\\";MOD:00039 - \\\"A protein modification that effectively converts an L-proline residue to 4-hydroxy-L-proline\\\"","keywords":"Osteoarthritis;MALDI Imaging;Extracellular Matrix;Cartilage;Subchondral Bone","pi":[{"name":"Birgit Schilling","email":"bschilling@buckinstitute.org","institution":"Buck Institute","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD051135","task":"c8ee2b4247994c4396007e1cffd0bcfb","id":"2718"}, {"dataset":"MSV000094447","datasetNum":"94447","title":"GNPS - CMMC_Bile_acid_derivatives_synthesis_04_01_2024","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1712013285000","created":"Apr. 1, 2024, 4:14 PM","description":"MS\/MS fragmentation data of Bile acid derivatives was acquired on Q Exactive-with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"187","fileSizeKB":"34939119","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acid;Peptiedes;CMMC","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"10bf84b3336743e897204ee57055478e","id":"2719"}, {"dataset":"MSV000094446","datasetNum":"94446","title":"Characterization of the human cardiomyocyte proteome response to Doxorubicin exposure","user":"saypaul","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711987272000","created":"Apr. 1, 2024, 9:01 AM","description":"Data from iPSC-derived cardiomyocytes from three different individuals treated with either 0.5 uM Doxorubicin or vehicle for 24 hours. The treatment was replicated three times for one of the individuals. Protein was extracted from the ten samples and subjected to NanoLC MS\/MS Analysis with data-independent acquisition.\n","fileCount":"21","fileSizeKB":"37637594","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cardiomyocyte;Doxorubicin","pi":[{"name":"Michelle C. Ward","email":"miward@utmb.edu","institution":"University of Texas Medical Branch at Galveston","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2cedc27bbd0141de9804d1b753cc7d7d","id":"2720"}, {"dataset":"MSV000094445","datasetNum":"94445","title":"GNPS - Brain energy metabolism adenosine mediated cAMP signaling in astrocytes.","user":"viragsagikiss","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711986684000","created":"Apr. 1, 2024, 8:51 AM","description":"Whole brain mouse central carbon targeted LCMS metabolomics.","fileCount":"44","fileSizeKB":"36844","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Xevo TQ-S","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"brain, energy metabolism, central carbon metabolites, mouse","pi":[{"name":"Virag Sagi-Kiss","email":"v.sagi-kiss@imperial.ac.uk","institution":"Imperial College London","country":"UK"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"02a1850ea69a4a84b84f9a124a1f550c","id":"2721"}, {"dataset":"MSV000094443","datasetNum":"94443","title":"GNPS - Discovery of Biofilm Inhibitors from the Microbiota of Marine Egg Masses","user":"lkyei","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711977565000","created":"Apr. 1, 2024, 6:19 AM","description":"Bacteria associated with marine egg masses cultured in liquid media","fileCount":"344","fileSizeKB":"161503646","spectra":"114829","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria (NCBITaxon:2)","instrument":"6520B Q-TOF LC\\\/MS","modification":"none","keywords":"Marine egg masses","pi":[{"name":"Emily Mevers","email":"emevers@vt.edu","institution":"Virginia Tech","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"995c0b75276a4b5e8ba5208fb768b146","id":"2722"}, {"dataset":"MSV000094441","datasetNum":"94441","title":"Molecular signatures of neurodegenerative diseases identified by proteomic and phosphoproteomic analyses in aging mouse brain ","user":"uma_aryal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711887785000","created":"Mar. 31, 2024, 5:23 AM","description":"A central hallmark of neurodegenerative diseases is the irreversible accumulation of misfolded proteins in the brain by aberrant phosphorylation. Understanding the mechanisms underlying protein phosphorylation and its role in pathological protein aggregation within the context of aging is crucial for developing therapeutic strategies aimed at preventing or reversing such diseases. Here, we applied multi-protease digestion and quantitative mass spectrometry to compare and characterize dysregulated proteins and phosphosites in the mouse brain proteome using three different age groups: young-adult (3-4 months), middle-age (10 months), and old mice (19-21 months). Proteins associated with senescence, neurodegeneration, inflammation, cell cycle regulation, the p53 hallmark pathway, and cytokine signaling showed significant age-dependent changes in abundances and level of phosphorylation. The findings identify a significant association between aging and the dysregulation of proteins involved in various pathways linked to neurodegenerative diseases with potential therapeutic implications. ","fileCount":"235","fileSizeKB":"261566227","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"aging, neurodegenerative disease, proteomics, phosphoproteomics, protein aggregation","pi":[{"name":"Uma K Aryal","email":"uaryal@purdue.edu","institution":"Purdue University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e3df80500e1249588bde5cc848c88fe4","id":"2723"}, {"dataset":"MSV000094439","datasetNum":"94439","title":"Coupland et al., Cryo-EM of synaptic vesicles reveals loading-induced V-ATPase dissociation","user":"Younlab_Toronto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711802906000","created":"Mar. 30, 2024, 5:48 AM","description":"This dataset consists of 4 raw mass spectrometry files and associated peak lists and results files, acquired on a Bruker timsTOF Pro 2 mass spectrometer operated in Data-Dependent Acquisition mode. Synaptic vesicle and cleared rat brain lysate samples were prepared and separated in SDS-PAGE gel, then processed for in-gel protease digestion by Claire Coupland. Mass spectrometric acquisition and database searches were performed by Network Biology Collaborative Centre at the Lunenfeld-Tanenbaum Research Institute. Mass spec results were analyzed by Ji-Young Youn and John Rubinstein. The files are associated with a manuscript by Coupland et al. that determines the structure of synaptic vesicle V-ATPases and their associated proteins using Cryo-EM structural analysis. Mass spectrometry analysis is used to determine the protein components in purified synaptic vesicles. John Rubinstein is the corresponding author for the manuscript and should be contacted for questions regarding this dataset (john.rubinstein@utoronto.ca). \n\n","fileCount":"173","fileSizeKB":"8216344","spectra":"0","psms":"38105","peptides":"17522","variants":"18961","proteins":"3425","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"rat;Rattus norvegicus (NCBITaxon:10116)","instrument":"timsTOF Pro 2","modification":"MOD:00408 - \\\"A protein modification that effectively replaces a residue amino or imino hydrogen with an acetyl group.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"Cryo electron microscopy, v-ATPase, synaptic vesicles","pi":[{"name":"John Rubinstein","email":"john.rubinstein@utoronto.ca","institution":"Molecular Medicine Program, The Hospital for Sick Children; Department of Biochemistry and Department of Medical Biophysics, The University of Toronto","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051100","task":"b04f3523c8ea4117a9272c127bc0e3d8","id":"2724"}, {"dataset":"MSV000094438","datasetNum":"94438","title":"Single-cell proteomics captures the Proteome Heterogeneity in Human iPSC-Derived Cardiomyocytes and Adult Cardiomyocytes","user":"bineka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711741593000","created":"Mar. 29, 2024, 12:46 PM","description":"Human induced pluripotent stem cell (IPSC)-derived cardiomyocytes (iCMs) have become important tools to model cardiovascular diseases and drug toxicology. Despite suggested transcriptomic heterogeneity in both iPSC and iCMs, the cellular proteome heterogeneity is poorly understood. Using cutting-edge single cell proteomics, we quantify the maturation from IPSC to iCMs and observed two distinct populations of iCMs with different metabolism, which recapitulates the single adult cardiomyocyte proteome populations albeit less mature.","fileCount":"44815","fileSizeKB":"3218139291","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"iPSCs;CMs;differentiation;single cell","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051092","task":"e576331ad1904dbbbcc7fe8456904854","id":"2725"}, {"dataset":"MSV000094437","datasetNum":"94437","title":"GNPS - Impact of early-life exposure to a potent aryl hydrocarbon receptor ligand on gut microbiota and host glucose homeostasis in C57BL\/6J male mice","user":"haihaba","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711723754000","created":"Mar. 29, 2024, 7:49 AM","description":"Background: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship. \r\nObjective: This study aimed to explore the association between early-life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life. \r\nMethods: This study utilized metagenomics, NMR- and mass spectrometry-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early-life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and mass spectrometry-based metabolomics.\r\nResults: TCDF-exposed mice exhibited disruption in the gut microbiome community structure and function, characterized by lower abundances of A. muciniphila, lower levels of cecal short chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), and a reduction in gut hormones GLP-1 and PYY. Importantly, microbial and metabolic phenotypes associated with early-life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, significantly affected the growth, physiology, gene expression, and metabolic activity of A. muciniphila, resulting in suppressed activity along the ILA pathway. \r\nConclusions: These data point to the complex effects of POPs on the host and microbiota, providing strong evidence that early-life, short-term, and self-limiting POP exposure can adversely impact the microbiome, persisting into later life with associated health implications. \r\n","fileCount":"164","fileSizeKB":"10410679","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exactive Pluse;Orbitrap Fusion Lumos;TripleTOF 5600+","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Persistent organic pollutants (POP);TCDF;mass spectrometry-based metabolomics;aryl hydrocarbon receptor (AHR);gut microbiome","pi":[{"name":"Andrew D. Patterson","email":"adp117@psu.edu","institution":"Penn State University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"13fb62bc133342e4b8f1f2192be9d407","id":"2726"}, {"dataset":"MSV000094436","datasetNum":"94436","title":"GNPS - 20240329_Aging_negative_RP_001","user":"Alesia","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711696494000","created":"Mar. 29, 2024, 12:14 AM","description":"fecal metabolome analysed by rp lc-ms_ms of 3, 9, 15, 24 and 28 months aged mice","fileCount":"30","fileSizeKB":"2131628","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"X500R QTOF","modification":"no","keywords":"feces | aging | metabolites","pi":[{"name":"Alesia Walker","email":"alesia.walker@helmholtz-munich.de","institution":"Helmholtz Munich","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5fdc194ebb014958b1024c881af61e12","id":"2727"}, {"dataset":"MSV000094435","datasetNum":"94435","title":"GNPS - Microbial iron limitation in the ocean's twilight zone","user":"SiderophoreResearcher","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711686867000","created":"Mar. 28, 2024, 9:34 PM","description":"The file GT13645.raw include data for Extended Data Figure 2, which is a sample for siderophores in seawater.\r\n\r\nThe file S3C2_T0_200mUF.raw include data for Extended Data Figure 3, which is a sample for siderophores in seawater after addition of 57Fe-siderophores.\r\n\r\nThe file GT12706_POM_20221123171512.raw include data for Extended Table 1, which is a sample for siderophores in suspended particles in seawater.","fileCount":"4","fileSizeKB":"2198071","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Seawater samples","instrument":"Dionex instrument model;Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Siderophore;Ocean;Fe","pi":[{"name":"Daniel Repeta","email":"drepeta@whoi.edu","institution":"Woods Hole Oceanographic Institution","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7439be618f5949ecb1c2eac35978dba4","id":"2728"}, {"dataset":"MSV000094434","datasetNum":"94434","title":"De novo nine-species benchmark peptide identifications for Casanovo and other methods","user":"melihyilmaz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711686590000","created":"Mar. 28, 2024, 9:29 PM","description":"Predicted peptides for the 9-species de novo sequencing benchmark MSV000090982 as described in Yilmaz et al. [Yilmaz2023]. FTP directory contains outputs of 5 de novo peptide sequencing methods on the 9-species benchmark: Casanovo, Casanovo_bm (benchmark), PointNovo, DeepNovo and Novor. Output files for Casanovo contain scan numbers and run names to allow matching to spectra files. [Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux*, R. Nelson, V. Ananth, S. Oh, and W. Noble,\"Sequence-to-sequence translation from mass spectra to peptides with a transformer model\", bioRxiv, 2023","fileCount":"381","fileSizeKB":"2939967","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vigna mungo (NCBITaxon:3915) | Solanum lycopersicum (NCBITaxon:4081) | Saccharomyces cerevisiae (NCBITaxon:4932) | Mus musculus (NCBITaxon:10090) | Methanosarcina mazei (NCBITaxon:2209) | Homo sapiens (NCBITaxon:9606) | Candidatus Thiodiazotropha endoloripes (NCBITaxon:1818881) | Bacillus subtilis (NCBITaxon:1423) | Apis mellifera (NCBITaxon:7460)","instrument":"Q Exactive","modification":"UNIMOD:1 - \\\\\\\\\\\\\\\"Acetylation.\\\\\\\\\\\\\\\" | UNIMOD:4 - \\\\\\\\\\\\\\\"Iodoacetamide derivative.\\\\\\\\\\\\\\\" | UNIMOD:5 - \\\\\\\\\\\\\\\"Carbamylation.\\\\\\\\\\\\\\\" | UNIMOD:7 - \\\\\\\\\\\\\\\"Deamidation.\\\\\\\\\\\\\\\" | UNIMOD:35 - \\\\\\\\\\\\\\\"Oxidation or Hydroxylation.\\\\\\\\\\\\\\\" | UNIMOD:385 - \\\\\\\\\\\\\\\"Loss of ammonia.\\\\\\\\\\\\\\\"","keywords":"de novo;benchmark","pi":[{"name":"William Noble","email":"wnoble@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0dcbdaaf6ccd487b8a102f2073ee3048","id":"2729"}, {"dataset":"MSV000094432","datasetNum":"94432","title":"GNPS - Data files for metabolomics ","user":"xcxu14","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711652950000","created":"Mar. 28, 2024, 12:09 PM","description":"mzXML files associated with Fig.S1B and Fig.S2C and D. Change of serum, spleen, and tumor metabolome over time.\r\n\r\nSee \"Knowns-new-Hilic25min-QE - Knowns-new-Hilic25min-QE.csv\" for retention time information.","fileCount":"26","fileSizeKB":"1317620","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus sp. (NCBITaxon:10095)","instrument":"Orbitrap Exploris 480 MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Serum metabolome;purines;artifacts","pi":[{"name":"Joshua Rabinowitz","email":"joshr@exchange.Princeton.EDU","institution":"Princeton University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4b241172c9254d50a0e6d005f94ff1fe","id":"2730"}, {"dataset":"MSV000094430","datasetNum":"94430","title":"Test MassIVE Dataset for Metadata and License","user":"lhenson","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711644184000","created":"Mar. 28, 2024, 9:43 AM","description":"Test dataset with example metadata and license file.\r\n\r\nNon-commercial license is granted to use this data. Attribution is required. Please see the attached license file prior to using the data","fileCount":"6","fileSizeKB":"134606","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Various","instrument":"Multiple Different Instruments","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Test","pi":[{"name":"Test","email":"info@versobio.com","institution":"Test","country":"US"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"99857eda7e34421d8d4fc0a998e713fe","id":"2731"}, {"dataset":"MSV000094429","datasetNum":"94429","title":"GNPS - Dataset Creation from GNPS Molcular Networking - 499f3454320146b0ac6caba3b0486ef4","user":"ndidonat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711642566000","created":"Mar. 28, 2024, 9:16 AM","description":"Combined water, methanol and chloroform soil extracts from week 12 of a California grassland soil root detritus experiment conducted under normal (~16% GWC) and reduced moisture (~8% GWC) conditions.\r\n","fileCount":"9","fileSizeKB":"398757","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"grassland soil extracts","instrument":"LTQ Orbitrap Velos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"soil organic matter;secondary metabolites;fungi;root detritus","pi":[{"name":"Nicole DiDonato","email":"ndidonat@gmail.com","institution":"PNNL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3664146e70c54027a5af8961dec713b3","id":"2732"}, {"dataset":"MSV000094428","datasetNum":"94428","title":"Development of a multiplexed LCMS assay for the quantitation of podocyte injury biomarkers nephrin, podocalyxin, and podocin in human urine","user":"cmoralesbetanzos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711641696000","created":"Mar. 28, 2024, 9:01 AM","description":"Targeted peptide immunoaffinity LCMS was conducted on clarified human urine using stable isotope labeled peptides for the absolute quantitation of nephrin, podocalyxin and podocin in samples from CKD patients and controls.","fileCount":"33","fileSizeKB":"926214","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QTRAP 6500+","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"podocytes;LC-MS;kidney injury;biomarkers;chronic kidney disease;urine","pi":[{"name":"Mireia Fernandez Ocana","email":"Mireia.FernandezOcana@pfizer.com","institution":"Pfizer Inc","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9aea96f40362425b8785451f43a5ee84","id":"2733"}, {"dataset":"MSV000094427","datasetNum":"94427","title":"Dysregulated Prion signaling induces calcium influx, protein kinase C activation, and NMDA receptor dependent excitotoxicity","user":"dmcclat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711639433000","created":"Mar. 28, 2024, 8:23 AM","description":"Neuronal hyperexcitability precedes synapse loss in certain neurodegenerative diseases, yet the synaptic membrane interactions and downstream signaling events remain unclear. The disordered amino terminus of the prion protein (PrPC) has been implicated in aberrant signaling in prion and Alzheimer\u2019s disease. To disrupt neuronal interactions and signaling linked to the amino terminus, we CRISPR-engineered a knockin mouse expressing mutant PrPC (G92N), generating an N-linked glycosylation site between 2 functional motifs. Mice developed seizures and necrosis of hippocampal pyramidal neurons, similar to prion-infected mice and consistent with excitotoxicity. Phosphoproteomics analysis revealed phosphorylated\r\nglutamate receptors and calcium-sensitive kinases, including protein kinase C (PKC). Additionally, 92N-PrPC-expressing neurons showed persistent calcium influx as well as dendritic beading, which was rescued by an N-methyl-d-aspartate receptor (NMDAR) antagonist. Finally, survival of Prnp92N mice was prolonged by blocking active NMDAR channels. We propose that dysregulated PrPC\/NMDAR-induced signaling can trigger an excitatory, inhibitory imbalance, spongiform degeneration, and neurotoxicity and that calcium dysregulation is central to PrPC-linked neurodegeneration.","fileCount":"29","fileSizeKB":"18613486","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"glycans;neuron","pi":[{"name":"Christina Sigurdson","email":"csigurdson@health.ucsd.edu","institution":"UC San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051060","task":"ac1268a453284cb2955c94e2ee20b3d0","id":"2734"}, {"dataset":"MSV000094426","datasetNum":"94426","title":"Effect of LPS on corpus luteum - TMT-based approach","user":"robertstr","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711622662000","created":"Mar. 28, 2024, 3:44 AM","description":"Effect of LPS on corpus luteum - TMT-based approach","fileCount":"9","fileSizeKB":"3672875","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sus scrofa (NCBITaxon:9823)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"pig;corpus luteum;TMT10 plex;LPS;inflammation","pi":[{"name":"Robert Stryinski ","email":"robert.stryinski@uwm.edu.pl","institution":"University of Warmia and Mazury in Olsztyn","country":"Poland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fcfb9ecf45ce4e4bbf4950d314c883ab","id":"2735"}, {"dataset":"MSV000094419","datasetNum":"94419","title":"Proteomic analysis of the probiotic Shewanella putrefaciens Pdp11 growing under different cultivation conditions ","user":"OliPG","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711586653000","created":"Mar. 27, 2024, 5:44 PM","description":"Assessment of in vitro postbiotic capabilities of the probiotic Shewanella putrefaciens Pdp11 growing under different cultivation conditions containing microalgae dietary supplements widely used in aquaculture","fileCount":"16","fileSizeKB":"16330142","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Shewanella sp. (NCBITaxon:50422)","instrument":"Easy nLC 1200 UHPLC system coupled to a Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer ","modification":"NA","keywords":"postbiotics;Shewanella sp. Pdp11;proteomic analysis ","pi":[{"name":"Miguel Angel Morinigo ","email":"morinigo@uma.es","institution":"University of Malaga ","country":"Spain"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"010cef6ee4954a07b0369613da48c36a","id":"2736"}, {"dataset":"MSV000094418","datasetNum":"94418","title":"Comprehensive metabolomic\/lipidomic characterization of patients with mitochondrial ATP synthase, short-chain acyl-CoA dehydrogenase and combined variant deficiencies","user":"AlesKvasnicka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711586255000","created":"Mar. 27, 2024, 5:37 PM","description":"Objective: This study aims to characterize the metabolic alterations in patients with inherited mitochondrial enzymopathies. We focused on targeted metabolomic, organic acid and lipidomic analyses of patients with TMEM70 deficiency (TMEM70d), short-chain acyl-CoA dehydrogenase deficiency (SCADd), and individuals with both deficiencies (TMEM70d-SCADd).\nMethods: Serum and urine samples were collected from patients with TMEM70d (n=13), SCADd (n=11), TMEM70d-SCADd (n=3), and controls (n=38). Analyses were conducted using high-performance liquid chromatography coupled with tandem mass spectrometry (LC-MS\/MS). Univariate and multivariate statistical evaluation was performed to identify significant metabolic differences between patient groups and controls.\nResults: Distinct metabolic profiles were observed in urine and serum samples of patients with TMEM70d, SCADd, and TMEM70d-SCADd compared to controls. Urinary metabolomics revealed significant elevations in butyrylcarnitine and metabolites related to branched-chain amino acid degradation in SCADd and TMEM70d-SCADd patients. Serum metabolomic analysis indicated alterations in pyruvate metabolism, citric acid cycle intermediates, and acylcarnitine metabolism in TMEM70d and TMEM70d-SCADd patients. Lipidomic analysis showed decreased levels of glycerophospholipids and sphingolipids across all patient groups.\nConclusion: Patients with TMEM70d, SCADd, and TMEM70d-SCADd exhibit distinct metabolic signatures characterized by disturbances in energy metabolism, amino acid degradation, and lipid homeostasis. The combination of TMEM70d and SCADd leads to synergistic metabolic effects, emphasizing the importance of comprehensive metabolic profiling in understanding complex mitochondrial disorders and identifying potential biomarkers for diagnosis and treatment monitoring.\n","fileCount":"20","fileSizeKB":"2204997","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QTRAP 6500+;ExionLC","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mitochondrial disorders;oxidative phosphorylation;TMEM70;SCAD;metabolomics;lipidomics","pi":[{"name":"David Friedecky","email":"david.friedecky@upol.cz","institution":"Palacky University Olomouc and Faculty Hospital Olomouc","country":"Czechia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e5dbb79fb94540719257c57cf97a8ce4","id":"2737"}, {"dataset":"MSV000094417","datasetNum":"94417","title":"O-GlcNAcome and Phosphoproteome","user":"ChiulabUCD","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711580508000","created":"Mar. 27, 2024, 4:01 PM","description":"Liver circadian clock and daily rhythmic transcriptome are highly responsive to metabolic cues generated from daily feeding activity. The mechanisms that mediate metabolic inputs to the whole rhythmic transcriptome are still under investigation. Here, we explored the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) that integrates circadian and metabolic signals, in the diurnal regulation of nuclear proteins. We found daily oscillation of overall nuclear protein O-GlcNAcylation in the liver of mice subjected to natural night time-restricted feeding (NRF). O-GlcNAcomic analysis revealed that 11.54% of 719 O-GlcNAcylated proteins are rhythmically O-GlcNAcylated. Proteins involved in gene expression were enriched, suggesting rhythmic O-GlcNAcylation may directly shape diurnal transcriptome. Furthermore, we showed that rhythmic O-GlcNAcylation could indirectly modulate diurnal transcriptome by interacting with phosphorylation. Specifically, several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. For example, O-GlcNAcylation may occur at a phosphor-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), regulating the stability and transcriptional output of CLOCK. Lastly, unnatural day time-restricted feeding (DRF) dampens O-GlcNAcylation rhythm, suggesting the disruption of diurnal transcriptome could be mediated by protein O-GlcNAcylation. In summary, our results provide mechanistic insights into metabolic regulation of diurnal transcriptome at PTM level and shed light on the deleterious effects of improper mealtimes.","fileCount":"169","fileSizeKB":"97676769","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Dionex instrument model","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Mouse;Circadian;PTM interplay","pi":[{"name":"Joanna Chiu","email":"jcchiu@ucdavis.edu","institution":"University of California, Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8b36400ad66440048867d2dad6a58eb8","id":"2738"}, {"dataset":"MSV000094416","datasetNum":"94416","title":"Analysis of histone PTMs in the choanoflagellate Salpingoeca rosetta","user":"gahan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711575469000","created":"Mar. 27, 2024, 2:37 PM","description":"Histone PTM data from two cell types of the choanoflagellate Salpingoeca rosettes : Slow swimmers and Thecate cells.","fileCount":"15","fileSizeKB":"30169630","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Salpingoeca rosetta (NCBITaxon:946362)","instrument":"Q Exactive","modification":"UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Choanoflagellate;protist","pi":[{"name":"David Booth","email":"David.Booth@ucsf.edu","institution":"University of California, San Francisco","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD051028","task":"e82db774a3594a6b9847c9ba12858424","id":"2739"}, {"dataset":"MSV000094415","datasetNum":"94415","title":"Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics ","user":"melihyilmaz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711568078000","created":"Mar. 27, 2024, 12:34 PM","description":"Ocean microbiome dataset published by May et al. [May2016] and the corresponding peptide identifications. The LC-MS\/MS spectra are from triplicate acquisitions of peptides, acquisitions 51-53 from the Bering Strait (BSt) and acquisitions 45-47 from the Chukchi Sea (CS). For each sampling location, there are two sets of peptide identifications: one based on a metapeptide database specific to the location and one based on a non-redundant environmental database. Peptide identifications were obtained with Tide search and Percolator as described in Yilmaz et al. [Yilmaz2023].\n\n[May2016] May, D. H. et al. \"An Alignment-Free Metapeptide Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing\", Journal of Proteome Research, 2016.\n\n[Yilmaz2023] Yilmaz, Melih et al. \"Sequence-to-sequence translation from mass spectra to peptides with a transformer model\", bioRxiv, 2023.","fileCount":"11","fileSizeKB":"3254676","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Various species in metaproteomics samples","instrument":"Q Exactive HF","modification":"UNIMOD:1 - \\\\\\\\\\\\\\\"Acetylation.\\\\\\\\\\\\\\\" | UNIMOD:4 - \\\\\\\\\\\\\\\"Iodoacetamide derivative.\\\\\\\\\\\\\\\" | UNIMOD:5 - \\\\\\\\\\\\\\\"Carbamylation.\\\\\\\\\\\\\\\" | UNIMOD:7 - \\\\\\\\\\\\\\\"Deamidation.\\\\\\\\\\\\\\\" | UNIMOD:35 - \\\\\\\\\\\\\\\"Oxidation or Hydroxylation.\\\\\\\\\\\\\\\" | UNIMOD:385 - \\\\\\\\\\\\\\\"Loss of ammonia.\\\\\\\\\\\\\\\"","keywords":"metaproteomics","pi":[{"name":"William Noble","email":"wnoble@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6ffc455c578a4e5da8b3088131467773","id":"2740"}, {"dataset":"MSV000094410","datasetNum":"94410","title":"GNPS - 20240327_Aging_negative_hilic_001","user":"Alesia","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711559412000","created":"Mar. 27, 2024, 10:10 AM","description":"fecal metabolome analysed by hilic lc-ms_ms of 3, 9, 15, 24 and 28 months aged mice","fileCount":"83","fileSizeKB":"2302282","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"maXis 4G","modification":"no","keywords":"feces | aging | metabolites","pi":[{"name":"Alesia Walker","email":"alesia.walker@helmholtz-munich.de","institution":"Helmholtz Munich","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"44196532e75f4562a7420571ffa0cba3","id":"2741"}, {"dataset":"MSV000094409","datasetNum":"94409","title":"GNPS - 20240327_Aging_positive_hilic_001","user":"Alesia","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711530517000","created":"Mar. 27, 2024, 2:08 AM","description":"fecal metabolome analysed by hilic lc-ms_ms of 3, 9, 15, 24 and 28 months aged mice","fileCount":"165","fileSizeKB":"1918399","spectra":"214024","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"maXis 4G","modification":"no","keywords":"feces;aging;metabolites","pi":[{"name":"Alesia Walker","email":"alesia.walker@helmholtz-munich.de","institution":"Helmholtz Munich","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e838639225f94422bd8d6654bcad70a2","id":"2742"}, {"dataset":"MSV000094408","datasetNum":"94408","title":"GNPS - Semaglutide ameliorates cardiac remodeling by optimizing energy substrate utilization and through the Creb5\/NR4a1 axis in male mice","user":"yulan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711514113000","created":"Mar. 26, 2024, 9:35 PM","description":"Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, RP China\r\nHubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, RP China","fileCount":"181","fileSizeKB":"4801213","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"ExionLC Series UHPLC","modification":"PRIDE:0000398","keywords":"metabolomics of Sema","pi":[{"name":"lan yu ma","email":"2017302180001@whu.edu.cn","institution":"Renmin Hospital of Wuhan University","country":"china"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"49db9bbad24e450aa2caa4b68fa70f7d","id":"2743"}, {"dataset":"MSV000094407","datasetNum":"94407","title":"TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics","user":"ARBasharat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711475361000","created":"Mar. 26, 2024, 10:49 AM","description":"E. coli proteins (300 ng) extracted from the sample were analyzed using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) coupled with an Ultimate 3000 (Thermo Fisher Scientific) reversed-phase liquid chromatography (RPLC) separation system with a C2 column (60 cm length, CoAnn Inc.). In the RPLC system, phase A was water with 0.1% formic acid (FA), and phase B was 60% acetonitrile (ACN) and 15% isopropanol (IPA) with 0.1% FA. A 98-min gradient of mobile phase B (0-5 min 5%, 5-7 min for 5% to 35%, 7-10 min for 35% to 50%, 10-97 min for 50% to 80%, 97-98 min from 80% to 99%) was applied with a flow rate of 400 nL\/min. \nE. coli proteins were analyzed using both DDA and DIA modes. In each mode, six runs were performed separately, with each targeting a specific m\/z range within the MS1 scan: 720-800, 800-880, 880-960, 960-1040, 1040-1120, and 1120-1200 m\/z. MS1 spectra were collected with a resolution of 240,000 (at 200 m\/z), 4 microscans, an automatic gain control (AGC) target value of 1x106, and a maximum injection time of 200 ms. MS\/MS spectra were obtained with a scan range of 400-2000 m\/z, a resolution of 60,000 (at 200 m\/z), 1 microscan, an AGC target value of 1x106, and a maximum injection time of 500 ms. Fragmentation was performed using higher-energy collisional dissociation (HCD) with 30% NCE. In the DDA runs, the top six precursor ions from each MS1 scan were isolated with a 3 m\/z window for MS\/MS analysis. The dynamic exclusion was set to 60 seconds. In the DIA runs, a 4 m\/z isolation window was used, resulting in a total of 20 MS\/MS spectra for each cycle. Three technical replicates were obtained for each experiment.","fileCount":"37","fileSizeKB":"31198703","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli K-12 (NCBITaxon:83333)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"data independent acquisition\t;top down proteomics\t;TDP;DIA;TopPIC;TopFD;TopDIA","pi":[{"name":"Xiaowen Liu","email":"xwliu@tulane.edu","institution":"Tulane University School of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0b40030be8ca47899e8784d4a267b659","id":"2744"}, {"dataset":"MSV000094406","datasetNum":"94406","title":"Chemical tools to define and manipulate interferon-induced Ubl protease USP18","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711468130000","created":"Mar. 26, 2024, 8:48 AM","description":"Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating interferon-induced ubiquitin-like (Ubl) modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) capable of selectively detecting USP18 activity over other ISG15 cross-reactive Ubl proteases by incorporating unnatural amino acids into the C-terminal tail of ISG15. Combining with a ubiquitin-based DUB ABP, the selective USP18 ABP is employed in a chemoprotemic platform to identify and assess inhibitors of DUBs including USP18. We further demonstrate that USP18 ABPs can be utilized to profile differential activities of USP18 in lung cancer cell lines, providing a strategy that will help define the activity-related landscape of USP18 in different disease states and unravel important (de)ISGylation-dependent biological processes.","fileCount":"10","fileSizeKB":"13864665","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"USP18, ISG15, DUB, activity-based protein profiling, chemoproteomic screening","pi":[{"name":"Euna Yoo","email":"euna.yoo@nih.gov","institution":"NCI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bce5b96ac6fe4e2c9763f351d54beba7","id":"2745"}, {"dataset":"MSV000094405","datasetNum":"94405","title":"GNPS - Metabolomics of Bacillus subtilis interactions with SynCom","user":"scottjarmusch11","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711445021000","created":"Mar. 26, 2024, 2:23 AM","description":"Dataset containing extracts from 5 membered synthetic communities containing various Bacillus subtilis mutants as well as monocultures.","fileCount":"84","fileSizeKB":"3398570","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis (NCBITaxon:1423);Pedobacter sp. D749;Rhodococcus globerulus (NCBITaxon:33008);Stenotrophomonas indicatrix (NCBITaxon:2045451);Chryseobacterium Sp. 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It mainly consists of two parts: Discovery of redundant nodes and Reasons of redundant nodes. The Discovery of redundant nodes section includes MS\/MS data of five different natural products with distinct compound structures, namely Ginseng Radix et Rhizoma (GR): GR-neg, Epimedii Folium (EF): EF-neg, Salviae Miltiorrhizae Radix et Rhizoma (SM): SM-neg, Bufonis Venenum (BV): BV-pos, and Aconiti Lateralis Radix Praeparata (AL): AL-pos. The Reasons of redundant nodes section includes MS\/MS data of GR and EF at different sample concentrations, as well as BV at different mass spectrometry parameters, such as 1-fold, 2-fold, and 10-fold dilution of GR samples (GR-1x dilution, GR-2x dilution, GR-10x dilution), 1-fold, 2-fold, and 10-fold dilution of EF samples (EF-1x dilution, EF-2x dilution, and EF-10x dilution), BV at different capillary voltages (BV-capillary-1500V-(1-6), BV-capillary-1750V-(1-6), BV-capillary-2000V-(1-6), BV-capillary-2250V-(1-6), and BV-capillary-2500V-(1-6)), BV at different sample cone voltages (BV-SC-10V-(1-6), BV-SC-20V-(1-6), BV-SC-30V-(1-6), BV-SC-40V-(1-6), and BV-SC-50V-(1-6)), and BV at different desolvation temperatures (BV-DT-300-(1-6), BV-DT-400-(1-6), and BV-DT-500-(1-6)).","fileCount":"90","fileSizeKB":"10152457","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ginseng Radix et Rhizoma;Bufonis Venenum;Epimedii Folium;Aconiti Lateralis Radix Praeparata;Salviae Miltiorrhizae Radix et Rhizoma","instrument":"SYNAPT G2-Si","modification":"No","keywords":"Natural products;In-depth analysis of molecular network;Redundant nodes","pi":[{"name":"Yuhao Zhang","email":"yuzh10040@163.com","institution":"Shanghai University of traditional Chinese medicine","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1cfe5e1027964a67ab4bdfe74926ce20","id":"2747"}, {"dataset":"MSV000094403","datasetNum":"94403","title":"GNPS - The role of ATP citrate lyase in myelin formation and maintenance","user":"earmstrong","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711405709000","created":"Mar. 25, 2024, 3:28 PM","description":"Formation of myelin by Schwann cells is tightly coupled to peripheral nervous system development and is important for neuronal function and long-term maintenance. Perturbation of myelin causes a number of specific disorders that are among the most prevalent diseases affecting the nervous system. Schwann cells synthesize myelin lipids de novo rather than relying on uptake of circulating lipids, yet one unresolved matter is how Acetyl CoA, a central metabolite in lipid formation is generated during myelin formation and maintenance. Recent studies have shown that glucose-derived Acetyl CoA itself is not required for myelination. Moreover, the importance of mitochondrially-derived Acetyl CoA has never been tested for myelination in vivo. Therefore, we have developed a Schwann cell-specific knockout of the ATP Citrate Lyase (Acly) gene to determine the importance of mitochondrial metabolism to supply Acetyl CoA in nerve development. Intriguingly, the ACLY pathway is important for myelin maintenance rather than myelin formation. In addition, ACLY is required to maintain expression of a myelin-associated gene program and to inhibit activation of the latent Schwann cell injury program.","fileCount":"10","fileSizeKB":"3876638","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:411 - \\\"Phenyl isocyanate.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:768 - \\\"Mono-methylated lysine labelled with Acetyl_heavy.\\\";acetyl labeling reagent heavy form (K);UNIMOD:1289 - \\\"Butyryl.\\\"","keywords":"ACLY knockout, sciatic nerve, histone PTM","pi":[{"name":"John Denu","email":"john.denu@wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"},{"name":"John Svaren","email":"john.svaren@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e923c22bd42340eda5a446110f033386","id":"2748"}, {"dataset":"MSV000094401","datasetNum":"94401","title":"Proteomic profile of hippocampus regions from the pilocarpine medial temporal lobe epilepsy model","user":"amcanto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711389583000","created":"Mar. 25, 2024, 10:59 AM","description":"Label-free Proteomic profile of the dentate gyrus (dorsal and ventral) and CA3 (dorsal and ventral) microdissected from the hippocampus of the pilocarpine model of Mesial Temporal Lobe Epilepsy. ","fileCount":"75","fileSizeKB":"59808817","spectra":"0","psms":"103868","peptides":"11158","variants":"14950","proteins":"2404","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"LTQ Orbitrap Velos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"epilepsy;hippocampus;dentate gyrus;label-free","pi":[{"name":"Iscia Lopes Cendes","email":"icendes@unicamp.br","institution":"University of Campinas","country":"Brazil"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD050962","task":"c4e39a8f6bea447fa34926c9b69c85df","id":"2749"}, {"dataset":"MSV000094400","datasetNum":"94400","title":"Differences in the Cerebral Amyloid Angiopathy Proteome in Alzheimers Disease and Mild Cognitive Impairment","user":"KanshinED1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711387246000","created":"Mar. 25, 2024, 10:20 AM","description":"Quantitative label-free proteomics study comparing brain samples from subjects with Cerebral amyloid angiopathy, Alzheimer desease and healthy Control groups.","fileCount":"35","fileSizeKB":"36852176","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"proteomics;cerebral amyloid angiopathy;Alzheimer disease","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyumc.org","institution":"NYU School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"2e8961e63cd2420e8c731f4010792428","id":"2750"}, {"dataset":"MSV000094397","datasetNum":"94397","title":"GNPS - 20240325_Natural Products Research and Innovation Center_Metabolomics_Workshop_Dataset","user":"bciap01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711366486000","created":"Mar. 25, 2024, 4:34 AM","description":"Fungal metabolites were extracted with a hydroalcoholic solution and partitioned between EtOAc. Analysis was done using Q-Exactive. In addition, Hydroalcoholic extracts from medicinal plants were also analyzed. 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It also includes the sequence database used for analysis and the MSPLIT spectral library which was generated from paired samples acquired in Data Dependent Acquisition (DDA) mode.\r\nAll streptavidin affinity purification, mass spectrometric acquisition, and data analysis was performed by Boris Dyakov. Samples were provided by Thomas Duchaine's lab (McGill University).\r\nThe files are associated with a manuscript in Cell Reports by Thivierge et al. that explores the paraspeckle-independent co-transcriptional regulation of nuclear microRNA biogenesis by SFPQ, wherein SFPQ is identified as a proximally-associated protein for DROSHA.\r\nOnly the Wildtype DROSHA bait data is used in the publication, but all files used in statistical analysis are provided.\r\nThomas Duchaine is the corresponding author of the manuscript (thomas.duchaine@mcgill.ca)\r\nAnne-Claude Gingras should be contacted for questions about this dataset (gingras@lunenfeld.ca)","fileCount":"116","fileSizeKB":"100640543","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;Proximity-dependent biotinylation;SFPQ;miRNA;Drosha;paraspeckles;lncRNA;nuclear exosome;RNA stability;transcription","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050949","task":"7262a764250a458699982f9d5910c05c","id":"2752"}, {"dataset":"MSV000094394","datasetNum":"94394","title":"GNPS - Spirolactone, an unprecedented antifungal beta-lactone spiroketal macrolidemacrolides from Streptomyces iranensis","user":"yyds","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711288752000","created":"Mar. 24, 2024, 6:59 AM","description":"Fungal infections pose a great threat to public health and the existing four classes of antifungals have limitations due to high toxicity, drug-drug interactions, and emerging drug-resistance. Streptomyces spp. represent an important source of antimicrobial substances, notably including the antifungal agent amphotericin B. The rapamycin-producer Streptomyces iranensis displayed strong antifungal activities against Aspergillus. Revisiting its genome revealed several intriguing biosynthetic gene clusters, including one unparalleled Type I polyketide synthase, which codes for uncharacterized metabolites. The identification of a novel macrolide spirolactone (1) was facilitated through CRISPR-based gene editing, HR-ESI-MS analysis, followed by fermentation and purification processes. Their structures and absolute configurations were confirmed by NMR, MS and X-ray crystallography. Spirolactone harbors an undescribed carbon skeleton with 13 chiral centers, featuring a rare beta-lactone moiety, a [6,6]-spiroketal ring, and an unprecedented 7-oxo-octylmalonyl-CoA extender unit. Spirolactone displayed profound antifungal effects against numerous fungal pathogens, e.g. the genus Talaromyces and several sections of Aspergillus including clinically relevant species such as Aspergillus niger and A. tubingensis (section Nigri), A. terreus (section Terrei) and the azol-resistant A. calidoustus (section Usti). Proteomics analysis revealed spirolactone potentially disrupted the integrity of fungal cell walls and induced the expression of stress-response proteins in A. niger. Spirolactone represents a new class of potential agents leading to combat fungal infections.","fileCount":"376","fileSizeKB":"159282","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces iranensis","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"spirolactone;Streptomyces iranensis","pi":[{"name":"Ling Ding","email":"lidi@dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a05cf4f6573844a488dbb6945cad2b23","id":"2753"}, {"dataset":"MSV000094393","datasetNum":"94393","title":"GNPS - CMMC_Reactions_of_BA_Derivatives_synthesis_Set_2","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711254487000","created":"Mar. 23, 2024, 9:28 PM","description":"MS\/MS fragmentation data of Bile acid derivatives acquired on Q Exactive - with\r\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"118","fileSizeKB":"24432611","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acid;Peptides;CMMC","pi":[{"name":"Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"24ae4e302b8546aba2a8440d1bcb9a1e","id":"2754"}, {"dataset":"MSV000094392","datasetNum":"94392","title":"Salinity-induced photorespiration in poplar vascular tissues facilitates nitrogen reallocation","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711251134000","created":"Mar. 23, 2024, 8:32 PM","description":"In poplar, cell-type specific proteomics responses were studied in leaf palisade and vascular cell types during salinity stress. Salinity induced-photorespiration in the leaf vascular tissue is associated with N reallocation processes triggered by the stress-induced reduction in C assimilation and growth at the whole plant level. Samples were digested with trypsin and analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.","fileCount":"395","fileSizeKB":"171498497","spectra":"0","psms":"3170799","peptides":"1037412","variants":"1106178","proteins":"85180","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Populus (NCBITaxon:3689)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"salinity;abiotic stress;trees;palisade;vascular;photorespiration;resource reallocation","pi":[{"name":"Amir H. Ahkami","email":"amir.ahkami@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD050927","task":"9418db6f976940a39b93d430e701106f","id":"2755"}, {"dataset":"MSV000094391","datasetNum":"94391","title":"GNPS - CMMC_BA_Derivatives_synthesis_1_set_of_Reactions","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711250541000","created":"Mar. 23, 2024, 8:22 PM","description":"MS\/MS fragmentation data of Bile acid derivatives acquired on Q Exactive-with\r\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"31","fileSizeKB":"5593313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acid;peptide;CMMC","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8ec1979529424d56bd2264b5b499d5b6","id":"2756"}, {"dataset":"MSV000094390","datasetNum":"94390","title":"Activity-dependent synthesis of Emerin gates neuronal plasticity via proteostasis regulation","user":"dmcclat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711233566000","created":"Mar. 23, 2024, 3:39 PM","description":"Neurons dynamically regulate their proteome in response to sensory input, a key process underlying experience-dependent structural and functional plasticity. Here, we characterized the visual experience-dependent nascent proteome within a brief, defined time window using an optimized metabolic labeling approach. Visual experience induces cell type-specific and age-dependent alterations in the nascent proteome and recruits proteostasis-related processes. We identified Emerin as the top activity-induced candidate plasticity protein and demonstrated that its activity-induced synthesis is transcription-independent. In contrast to its well-studied nuclear localization and function in myocytes, activity-induced neuronal Emerin is abundant in the ER and broadly inhibits protein synthesis, including synaptic proteins. Downregulating Emerin increases synaptic density, however, it shifts dendritic spines from predominantly mushroom morphology to filopodia, leading to decreased network connectivity, visual responses and visual information processing. Our findings support a visual experience-dependent feed-forward role for Emerin in gating neuronal plasticity through negative regulation of translation. ","fileCount":"63","fileSizeKB":"138672015","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"azidonorleucine","keywords":"cell type-specific proteomics;metabolic protein labeling;sensory experience-dependent plasticity;Emerin","pi":[{"name":"Hollis T. Cline","email":"cline@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050926","task":"7fadf7854abe47819d1db5d9898ed5d0","id":"2757"}, {"dataset":"MSV000094389","datasetNum":"94389","title":"An accessible workflow for high sensitivity proteomics using Parallel Accumulation - Serial Fragmentation (PASEF)","user":"patricias","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711192505000","created":"Mar. 23, 2024, 4:15 AM","description":"Deep and accurate proteome analysis is crucial for understanding cellular processes and disease mechanisms, however, it is also challenging to implement in routine settings. In this protocol we combine a robust and accessible chromatographic platform with an equally robust and high-performance mass spectrometric set up, to enable routine yet in-depth proteome coverage for a broad community. This entails tip-based sample preparation and pre-formed gradients combined with trapped ion mobility - quadrupole - time-of-flight mass spectrometry. It enables parallel accumulation - serial fragmentation (PASEF), in which all ions are used but spectra are resolved by ion mobility. Combined with data-independent acquisition (dia-PASEF), it offers high peak sampling rates and near-complete ion coverage. Here we explain how to balance quantitative accuracy, specificity, proteome coverage, and sensitivity by choosing best PASEF and DIA method parameters. The protocol streamlines the liquid chromatography - mass spectrometry setup and enables PASEF method generation and evaluation for varied samples. Our py_diAID tool automatically generates acquisition schemes where isolation windows are optimally positioned on the mass-to-charge and ion mobility plane. Hands-on time is three hours, and simple biological projects can be performed in three days. The implementation shown here allows reproducible quantification of 7,300 proteins in a human cancer cell line in 21 min with quadruplicate single-shot injections and 27,000 phosphosites in 21 min from for phospho-enriched quadruplicates. Synchro-PASEF, a next-generation scan mode, currently offers proteomic depth comparable to that of dia-PASEF. When analyzed with AlphaDIA, it showed superior quantitative reproducibility owing to its drastically reduced cycle times and high sampling efficiency.","fileCount":"47","fileSizeKB":"374240269","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro;timsTOF Ultra","modification":"MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"TIMS;PASEF;data-independent acquisition ;scan mode;TOF","pi":[{"name":"Matthias Mann","email":"mmann@biochem.mpg.de","institution":"Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 D-82152 Martinsried","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050922","task":"9419c99395a545a3810450a14a3b5e47","id":"2758"}, {"dataset":"MSV000094388","datasetNum":"94388","title":"APOBEC2 Safeguards Skeletal Muscle Cell Fate through Regulating Transcription of Non-Muscle Genes during Myoblast Differentiation","user":"Monod","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711166776000","created":"Mar. 22, 2024, 9:06 PM","description":"The apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) family is comprised of nucleic acid editors with roles ranging from antibody diversification to RNA editing. APOBEC2, a member of this family with an evolutionarily conserved nucleic acid binding cytidine deaminase domain, has neither an established substrate nor function. Using a cellular model of muscle differentiation where APOBEC2 is inducibly expressed, we confirmed that APOBEC2 does not have the attributed molecular functions of the APOBEC family, such as RNA editing, DNA demethylation, and DNA mutation. Instead, we found that during muscle differentiation APOBEC2 occupied a specific motif within promoter regions; its removal from those regions resulted in transcriptional changes. Mechanistically, these changes reflect the direct interaction of APOBEC2 with histone deacetylase (HDAC) transcriptional corepressor complexes. We also found that APOBEC2 could bind DNA directly, in a sequence-specific fashion, suggesting that it functions as a recruiter of HDAC to specific genes whose promoters it occupies. These genes are normally suppressed during muscle cell differentiation and their suppression may contribute to the safeguarding of muscle cell fate. Altogether, our results reveal a novel role for APOBEC2 within the APOBEC family.","fileCount":"44","fileSizeKB":"37327404","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"transcriptional regulator;muscle differentiation;DNA binding;APOBEC family;BioID","pi":[{"name":"Javier Marcelo Di Noia","email":"javier.marcelo.di.noia@ircm.qc.ca","institution":"IRCM","country":"Canada"},{"name":"Nina F Papavasiliou","email":"n.papavasiliou@dkfz-heidelberg.de","institution":"Heidelberg University","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"941ef7fb08f2415e9ab61e050d5fb897","id":"2759"}, {"dataset":"MSV000094386","datasetNum":"94386","title":"Phylogeny and bioactivity mining of plant-associated Paenibacillus","user":"machushynets","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711159985000","created":"Mar. 22, 2024, 7:13 PM","description":"In the present study we adopt a GNPS MN approach to provide insight into chemical structures and diversity of Paenibacillus specialised metabolites and facilitate the discovery of new natural products. Dataset includes the LC-MS\/MS data for extracts of 227 plant-associated Paenibacillus spp, Known lipopeptide classes as polymyxins, tridecaptins, fusaricidins and paenibacterins were dereplicated. ","fileCount":"11","fileSizeKB":"25336","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Paenibacillus strain collection","instrument":"LCMS-IT-TOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"NRPs, Paenibacillus, plant-associated bacteria, lipopeptides","pi":[{"name":"Gilles van Wezel ","email":"g.wezel@biology.leidenuniv.nl","institution":" Institute of Biology, Leiden University,","country":"The Netherlands"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"9e0a3c526cb443d79f6ac153f93a06f3","id":"2760"}, {"dataset":"MSV000094385","datasetNum":"94385","title":"GNPS - Annotation of DOM Metabolomes with Ultrahigh Resolution Mass Spectrometry Libraries","user":"coffe198","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711152573000","created":"Mar. 22, 2024, 5:09 PM","description":"This dataset contains LC-MS metabolomic data collected on an Orbitrap IQ-X from axenic Phaeodactylum tricornutum (P. tricornutum) cultures after 1, 7, and 16 days of growth in iron-replete (1 uM) and iron limited (10 nM) conditions. Additionally, there is a pooled sample from t16 that was analyzed on the 21T FT-ICR MS at the National High Magnetic Field Laboratory that was used to generate a molecular formula library to annotate P. tricornutum's metabolome. ","fileCount":"44","fileSizeKB":"15966747","spectra":"1397484","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Phaeodactylum tricornutum (NCBITaxon:2850)","instrument":"Orbitrap IQ-X (Thermo Scientific Instrument Model);21T FT-ICR MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Phaeodactylum tricornutum;iron limitation","pi":[{"name":"Rene Boiteau","email":"reneboiteau@oregonstate.edu","institution":"Oregon State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1850b92f8dd04f42b7d6daac606240ad","id":"2761"}, {"dataset":"MSV000094383","datasetNum":"94383","title":"Subsection and proteomic analysis of single algael cells on multiple TOF mass spectrometers","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711141029000","created":"Mar. 22, 2024, 1:57 PM","description":"Single cells were physically sectioned into 6 distinct fractions, processed and analyzed on a TIMSTOF Flex, TIMSTOF SCP and ZenoTOF mass analyzer using both DDA and DIA methods. ","fileCount":"384","fileSizeKB":"9258330","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caulerpa taxifolia (NCBITaxon:76313)","instrument":"timsTOF SCP;ZenoTOF 7600","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Subcellular proteomics;Single cell proteomics","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050912","task":"3bf5f0066cfe408c97ff0b4e493a86d6","id":"2762"}, {"dataset":"MSV000094382","datasetNum":"94382","title":"GNPS - CMMC_CDCA_reactions_with_dipeptide","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711139539000","created":"Mar. 22, 2024, 1:32 PM","description":"MS\/MS fragmentation data of CDCA and Tripeptide acquired on Q Exactive - with\r\nchromatographic separation on a Phenomenex polar C18 column.","fileCount":"3","fileSizeKB":"486292","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acids;Dipeptide;CMMC","pi":[{"name":"Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b993638d2db84fd0b272e016d768cdd7","id":"2763"}, {"dataset":"MSV000094381","datasetNum":"94381","title":"A multi-organ proteomic atlas of a murine model of extreme age","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711139446000","created":"Mar. 22, 2024, 1:30 PM","description":"diaPASEF analysis of 16 mouse organs from 4x 12 week and 84 week old male mice","fileCount":"304","fileSizeKB":"42374140","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF fleX","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"aging","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD050910","task":"620846ff116e46e6b66769968842cc1d","id":"2764"}, {"dataset":"MSV000094379","datasetNum":"94379","title":"BioID proximity labeling of interactome using BirA* tagged IRE1 ","user":"Kurt_Dejgaard2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711121662000","created":"Mar. 22, 2024, 8:34 AM","description":"BioID proximity interactomics, using Ire1 alpha and -beta as baits, in stably expressing HEK293 cells","fileCount":"50","fileSizeKB":"6076865","spectra":"0","psms":"199778","peptides":"34629","variants":"38192","proteins":"8663","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"homo sapiens","instrument":"Orbitrap Exploris 240","modification":"ox-Met","keywords":"BioID, IRE1, Human","pi":[{"name":"Kurt Dejgaard","email":"kurt.dejgaard@mcgill.ca","institution":"McGill University","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"96a1394ea5ef4a67a8401e132abbcc92","id":"2765"}, {"dataset":"MSV000094375","datasetNum":"94375","title":"Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation","user":"mviolette","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1711046468000","created":"Mar. 21, 2024, 11:41 AM","description":"Ten micrograms of each sample were reduced and alkylated followed by trypsin digestion using a suspension trap (S-trap). An SPQC was made by combining equal volumes of each sample. After lyophilization and reconstitution of the sample in 20 uL, 1-2 uL of each was analyzed by LC-MS\/MS using a 30 min gradient on a Thermo Vanquish Neo coupled to a Thermo Orbitrap Astral via a Nanospray Flex ionization source.\nBriefly, the sample was first trapped on a PepMap C18 0.3 mm x 5 mm trapping column (50 ul\/min at 99.9\/0.1 v\/v water\/acetonitrile), followed by analytical separation using a 1.5 um 150um ID x 8cm (PepSep) column with a 20 min gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 500 nanoliters\/minute (nL\/min) with a column temperature of 55C. Data collection on the Orbitrap Astral mass spectrometer was performed in a data-independent acquisition (DIA) mode of acquisition with a r=240,000 (@ m\/z 200) full MS scan every 0.6s from m\/z 380-980 with an AGC target of 500%. DIA MS\/MS scans were acquired in the Astral analyzer using fixed windows of 4 m\/z from m\/z 380, target AGC of 500% and max fill time of 6 ms. HCD collision energy setting of 27% was used for all MS2 scans. \nRaw MS data was demultiplexed and converted to *.htrms format using HTRMS converter and processed in Spectronaut 18 (Biognosys). A spectral library was built using direct-DIA searches which used a Mus muculus database, downloaded from Uniprot on 4\/08\/23, and appended the transgene APOBEC1-YTH as well as contaminant sequences using FragPipe. Search settings included N-terminal trypsin\/P specificity up to 2 missed cleavages; peptide length from 7-52 amino acids with the following modifications: acetyl (N-term), carbamidomethyl(Cys) and oxidation (M). For DIA analysis, default extraction, calibration, identification and protein inference settings were used. Normalization, imputation and protein quantification was performed using an in-house script. \n","fileCount":"45","fileSizeKB":"383660183","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Astral","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"m6A (or N6-methyladenosine);DART-seq;RNA modifications;Transgenic Mouse Characterization","pi":[{"name":"Kate Meyer","email":"kate.meyer@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD050870","task":"b89a673a1cc648cfacea78ba940e729d","id":"2766"}, {"dataset":"MSV000094373","datasetNum":"94373","title":"Proteomic characterization of epithelial and endothelial cells from human bronchopulmonary dysplasia lung","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710977921000","created":"Mar. 20, 2024, 4:38 PM","description":"Proteomic data from human BPD lung; normal and BPD lungs for comparison; 5 biological replicates. The frozen lung suspension was received from BRINDL (the Biorepository for Investigation of Neonatal Diseases of the Lung) at the University of Rochester. FACS sorting was done to isolate epithelial and endothelial populations using specific cell surface markers. MicroPOTs sample preparation was utilized, followed by trypsin digestion, then LC-MS\/MS analysis. Data was searched with MSFragger using PNNL's DMS processing pipeline.","fileCount":"88","fileSizeKB":"35252557","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"proteomics;FACS;lung","pi":[{"name":"Mereena George Ushakumary","email":"mereena.ushakumary@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"a144d0abae8d423186bafd8752ee0d4d","id":"2767"}, {"dataset":"MSV000094370","datasetNum":"94370","title":"PPH24 - Botrytis cinerea Steroidal glycoalkaloids","user":"iris66","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710957326000","created":"Mar. 20, 2024, 10:55 AM","description":"Multiple mechanisms of the grey mould Botrytis cinerea to detoxify plant antifungal steroidal glycoalkaloids","fileCount":"15","fileSizeKB":"1291179","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Botrytis cinerea (NCBITaxon:40559)","instrument":"LC-QExactive Plus Orbitrap FTMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Botrytis cinerea - steroidal glycoalkaloids","pi":[{"name":"Iris Kappers","email":"iris.kappers@wur.nl","institution":"Wageningen University","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3f44233744814b409eb420fb6bec10e1","id":"2768"}, {"dataset":"MSV000094368","datasetNum":"94368","title":"Identification of 187AA unique peptides by mass spectrometry 2","user":"huzhijuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710910823000","created":"Mar. 19, 2024, 10:00 PM","description":"Identification of 187AA unique peptides by mass spectrometry and detection of 187AA by mass spectrometry in 4 human cells (293T, SK-hep1, ESC-derived cardiomyocytes) and 1mouse cell(R1).","fileCount":"150","fileSizeKB":"22886848","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus (NCBITaxon:10088)","instrument":"timsTOF Pro","modification":"none","keywords":"187AA MS","pi":[{"name":"xingguo liu","email":"liu_xingguo@gibh.ac.cn","institution":"Guangzhou Institutes of Biomedicine and Health Chinese Academy of Science","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"96c7fdc5fb314b25b90b5df9d7dfc8a5","id":"2769"}, {"dataset":"MSV000094367","datasetNum":"94367","title":"Post-translational Regulation of the Response to Different Exercise Modes in Muscle","user":"carriejo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710909582000","created":"Mar. 19, 2024, 9:39 PM","description":"Different modes of acute exercise (a single bout) and chronic exercise (12 weeks of training) result in different post-translational (acetyl and phospho) responses in skeletal muscle. We also include global proteomics as well as metabolomics and transcriptomics data indicating that the distinct metabolic responses to each type of exercise corresponds to the PTM responses. \r\n","fileCount":"497","fileSizeKB":"369275492","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"post-translational modifications (PTM);phosphorylation;acetylation;exercise;muscle;proteome","pi":[{"name":"Nair, K Sreekumaran, M.D., Ph.D.","email":"Nair@mayo.edu","institution":"Mayo Clinic","country":"United States"},{"name":"Pataky, Mark W., Ph.D., M.S.","email":"Pataky.Mark@mayo.edu","institution":"Mayo Clinic","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050786","task":"15360a1d2e954e8fb6a7ae70f26ddbbe","id":"2770"}, {"dataset":"MSV000094366","datasetNum":"94366","title":"Identification of 187AA unique peptides by mass spectrometry","user":"huzhijuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710906689000","created":"Mar. 19, 2024, 8:51 PM","description":"Identification of 187AA unique peptides by mass spectrometry and detection of 187AA by mass spectrometry in 5 human cells (293F 293T SK-hep1 ESC-derived cardiomyocytes) and 1mouse cell(R1).","fileCount":"21","fileSizeKB":"3090304","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus (NCBITaxon:10088)","instrument":"timsTOF Pro","modification":"none","keywords":"187AA MS","pi":[{"name":"xingguo liu","email":"liu_xingguo@gibh.ac.cn","institution":"Guangzhou Institutes of Biomedicine and Health Chinese Academy of Science","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc7f23ad73924c87aec6f5854e3d7445","id":"2771"}, {"dataset":"MSV000094364","datasetNum":"94364","title":"GNPS - Dataset Creation from GNPS Molcular Networking - DOM metabolization from cyanobacterial and non cyanobacterial diazotrophs","user":"MarineValletMPICE","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710877020000","created":"Mar. 19, 2024, 12:37 PM","description":"In collaboration with Mar Benavides (CNRS, France)","fileCount":"39","fileSizeKB":"616485","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Thalassiosira pseudonana (NCBITaxon:35128);Synechococcus sp. (NCBITaxon:1131)","instrument":"Q Exactive Plus;Dionex instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Dissolved Organic Matter;Algae;Cyanobacteria;Diatoms;Diazotrophs;UHPLC-HRMS;Metabolization;Metabolomics;Aquatic ecology","pi":[{"name":"Dr. Marine Vallet","email":"mvallet@ice.mpg.de","institution":"Friedrich Schiller University Jena, Max Planck Institute for Chemical Ecology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5654e8d8311a467c9abd813aec054c96","id":"2772"}, {"dataset":"MSV000094363","datasetNum":"94363","title":"Junctophilin 2 protein complex in WT and FKBP12 deficient mice heart","user":"syjung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710873761000","created":"Mar. 19, 2024, 11:42 AM","description":"To determine if the absence of FKBP12 in cardiac tissue alters JPH2 interactions with other dyadic proteins, we immunoprecipitated JPH2 from hearts of FL, MCK-FKD, MHC-Cre+ only, and MHC-FKD mice. Specific proteins were identified in the IPs from the FL mice and included JPH2, CASQ2 , SPEG, RYR2, CACNA1c, CACNB2, ESD, CMYA5, and LRRC10.","fileCount":"229","fileSizeKB":"182748415","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Junctophilin 2 ;FKBP12 deficient mice","pi":[{"name":"Sung Yun Jung","email":"syjung@bcm.edu","institution":"Baylor College of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050775","task":"1f63e4141a3b407ab116bd348e897548","id":"2773"}, {"dataset":"MSV000094362","datasetNum":"94362","title":"TopDIA - temp data - file upload issue","user":"ARBasharat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710869501000","created":"Mar. 19, 2024, 10:31 AM","description":"E. coli proteins (300 ng) extracted from the sample were analyzed using an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) coupled with an Ultimate 3000 (Thermo Fisher Scientific) reversed-phase liquid chromatography (RPLC) separation system with a C2 column (60 cm length, CoAnn Inc.). In the RPLC system, phase A was water with 0.1% formic acid (FA), and phase B was 60% acetonitrile (ACN) and 15% isopropanol (IPA) with 0.1% FA. A 98-min gradient of mobile phase B (0-5 min 5%, 5-7 min for 5% to 35%, 7-10 min for 35% to 50%, 10-97 min for 50% to 80%, 97-98 min from 80% to 99%) was applied with a flow rate of 400 nL\/min. \r\nE. coli proteins were analyzed using both DDA and DIA modes. In each mode, six runs were performed separately, with each targeting a specific m\/z range within the MS1 scan: 720-800, 800-880, 880-960, 960-1040, 1040-1120, and 1120-1200 m\/z. MS1 spectra were collected with a resolution of 240,000 (at 200 m\/z), 4 microscans, an automatic gain control (AGC) target value of 1x106, and a maximum injection time of 200 ms. MS\/MS spectra were obtained with a scan range of 400-2000 m\/z, a resolution of 60,000 (at 200 m\/z), 1 microscan, an AGC target value of 1x106, and a maximum injection time of 500 ms. Fragmentation was performed using higher-energy collisional dissociation (HCD) with 30% NCE. In the DDA runs, the top six precursor ions from each MS1 scan were isolated with a 3 m\/z window for MS\/MS analysis. The dynamic exclusion was set to 60 seconds. In the DIA runs, a 4 m\/z isolation window was used, resulting in a total of 20 MS\/MS spectra for each cycle. Three technical replicates were obtained for each experiment.","fileCount":"41","fileSizeKB":"32681974","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli K-12 (NCBITaxon:83333)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"data independent acquisition;top down proteomics;TDP;DIA;TopPIC;TopFD;TopDIA","pi":[{"name":"Xiaowen Liu","email":"xwliu@tulane.edu","institution":"Tulane University School of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"eb3af779fc9242988c4806cee52e7e83","id":"2774"}, {"dataset":"MSV000094358","datasetNum":"94358","title":"GNPS - MS2 spectra from Streptomyces bacteria containing fluorinated compounds and terminal alkynes","user":"atekel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710847657000","created":"Mar. 19, 2024, 4:27 AM","description":"MS2 spectra from Streptomyces aureorectus (nucleocidin, aurerenin) and Streptomyces cattleya (terminal alkynes, fluorodeoxyadenosine). Grown on MS agar, extracted with 50\/50 water\/ethanol and sonication. ","fileCount":"10","fileSizeKB":"14","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces cattleya (NCBITaxon:29303);Streptomyces aureorectus (NCBITaxon:285571)","instrument":"Orbitrap ID-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces;Organofluorines;Nucleosides;alkynes;sulfamates","pi":[{"name":"Tomas Pluskal","email":"tomas.pluskal@uochb.cas.cz","institution":"Institute of Organic Chemistry and Biochemistry of the CAS","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e044d048bf084334b3f2006a4432262a","id":"2775"}, {"dataset":"MSV000094357","datasetNum":"94357","title":"GNPS - 2024039_KastoriaBiomass_9.8mg_25MeOH","user":"Sofia_Iliakop","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710847034000","created":"Mar. 19, 2024, 4:17 AM","description":"Biomass extract from Lake Kastroria in Greece. Untargeted metabolomics, DDA, ESI+\r\nCE 60-80eV\r\nmass range: 50-1300","fileCount":"8","fileSizeKB":"227095","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lake Biomass","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanotoxins","pi":[{"name":"Tri Kaloudis","email":"t.kaloudis@inn.demokritos.gr","institution":"NCSR Demokritos","country":"Greece"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"dd277b81492546648a888075ad4513f0","id":"2776"}, {"dataset":"MSV000094355","datasetNum":"94355","title":"GNPS - Effect of itaconate and 4-octylitaconate on the metabolome of VSV infected cells","user":"rinschen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710841029000","created":"Mar. 19, 2024, 2:37 AM","description":"Metabolites extraction.\r\nMetabolites were extracted from cells on ice using 800 ul 100% methanol for viral inactivation, followed by 200 ul of ice cold HPLC-grade water. The cell solutions were vortexed for 10 seconds and incubated at -20 degrees C for 2 h. Then, the cell solutions were centrifuged at 4 degrees C, 16 000 g for 20 min, and the supernatants were transferred to 1.5 ml Eppendorf tubes. The supernatants were dried down in a speedvac (Labconco Centrivap) at 8oC. The dried metabolite extracts were resuspended in 100 ul of acetonitrile-water (1:1, v\/v) and sonicated for 10 min in ice water. The solution was centrifuged at 4 degrees C, 16 000 g for 20 min. The supernatants were transferred to a 96-well plate (Greiner) and were subjected to targeted metabolomics LC-MS\/MS analysis using a list of known itaconate-related metabolites. A quality control sample was prepared by pooling together 5ul of all samples and was used to observe the instrument performance during the run.\r\n\r\nTargeted metabolomics analysis and mass spectrometry.\r\nTargeted metabolomic analysis was performed on a triple quadrupole (QQQ) mass spectrometer (Agilent Triple Quadrupole 6495C, San Diego, CA), coupled to an ultra-high pressure liquid chromatography system (UPLC) system (1290 Infinity, Agilent Technologies) as previously described 81. Data were acquired with Agilent MassHunter Workstation Data Acquisition (version 10.1). A CSH Phenyl-hexyl column (1.7 um, 1.0 x 100 mm) (Waters, Taastrup, Denmark) was used for metabolites separation. Collision energies and product ions (MS2 or quantifier and qualifier ion transitions) were optimized. Electrospray ionisation source conditions were set as follows: gas temperature, 200 degrees C; gas flow, 15 L\/min; Nebulizer, 25 psi; sheath gas temperature, 325 degrees C; cap voltage, 3000 V; and nozzle voltage, 500 V. For the liquid chromatography, the following parameters were used. The gradient consisted of buffer A, and buffer B. Buffer A was 99.9% H2O and 0.1% formic acid. Buffer B was 99.9% acetonitrile and 0.1% formic acid. The gradient with A\/B ratios were as follows: T0, 99:1; T2.5, 99:1; T6, 86.9:13.10; T7, 1:99; T8.5, 1:99; T9, 99:1; T10, 99:1. The flow rate was 150ul\/min. Three microliters of sample were injected. Multi reaction monitoring (MRM) was used. A standard curve was recorded and integrated using the mass hunter platform (Agilent). The transitions used for 4-octyl-itaconic acid were 241.14 -> 111 (quantifier, collision energy - 12 V), 241.14 -> 67.1 (qualifier, collision energy - 24 V). The transitions for itaconic acid were the following: 129.02 -> 85.1 (quantifier, collision energy - 8 V), 129.02 -> 41.2 (qualifier, collision energy - 12 V). Retention time for 4-octyl itaconic acid was 8.2 min, and 2.0 min for itaconic acid.\r\n\r\nTargeted metabolomics data analysis.\r\nTransition lists, retention time and raw data were loaded into Skyline (version 23.1) 82. Then, peaks were evaluated and integrated, and intensities were exported. The area under the curve of the quantifiers was used for further analysis. Data were plotted using python v3.9 83 , and the packages matplotlib v3.5.1, numpy v1.22.2 83, pandas v1.4.1, seaborn v0.12.0, statannotations v0.4.4. T-test independent was used for statistical analysis.","fileCount":"54","fileSizeKB":"60823","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"6495C Triple Quadrupole LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"VSV infection","pi":[{"name":"Markus Rinschen","email":"rinschen@biomed.au.dk","institution":"aarhus University","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"47883b17d55b400f89eeba94c6e6cf8d","id":"2777"}, {"dataset":"MSV000094354","datasetNum":"94354","title":"Identification and characterization of novel pathogen antigens and epitopes and their impact on self MHC class I immunopeptidomes by applying PEPSeek software","user":"john_cormican","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710838951000","created":"Mar. 19, 2024, 2:02 AM","description":"Analysis of the pathogen-derived peptides presented via MHC class I pathway of infected cells is a cutting-edge strategy to identify epitope candidates suitable for vaccine development. This dataset contains raw data from mass spectrometry measurements of the immunopeptidomes of HeLa cells infected with Chlamydia trachomatis and mouse macrophage cells infected with Listeria monocytogenes along with cognate control files, search results from standard search engine approaches, and PEPSeek outputs with pathogen epitopes identified. We further provide search engine and PEPSeek outputs for reanalysis of data from immunopeptidomes of multiple human cell lines infected SARS-COV2 and Listeria monocytogenes. Finally, we include raw files and analysis of files for synthetic peptide measurements of a sample of pathogen epitopes identified which provided validation of the identified peptides through spectral comparison.","fileCount":"256","fileSizeKB":"40533036","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Chlamydia trachomatis (NCBITaxon:813);Listeria monocytogenes (NCBITaxon:1639);Mus musculus (NCBITaxon:10090);Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)","instrument":"Orbitrap Fusion;Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"immunopeptidomics;pathogen;MHC-I","pi":[{"name":"Dr. Juliane Liepe","email":"juliane.liepe@mpinat.mpg.de","institution":"Max Planck Institute for Multidisciplinary Sciences","country":"Germany"},{"name":"Michele Mishto","email":"michele.mishto@kcl.ac.uk","institution":"King's College London and the Francis Crick Institute","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da4ff8b7f75c4f3a86dd4ce2731b6122","id":"2778"}, {"dataset":"MSV000094353","datasetNum":"94353","title":"GNPS Nostoc extracts for Cyanopeptolins detection","user":"Sofia_Iliakop","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710834907000","created":"Mar. 19, 2024, 12:55 AM","description":"CCNP1411 culture extracts in 75%MeOH, CH2Cl2-ACN and CH2Cl2-MeOH were analyzed in an Impact II QToF instrument for cyanopeptolins detection. ","fileCount":"19","fileSizeKB":"555188","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nostoc sp. (NCBITaxon:1180)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanopeptolins","pi":[{"name":"Hanna Mazur-Marzec ","email":"hanna.mazur-marzec@ug.edu.pl","institution":"University of Gdansk","country":"Poland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ff1bdd45dd55411780d05a71d8ac0552","id":"2779"}, {"dataset":"MSV000094352","datasetNum":"94352","title":"Deep, Unbiased and Quantitative mass spectrometry-based plasma proteome analysis of personalized response to mRNA COVID-19 vaccine","user":"alexcampos","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710813221000","created":"Mar. 18, 2024, 6:53 PM","description":"Global efforts against COVID-19 have vaccinated a significant portion of the world population in recent years. Combating the COVID-19 pandemic with mRNA vaccines playinged a pivotal role in global immunization effort. However, individual responses to these vaccines vary, leading to diverse vaccination efficacy. Despite significant progress, full understanding of the molecular mechanisms driving the personalized immune response to COVID-19 vaccine remains elusive. To address this gap, we combined a novel nanoparticle-based proteomic workflow with tandem mass tag (TMT) labeling, to quantitatively assess the proteomic changes in a cohort of 12 volunteers following two doses of the Pfizer-BioNTech mRNA COVID-19 vaccine. This optimized protocol seamlessly integrates comprehensive proteome analysis with enhanced throughput by leveraging the enrichment of low-abundant plasma proteins by engineered nanoparticles. Our data demonstrate the ability of this nanoparticle-based workflow to quantify over 3,000 proteins from 48 human plasma samples, providing the deepest view into COVID-19 vaccine-related plasma proteome study. We identified 69 proteins exhibiting a boosted response to the vaccine after the second dose. Additionally, 74 proteins were differentially regulated between seven volunteers, who contracted COVID-19 despite receiving two doses of the vaccine, and the ones who did not contract COVID-19. These findings offer valuable insights into individual variability in response to vaccination, demonstrating the potential of personalized medicine approaches in vaccine development.","fileCount":"86","fileSizeKB":"43442020","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Plasma proteomics;COVID-19 vaccine;Immune response;Nanoparticle-based Workflow;Personalized Response","pi":[{"name":"Alex Rosa Campos","email":"arosacampos@sbpdiscovery.org","institution":"Sanford Burnham Prebys Medical Discovery Institute","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD050749","task":"415d33cd72cf4434ba2c3e7974fdb4b4","id":"2780"}, {"dataset":"MSV000094351","datasetNum":"94351","title":"Sustained bacterial N2O reduction at acidic pH","user":"ghe3","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710809116000","created":"Mar. 18, 2024, 5:45 PM","description":"This dataset contains MS data generated in manuscript 'Sustained bacterial N2O reduction at acidic pH'.","fileCount":"11","fileSizeKB":"3020232","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Serratia (NCBITaxon:613);Desulfosporosinus (NCBITaxon:79206)","instrument":"Exactive Plus","modification":"NA","keywords":"N2O reduction;acidic soils;Environmental microbiology;Microbial physiology;Co-culture EV","pi":[{"name":"Frank E. 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For more detailed information, please contact Dr.Chang Liu (hichang813@uri.edu)","fileCount":"37","fileSizeKB":"371568975","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 5600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"anti-ferroptosis, CBD, proteomics, keratinocytes","pi":[{"name":"Navindra Seeram","email":"bbrluri@gmail.com","institution":"university of rhode island","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1a0d1e7ab93143d7bc19212082db240c","id":"2783"}, {"dataset":"MSV000094347","datasetNum":"94347","title":"SDS22 coordinates the assembly of holoenzymes from nascent protein phosphatase-1","user":"madamo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710790134000","created":"Mar. 18, 2024, 12:28 PM","description":"SDS22 forms an inactive complex with nascent protein phosphatase-1 (PP1) and Inhibitor-3 (I3). SDS22:PP1:I3 is a substrate for the ATPase p97\/VCP, which liberates PP1 for binding to canonical regulatory subunits. The exact role of SDS22 in PP1-holoenzyme assembly remains elusive. Here, we show that SDS22 prevents the aggregation of nascent PP1. In the absence of SDS22, PP1 was gradually lost, resulting in substrate hyperphosphorylation and a proliferation arrest. A human patient with an unstable SDS22 mutant also expressed reduced levels of PP1 and suffered from neurodevelopmental retardation. We furthermore found that SDS22 directly binds to I3 and that this is essential for the stable assembly of SDS22:PP1:I3, the recruitment of p97\/VCP, and the extraction of SDS22 during holoenzyme assembly. SDS22 with a disabled I3-binding site co-transfered with PP1 to canonical regulatory subunits, thereby forming non-functional holoenzymes. Our data show that SDS22, by its ability to bind to both PP1 and I3, integrates the major steps of PP1 holoenzyme assembly.","fileCount":"162","fileSizeKB":"29548113","spectra":"0","psms":"1028791","peptides":"671472","variants":"836380","proteins":"20038","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"SDS22;PP1;ATPase;I3;holoenzyme","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"The Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050733","task":"7fa2a943422148c19d91e017a0caf990","id":"2784"}, {"dataset":"MSV000094340","datasetNum":"94340","title":"Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response","user":"ga87gah","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710750816000","created":"Mar. 18, 2024, 1:33 AM","description":"The DNA-damaging agent gemcitabine (GEM) is a first-line treatment for pancreatic cancer but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs including kinase inhibitors but the experimental evidence for such rational is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 140 clinical kinase inhibitors and observed strong synergy for the ATR inhibitor Elimusertib in most cell lines. Dose-dependent phosphoproteome profiling of four ATR inhibitors following DNA damage induction by GEM revealed a strong block of the DNA damage response pathway including phosphorylated pS468 of CHEK1 as the underlying mechanism of drug synergy. The current work provides a strong rationale for why the combination of GEM and ATR inhibition may be useful for the treatment of PDAC patients and constitutes a rich phenotypic and molecular resource for further investigating effective drug combinations.","fileCount":"1421","fileSizeKB":"287518196","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00696 - \\\"A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate').\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\"","keywords":"decryptM;Phosphorylation;Kinase Inhibitor;Kinobeads;Pancreatic cancer","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Technical University of Munich (TUM)","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050707","task":"a17b8eb584014148815f77235f98d8de","id":"2785"}, {"dataset":"MSV000094339","datasetNum":"94339","title":"Comparative multi-omic analysis of fallopian tube fimbria from BRCA mutation carriers and control women","user":"Martolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710729874000","created":"Mar. 17, 2024, 7:44 PM","description":"Integrated transcriptomic, epigenomic, and proteomic analysis of histologically normal fallopian tubes (FTs) fimbria from BRCA mutant carriers and controls. This study was undertaken to test the hypothesis that there are molecular alterations in FTs from BRCA mutant carriers that contribute to field cancerization and high-grade serous risk. We address the limitations of prior molecular profiling studies of BRCA mutant FTs by controlling for covariates known to influence the molecular and cellular landscape of the FT.","fileCount":"3444","fileSizeKB":"550964437","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF fleX MALDI-2","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00964 - \\\"modification from DeltaMass\\\"","keywords":"multi-omics;fallopian tube fimbria;ovarian cancer;FFPE;BRCA","pi":[{"name":"Jarrod Marto","email":"jarrod_marto@dfci.harvard.edu","institution":"DFCI","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"36f5a33e9ef240c29943344c56b01e60","id":"2786"}, {"dataset":"MSV000094338","datasetNum":"94338","title":"GNPS - 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This intracellular isoform enhanced mitochondrial function. To understand its molecular mechanism, we performed affinity-purification coupled to mass spectrometry using MDCK cell lysate expressing UMOD variant. We prepared MDCK cells which express mock (negative control), wild-type human UMOD or alternatively spliced human UMOD. UMOD was isolated by Immunoprecipitation and interacting proteins were identified by mass spectrometry proteomics analysis.","fileCount":"16","fileSizeKB":"4620626","spectra":"0","psms":"378785","peptides":"228386","variants":"353901","proteins":"52267","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Canis lupus familiaris (NCBITaxon:9615);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"uromodulin;MDCK;protein protein interactions","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"},{"name":"Tarek M. 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Senescent cells release senescence-associated secretory phenotype (SASP), including exosomes that may act as signal transducers between distal tissues, propagating secondary senescence and signaling throughout the body. However, the composition of exosome SASP remains underexplored, presenting an opportunity for novel unbiased discovery. Here, we present a detailed lipidomic analysis of exosome SASP using mass spectrometry from senescent primary human lung fibroblasts and human plasma from young and older individuals. 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Raw MS data were processed using Max Quant (version 2.0, Cox and Mann 2008), Perseus software (version 2.0.6.0)(Tyanova et al.,2016), and human entries of uniprot DB. Proteins were stated identified by a false discovery rate of 0.01 on protein and peptide level.","fileCount":"559","fileSizeKB":"528949783","spectra":"0","psms":"12197050","peptides":"2695664","variants":"5866919","proteins":"85199","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"SOD2;UBR1;UBR2;amino acid starvation;protein degradation;drug resistance;cancer;leukemia","pi":[{"name":"PD Dr. Laura Hinze","email":"hinze.laura@mh-hannover.de","institution":"Hannover Medical School","country":"Germany"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"87c923ec6a7f455fbe4cb37b11480b30","id":"2793"}, {"dataset":"MSV000094324","datasetNum":"94324","title":"GNPS - 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The human CTLH complex forms distinct supramolecular ring-shaped structures dependent on the multimerization of WDR26 or muskelin beta-propeller proteins. Here, we find that, in human cells, CTLH complex E3 ligase activity is dictated by a dynamic exchange between WDR26 and muskelin in tandem with muskelin autoregulation. Proteomic experiments revealed that complex-associated muskelin protein turnover is a major ubiquitin-mediated degradation event dependent on the CTLH complex in unstimulated HeLa cells. We observed that muskelin and WDR26 binding to the scaffold of the complex is interchangeable, indicative of the formation of separate WDR26 and muskelin complexes, which correlated with distinct proteomes in WDR26 and muskelin knockout cells. We found that mTOR inhibition-induced degradation of Pro\/N-degron containing protein HMGCS1 is distinctly regulated by a muskelin-specific CTLH complex. Finally, we found that mTOR inhibition also activated muskelin degradation, likely as an autoregulatory feedback mechanism to regulate CTLH complex activity. Thus, rather than swapping substrate receptors, the CTLH E3 ligase complex controls substrate selectivity and its autoregulation through exchanging its beta-propeller oligomeric subunits WDR26 and muskelin. 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","fileCount":"133","fileSizeKB":"63431857","spectra":"2146055","psms":"1518342","peptides":"86194","variants":"149924","proteins":"28596","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"POLR2I, RPB9, T-REx Flp-In HEK293, miniTurbo, biotin, streptavidin, LC-MS","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050608","task":"8fbfbf9eac5f4bb3b3ef94974b2c1127","id":"2800"}, {"dataset":"MSV000094312","datasetNum":"94312","title":"Unbiased mapping of Thr4 phosphorylation on RNA Pol II CTD indicates role in elongation and 3'-end processing","user":"bfloyd","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710352662000","created":"Mar. 13, 2024, 10:57 AM","description":"RNA polymerase II relies on a repetitive sequence domain (YSPTSPS) within its largest subunit to orchestrate transcription. While the significance of phosphorylation on Ser2\/Ser5 is well-established, the role of Thr4 remains enigmatic. Thr4 phosphorylation has been implicated in elongation, termination, and mRNA processing, yet it has only been detected after transcription end sites, presenting a paradox. Our investigation revealed that Thr4 phosphorylation is initially obscured by flanking Ser5 phosphorylation at the onset of transcription. By selectively removing this masking effect using a phosphatase, we unveiled the true genomic location of this evolutionarily conserved phosphorylation mark, shedding light on Thr4 phosphorylation cellular functions. Subsequent proteomic analyses unearthed that many proteins previously associated with Ser2 are actually recruited to transcription via Thr4. Crucially, Thr4 phosphorylation primes Ser2 phosphorylation, leading to lethal defects in 3'-end processing. Our findings delineate the true genomic location and function of this \"phantom\" mark, prompting a reassessment of functional assignments of the CTD heptad.","fileCount":"38","fileSizeKB":"26734940","spectra":"0","psms":"118973","peptides":"12928","variants":"12928","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Phosphorylation;PPI","pi":[{"name":"Edward Marcotte","email":"marcotte@icmb.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050595","task":"2603f81f2bc24baa822d076e1a9dacd9","id":"2801"}, {"dataset":"MSV000094311","datasetNum":"94311","title":"Top-Down Proteomics Identifies Plasma Proteoform Signatures of Liver Cirrhosis Progression","user":"mikehollas123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710344487000","created":"Mar. 13, 2024, 8:41 AM","description":"Cirrhosis, advanced liver disease, affects 2-5 million Americans. While most patients have compensated cirrhosis and may be fairly asymptomatic, many decompensate and experience life-threatening complications such as gastrointestinal bleeding, confusion (hepatic encephalopathy), and ascites, reducing life expectancy from 12 to less than 2 years. Among the patients with compensated cirrhosis, identifying patients at high risk of decompensation is critical to optimize care, reduce morbidity and mortality. This is important to preferentially direct them towards specialty care which cannot be provided to all patients with cirrhosis. We used discovery Top-down Proteomics (TDP) to detect differentially expressed proteoforms (DEPs) in the plasma of patients with cirrhosis with the goal to identify candidate biomarkers of disease progression. 663 DEPs were identified across three stages of cirrhosis (compensated, compensated with portal hypertension, and decompensated), of which 115 derived from proteins enriched in the liver at a transcriptional level and discriminated the progressive stages of cirrhosis. Enrichment analyses demonstrated DEPs are involved in numerous metabolic, oxidative, immunological, and hematological processes known to be impacted by cirrhosis progression. We have preliminarily defined the plasma proteoform signatures of cirrhosis patients, setting the stage for ongoing discovery and validation of biomarkers for early diagnosis, risk stratification, and disease monitoring.","fileCount":"182","fileSizeKB":"379300445","spectra":"948120","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Cirrhosis;TopDown;Label Free Quant","pi":[{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"04f249ea07764d65bf1d5f07459646c6","id":"2802"}, {"dataset":"MSV000094310","datasetNum":"94310","title":"Target deconvolution of SW016789 in human and mouse Beta cells","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710344366000","created":"Mar. 13, 2024, 8:39 AM","description":"The target of SW016789 is unknown (PMCID: PMC9225822). This compound was identified in a high-throughput screen for insulin secretion modulators and was subsequently discovered to cause hypersecretory stress in beta cells. A photoaffinity probe was designed, Z629, based upon the structure of SW016789. Photo-crosslinking, click chemistry to biotin, and affinity purification with streptavidin-agarose was used to enrich for potential binding partners. Experiments were performed in both mouse MIN6 and human EndoC-BetaH1 beta cells. Enriched proteins were identified based on the ratio of PSMs detected in Z629 vs DMSO treatments. Candidate proteins (>2-fold) were filtered based on a >2-fold enrichment in Z629\/DMSO and >1 PSM for Z629 in both MIN6 and EndoC-BetaH1. Pathway analysis indicated a role for the Vdac family of proteins which were previously identified to have an important role in Beta-cells during type 2 diabetes (PMCID: PMC6331340). Vdac1 was therefore chosen for validation studies.","fileCount":"21","fileSizeKB":"3522318","spectra":"0","psms":"146621","peptides":"98452","variants":"131819","proteins":"69958","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"pancreatic Beta cells;AP-MS\/MS;Vdac","pi":[{"name":"Amber L. 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The second part is focused on the identification of new interacting proteins for phot2.\nCharacterization of proteins important for signaling leading to chloroplast avoidance. PHOT2-GFP wild type and PHOT2-V392L-GFP muteins were immunoprecipitated from leaves of transgenic Arabidopsis plants, either dark-adapted or irradiated with low or high blue light. Proteins identified by Mass Spectrometry as interacting with wild-type PHOT2-GFP and PHOT2-V392L-GFP were compared to identify proteins putatively involved in chloroplast avoidance. Phosphorylation profiles of PHOT2-GFP wild type and PHOT2-V392L-GFP were analyzed to distinguish between phosphorylation sites characteristic for chloroplast accumulation and avoidance.","fileCount":"29","fileSizeKB":"47582886","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Q Exactive","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phototropin;interactome;blue light","pi":[{"name":"Justyna Labuz","email":"justyna.sojka@uj.edu.pl","institution":"Malopolska Centre of Biotechnology, Jagiellonian University","country":"Poland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"bf0b59b06c2c490887dfe6b08b12263a","id":"2804"}, {"dataset":"MSV000094307","datasetNum":"94307","title":"Multi-omics discovery of hallmark protein and lipid features of circulating small extracellular vesicles in humans","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710330894000","created":"Mar. 13, 2024, 4:54 AM","description":"Extracellular vesicles (EVs) are now being increasingly recognized as an essential signalling entity in human plasma, linking them to health and various diseases. Still, their core protein and lipid componentry, which epicentres EV form and function, remains poorly defined. Achieving this unmet milestone remains greatly hindered by abundant non-vesicular extracellular plasma components (non-EVs) in mass spectrometry-based analyses. Here, we performed high-resolution density gradient fractionation of over 80 human plasma samples to isolate circulating EVs, and systematically construct their quantitative proteome (4500 proteins) and lipidome (829 lipids) landscapes. This led to the discovery of a highly conserved panel of 182 proteins (ADAM10, STEAP23, STX7) and 52 lipids (PS, PIPs, Hex2Cer, PAs), providing a deep survey of hallmark molecular features and biological pathways intrinsic to circulating EVs. Our efforts also mapped the surfaceome diversity, identifying 126 proteins on EV surface. We further establish a set of 42 proteins and 114 lipids features that served as hallmark features of non-EV particles in plasma. We submit ADAM10 and PS(36:1) as conserved EV biological markers that enable precise differentiation between EV and non-EV particles. Our findings, which can be explored via open-source Shiny web tool will serve as a valuable repository to the research community for a clearer understanding of circulating EV biology. 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanotoxins","pi":[{"name":"Tri Kaloudis","email":"t.kaloudis@inn.demokritos.gr","institution":"NCSR Demokritos","country":"Greece"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"be1dcff6cc2f4b89b456217f7d3ec08d","id":"2807"}, {"dataset":"MSV000094304","datasetNum":"94304","title":"GNPS [D-Asp3] Microcystins, Cylindrospermopsins, Anatoxins","user":"Sofia_Iliakop","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710322012000","created":"Mar. 13, 2024, 2:26 AM","description":"1: [D-Asp3] Microcystin-LR, [D-Asp3] Microcystin-RR, Microcystin-HilR 200ppb \n2: 13C4(+)-Anatoxin-a, Homoanatoxin-a, CYN, 7-epi-CYN, 7-deoxy-CYN 200ppb\nStandard solutions\nCollision Energy: 40eV-60eV","fileCount":"9","fileSizeKB":"147568","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cyanobacteria (NCBITaxon:1117)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanotoxins","pi":[{"name":"Tri Kaloudis","email":"t.kaloudis@inn.demokritos.gr","institution":"NCSR Demokritos","country":"Greece"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7eed7bde63ea49819dd5ea95dcac202b","id":"2808"}, {"dataset":"MSV000094303","datasetNum":"94303","title":"GNPS Microcystins and Nodularin standards","user":"Sofia_Iliakop","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710319589000","created":"Mar. 13, 2024, 1:46 AM","description":"Anabaenopeptin A, Anabaenopeptin B, Microcystin-LA, Microcystin-LF, Microcystin-LR, Microcystin-LW, Microcystin-LY, Microcystin-RR, Microcystin-YR, Microcystin-HtyR, Microcystin-HilR, Nodularin\nStandard solution 200ppb\nCollision Energy: 40eV-60eV\n","fileCount":"59","fileSizeKB":"1707268","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cyanobacteria (NCBITaxon:1117)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanotoxins","pi":[{"name":"Tri Kaloudis","email":"t.kaloudis@inn.demokritos.gr","institution":"NCSR Demokritos","country":"Greece"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ae042df7f17247fc87bae7df23635591","id":"2809"}, {"dataset":"MSV000094301","datasetNum":"94301","title":"Barbatia virescens proteins_bcbp-1 and bcbp-2","user":"jiminchoi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710306891000","created":"Mar. 12, 2024, 10:14 PM","description":"MSMS data from B. virescense proteins (Bcbp-1, Bcbp-2)","fileCount":"4","fileSizeKB":"23853","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Barbatia virescens (NCBITaxon:6559)","instrument":"Easy n-LC and LTQ Orbitrap XL mass spectrometers","modification":"fixed modification, carbamidomethylation at cysteine residues; variable modification, oxidation at methionine residues","keywords":"barbatia;barbatia virescense;EGF;adhesion","pi":[{"name":"JIMIN CHOI","email":"jmjm334@postech.ac.kr","institution":"POSTECH","country":"South Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050572","task":"3a043a8e07184f75941823365e7c2964","id":"2810"}, {"dataset":"MSV000094300","datasetNum":"94300","title":"GNPS - Cholic acid reaction with mixture of 400 Tripeptides SXX","user":"apatan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710288437000","created":"Mar. 12, 2024, 5:07 PM","description":"MS\/MS fragmentation data of Cholic acid and tripeptide acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"3","fileSizeKB":"150638","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bile acid;Tripeptides;CMMC","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"690a96ef62d841fe9e7c76ed6eee63d2","id":"2811"}, {"dataset":"MSV000094299","datasetNum":"94299","title":"GNPS - Comprehensive Untargeted Lipidomic Profiling of Third Generation Lentiviral Vectors and Packaging Cells: Raw LCMS Data","user":"joshuaroberts","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710287631000","created":"Mar. 12, 2024, 4:53 PM","description":"Untargeted high-resolution lipidomics data of HEK 293T packaging cells and lentiviral vectors (LV) in cell culture media. HEK 293T cells are treated with either vehicle control (DMSO), myriocin (positive control), expressing the VSV G protein or producing 3rd generation LV. LV are concentrated from HEK 293T cell culture media using ultracentrifugation. HEK 293T culture media from untransfected cells is also concentrated by ultracentrifugation and acquired as a lipidomics blank which is used to subtract the abundance of background lipids from the LV samples. Also included, is a diltution series of fetal bovine serum lipid extract (FBS) which is used to asses the linear dynamic range of the instrument.","fileCount":"7686","fileSizeKB":"62811247","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Lentivirus (NCBITaxon:11646)","instrument":"Agilent 6546 QToF","modification":"Not applicable","keywords":"Lipidomics;HEK 293T;Lentiviral Vectors","pi":[{"name":"Jeffrey C. Smith","email":"jeffcsmith@cunet.carleton.ca","institution":"Carleton University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"604c77163ea342a3a167fe74fe339464","id":"2812"}, {"dataset":"MSV000094298","datasetNum":"94298","title":"A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology","user":"zzyingying753","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710282385000","created":"Mar. 12, 2024, 3:26 PM","description":"A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Two distinct types of computational methodologies have emerged: one focuses on analyzing clustering of mutations within protein sequences and 3D structures, while the other characterizes mutations by leveraging the topology of protein-protein interaction network. Their insights are largely non-overlapping, offering complementary strengths. Here, we established a unified, end-to-end 3D structurally-informed protein interaction network propagation framework, NetFlow3D, that systematically maps the multiscale mechanistic effects of somatic mutations in cancer. The establishment of NetFlow3D hinges upon the Human Protein Structurome, a comprehensive repository we compiled that incorporates the 3D structures of every single protein as well as the binding interfaces of all known protein interactions in humans. NetFlow3D leverages the Structurome to integrate information across atomic, residue, protein and network levels: It conducts 3D clustering of mutations across atomic and residue levels on protein structures to identify potential driver mutations. It then anisotropically propagates their impacts across the protein interaction network, with propagation guided by the specific 3D structural interfaces involved, to identify significantly interconnected network \"modules\", thereby uncovering key biological processes underlying disease etiology. Applied to 1,038,899 somatic protein-altering mutations in 9,946 TCGA tumors across 33 cancer types, NetFlow3D identified 12,378 significant 3D clusters throughout the Human Protein Structurome, of which ~54% would not have been found if using only experimentally-determined structures. It then identified 28 significantly interconnected modules that encompass ~8-fold more proteins than applying standard network analyses.","fileCount":"22","fileSizeKB":"10510857","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human 293T cells","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cancer Genomics;3D Protein Structure;Interactome;Protein-Protein Interaction Network;TMT;IP-MS","pi":[{"name":"Haiyuan Yu","email":"haiyuan.yu@cornell.edu","institution":"Cornell University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050561","task":"9413e64fd9da4254924538fd8e265914","id":"2813"}, {"dataset":"MSV000094297","datasetNum":"94297","title":"Brain-wide alterations revealed by spatial transcriptomics and proteomics in COVID-19 infection","user":"JSha","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710277443000","created":"Mar. 12, 2024, 2:04 PM","description":"Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. We performed proteomics profiling across eight cortical and subcortical brain regions, frontal lobe, temporal lobe, occipital lobe, hippocampus, thalamus, basal ganglia, midbrain, and pons, using postmortem brain samples from severe acute COVID-19 patients and matched controls (n=16), all preserved as formalin-fixed paraffin-embedded (FFPE) tissue. Integrating proteomics and additional transcriptomic analyses, we identified board dysregulation of mitochondrial and synaptic pathways in deep-layer excitatory neurons and changes exhibited similarities with those seen in various age-related neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease (AD).","fileCount":"96","fileSizeKB":"87708024","spectra":"18189217","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"K-TMTpro;UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"severe acute COVID-19, postmortem human brains, proteomics, neurodegeneration, mitochondrial defects ","pi":[{"name":" Daniel H. Geschwind","email":"dhg@mednet.ucla.edu","institution":"UCLA School of Medicine, Department of Neurology, Psychiatry, and Human Genetics","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"782dd7cbc6f6486eb515b8c9e4b0f5d5","id":"2814"}, {"dataset":"MSV000094296","datasetNum":"94296","title":"GNPS - Comprehensive Untargeted Lipidomic Profiling of Third Generation Lentiviral Vectors and Packaging Cells: Raw LCMS Data","user":"joshuaroberts","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710276570000","created":"Mar. 12, 2024, 1:49 PM","description":"Untargeted high-resolution lipidomics data of HEK 293T packaging cells and lentiviral vectors (LV) in cell culture media. HEK 293T cells are treated with either vehicle control (DMSO), myriocin (positive control), expressing the VSV G protein or producing 3rd generation LV. LV are concentrated from HEK 293T cell culture media using ultracentrifugation. HEK 293T culture media from untransfected cells is also concentrated by ultracentrifugation and acquired as a lipidomics blank which is used to subtract the abundance of background lipids from the LV samples. Also included, is a diltution series of fetal bovine serum lipid extract (FBS) which is used to asses the linear dynamic range of the instrument.","fileCount":"7686","fileSizeKB":"62811247","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Lentivirus (NCBITaxon:11646)","instrument":"Agilent 6546 QToF","modification":"Not applicable","keywords":"Lipidomics, HEK 293T, Lentiviral Vectors","pi":[{"name":"Jeffrey C. Smith","email":"jeffcsmith@cunet.carleton.ca","institution":"Carleton University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6e5eb284e04b47499dbfdce0f23b60b7","id":"2815"}, {"dataset":"MSV000094294","datasetNum":"94294","title":"B._Raktan_Ahmed_P131_VS15_2024","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710261813000","created":"Mar. 12, 2024, 9:43 AM","description":"This dataset consists of 363 raw MS files and associated peak lists and result files, acquired on a TripleTOF 6600 mass spectrometer operated in Data Independent Acquisition mode (SWATH). It also includes the sequence database used for analysis and the MSPLIT spectral library which was generated from paired samples acquired in Data Dependent Acquisition (DDA) mode.\nAll sample generation, streptavidin affinity purification, mass spectrometric acquisition, and data analysis was performed by B. Raktan Ahmed.\nThe files are associated with a manuscript submitted for publication by Dyakov et al. that provides a spatial map of nuclear body-associated proteins with a focus on the paraspeckle and nuclear speckle. \nAnne-Claude Gingras is the corresponding author of the manuscript and should be contacted for questions about this dataset (gingras@lunenfeld.ca).\n\nThis submission is associated with 4 Supplementary Files (in addition to this README file):\nTable 1 describes the composition of this dataset\nTable 2 lists the protein evidence for the entire dataset\nTable 3 lists the SAINT output (results) \n\nInternal reference from the Gingras lab ProHits implementation:\nProject: P131\nExport version VS15\nSAINT Task ID: 6779\n","fileCount":"362","fileSizeKB":"259689697","spectra":"0","psms":"222772","peptides":"49841","variants":"57909","proteins":"34831","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;Proximity-dependent biotinylation;Protein-protein interaction;RNA biology;Nuclear bodies ;Nuclear speckle ;Splicing speckle;Paraspeckle","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050558","task":"f42e13f964234d80a7f6053fa40a3af4","id":"2816"}, {"dataset":"MSV000094293","datasetNum":"94293","title":"Minimal Change Disease: a proteomics approach ","user":"ioanapralea","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710233648000","created":"Mar. 12, 2024, 1:54 AM","description":"This study aimed to shed light on the potential pathophysiology of MCD by using glomerular proteomic analysis. Shotgun proteomics using label-free quantitative mass spectrometry was performed on formalin-fixed, paraffin-embedded (FFPE) renal biopsies from two groups of samples: control (CTR) and MCD. Glomeruli were excised from FFPE renal biopsies using laser capture microdissection (LCM), and a single-pot solid-phase-enhanced sample preparation (SP3) digest method was used to improve yield and protein identifications. ","fileCount":"434","fileSizeKB":"121509711","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"minimal change disease;label-free proteomics;podocyte cytoskeleton;laser capture microdissection","pi":[{"name":"Iuga Cristina-Adela","email":"iugac@umfluj.ro","institution":"MEDFUTURE Research Center for Advanced Medicine","country":"Romania"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2799588823c547dba1b6a3fe807af9a7","id":"2817"}, {"dataset":"MSV000094292","datasetNum":"94292","title":"synthesized of 2H,2Cl-PFOA from 2H,2H-PFOA or from 6:2 FTOH.","user":"Bing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710227389000","created":"Mar. 12, 2024, 12:09 AM","description":"synthesized of 2H,2Cl-PFOA from 2H,2H-PFOA or from 6:2 FTOH.","fileCount":"4","fileSizeKB":"1307292","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthesized PFAS","instrument":"Orbitrap Exploris 480 (Thermo Scientific instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PFAS synthesized","pi":[{"name":"Wang Xuebing","email":"wangxuebing@nju.edu.cn","institution":"Nanjing University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"17a1f6c86763492698574cd4556f010b","id":"2818"}, {"dataset":"MSV000094290","datasetNum":"94290","title":"Fervidibacter sacchari diferential proteomics under different growth conditions","user":"nnou","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710175850000","created":"Mar. 11, 2024, 9:50 AM","description":"Fervidibacter sacchari PD1 cells were grown with beta-glucan, gellan gum, locust bean gum, starch, or xyloglucan as sole carbon\/energy sources. Cellular and secreted proteins under each condition were analyzed with DIA proteomics.","fileCount":"25","fileSizeKB":"35733856","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Candidatus Fervidibacter sacchari (NCBITaxon:1448929)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"hyperthermophile armatimonadota fervidibacteria polysaccharide","pi":[{"name":"Brian P. Hedlund","email":"brian.hedlund@unlv.edu","institution":"University of Nevada","country":"USA"},{"name":"Marike Palmer","email":"Marike.Palmer@umanitoba.ca","institution":"University of Manitoba","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050537","task":"c1fe9f9b8bec4663b307a0548cb5aae8","id":"2819"}, {"dataset":"MSV000094288","datasetNum":"94288","title":"GNPS - Cryogenic tissue homogenization as an alternative to adjacent fresh-frozen biopsy use for multi-omics analysis","user":"Dali77","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710141734000","created":"Mar. 11, 2024, 12:22 AM","description":"Background: The majority of multi-omics studies make use of adjacent fresh-frozen tissue pieces for different analyses. This approach however is not considering the intrinsic tissue heterogeneity and can lead to a biological mismatch of different omics layers. To overcome this limitation, we here propose an alternative approach where tissue is cryogenically pulverized and lyophilized, obtaining a homogenous tissue powder that can be used for subsequent omics studies. The purpose of this study was to investigate how omics analysis differ or coincide when comparing adjacent tissue slices to homogenized powder using three major mammalian organs from a wildtype mouse model.\r\nMethods: Healthy fresh-frozen and pulverized-lyophilized mouse tissue from brain, kidney, and liver was subjected to DNA methylation and genome sequencing (genomics), RNA sequencing (transcriptomics), protein (proteomics), and metabolite (metabolomics) analysis. Obtained analytical results were investigated by statistical and quality control measures, including dendrograms, correlation analysis, principal component analysis, RNA integrity, feature coverage, and energy charge estimation.\r\nResults: DNA methylation was not affected differently by the two different tissue processing methods. The RNA integrity obtained was comparable between fresh-frozen tissue slicing and pulverization-lyophilization. The coverage of gene transcripts, proteins, and metabolites was preserved similarly by both methodological approaches. Overall the pulverization-lyophilization approach resulted in a reduced heterogeneity between biological replicates.\r\nConclusions: Cryogenically pulverized and lyophilized tissue preserves the most important cellular molecular features, such as RNA integrity, DNA methylation status, gene transcript, protein, and metabolite coverage. Therefore, it is a suitable alternative method for improved multi-omics analysis, providing reduced sample heterogeneity, beneficial for batch reproducibility, as well as easier transportation and storage conditions due to complete water removal.\r\n","fileCount":"30","fileSizeKB":"69967412","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Cryogenic pulverization, lyophilization, tissue omics, metabolomics, proteomics, RNA sequencing, transcriptomics, DNA methylation, genomics","pi":[{"name":"Dr.Mohamed Ali Jarboui","email":"mohamed-ali.jarboui@uni-tuebingen.de","institution":"Medical Bioanalytics, University Clinic Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD050521","task":"fc4ef0e54fac4117ae63944375e60ed6","id":"2820"}, {"dataset":"MSV000094287","datasetNum":"94287","title":"The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 monoclonal antibodies","user":"alejandro1018","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1710139590000","created":"Mar. 10, 2024, 11:46 PM","description":"Antibodies are central to the immune response against microbes. We have previously generated an opsonic IgG1 monoclonal antibody, Ab25, targeting the M protein of Streptococcus pyogenes. Here, we engineered Ab25 into the IgG2-4 subclasses. Despite reduced binding, the IgG3 version demonstrated enhanced opsonic function. Molecular dynamics (MD) simulations showed that IgG3s Fc exhibits extensive mobility in 3D space relative to the antigen due to its extended hinge region. The MD simulations also showed altered Fab-antigen interactions, in line with IgG3s diminished affinity. We explored the impact of hinge-engineering by generating a panel of IgG antibodies, IgGhxx, containing the CH1-3 domains of IgG1 and different segments of IgG3s hinge. Hinge-engineering enhanced opsonic function, with the most potent hinge having 47 amino acids. IgGh47 exceeded the parent IgG1 and, in some instances, the IgG3 version. The IgGh47 was protective against Streptococcus pyogenes in a systemic infection mouse model, contrary to parent IgG3 and IgG1. The in vitro phenotype of IgGh47 was generalizable to clinical isolates with different emm types. Finally, we generated IgGh47 versions of anti-SARS-CoV-2 mAbs, which exhibited strongly enhanced in vitro opsonic function compared to the original IgG1s. 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We identified over 250 proteins preferentially associated with pgRNA from the packaging competent version of the virus. These included proteins known to support capsid formation, enhance viral gene expression, catalyze nucleocapsid dephosphorylation, and bind to N6-methylations on the viral genome. 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In recent years, wildfire events have been increasing in both number and severity within the region. Currently, there is an extensive body of research from the wine industry on the impact of smoke taint in grapes, however, research investigating smoke taint in hops is limited. This study aims to characterize smoke taint in hops through laboratory simulated wildfire smoke exposure coupled with chemical profiling by nontargeted gas chromatography-mass spectrometry (GC-MS). Results reveal that the chemical profiles of smoked hops varied across fuel types. Specifically, several known smoke taint markers, including guaiacol and 4-methylguaiacol, as well as previously unreported compounds such xylopyranose were observed to be elevated in smoked hops compared to controls. This research provides a foundation for future studies to investigate various fuel types and their varying effects on hop quality.","fileCount":"90","fileSizeKB":"759225","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Humulus lupulus (NCBITaxon:3486)","instrument":"GC-MS","modification":"NA","keywords":"hops;smoke taint;GC-MS;SPME;nontargeted","pi":[{"name":"Jessica Prenni","email":"jprenni@colostate.edu","institution":"Colorado State University","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"89dc9b5a66e84243ad18e1202bd56fee","id":"2839"}, {"dataset":"MSV000094245","datasetNum":"94245","title":"Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma","user":"benjamin_hempel","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709733861000","created":"Mar. 6, 2024, 6:04 AM","description":"Canine cutaneous histiocytoma (CCH) is a tumor originating from dermal Langerhans cells, especially affecting young dogs. The common spontaneous regression of CCH makes it an interesting model in comparative oncology research. Here, we asked which specific immuno-oncological dynamics underlie spontaneous regression of CCH on mRNA and protein levels. QuantSeq 3' mRNA sequencing with functional overrepresentation analysis and an nCounter RNA hybridization assay were employed on CCH samples representing three different tumor stages. Additionally, samples were subjected to matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI).","fileCount":"13","fileSizeKB":"10605382","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Canis lupus familiaris (NCBITaxon:9615)","instrument":"ultrafleXtreme;Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Canine Cutaneous Histiocytoma;Mass Spectrometry Imaging;Proteomics","pi":[{"name":"Benjamin-Florian Hempel","email":"benjamin.hempel@fu-berlin.de","institution":"Freie University Berlin","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050403","task":"0456d42def634012bbd67bfc72b95524","id":"2840"}, {"dataset":"MSV000094244","datasetNum":"94244","title":"Bacterial RNA promotes proteostasis through inter-tissue communication in C. elegans","user":"verizy27","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709710950000","created":"Mar. 5, 2024, 11:42 PM","description":"Life expectancy has been increasing over the last decades, which is not matched by an increase in healthspan. Besides genetic composition, environmental and nutritional factors influence both health- and lifespan. Diet is thought to be a major factor for healthy ageing. Here, we show that dietary RNA species extend healthspan in C. elegans. Inherent bacterial-derived double stranded RNA reduces protein aggregation in a C. elegans muscle proteostasis model. This beneficial effect depends on low levels of systemic selective autophagy, the RNAi machinery in the germline, even when the RNA is delivered through ingestion in the intestine and the integrity of muscle cells. Our data suggest a requirement of inter-organ communication between the intestine, the germline and muscles. Our results demonstrate that bacterial-derived RNAs elicit a systemic response in C. elegans, which protects the animal from protein aggregation during ageing. We provide evidence that low stress levels are beneficial for healthspan.","fileCount":"22","fileSizeKB":"26402366","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"C. elegans, proteostasis, Bacterial RNA","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050390","task":"9775373687f4439b80b87162378b63af","id":"2841"}, {"dataset":"MSV000094243","datasetNum":"94243","title":"CDKN1B (p27kip1) enhances drug tolerant persister CTCs by restricting polyploidy following mitotic inhibitors","user":"whaas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709699478000","created":"Mar. 5, 2024, 8:31 PM","description":"BRx82 and BRx142 were cell cultures derived from breast cancer circulating tumor cells and propagated ex-vivo. To study early changes that transpire under mitosis inhibiting chemotherapy, these cultures were subjected to a 16 hours exposure to docetaxel (10nM or DMSO as vehicle control) and then cultured for a total of 4 days.\n\nThe experiments were done using an Orbitrap Fusion (proteomics) or an Orbitrap Fusion Lumos (phosphoproteomics) mass spectrometer. Multiplexing was achieved using either TMT10 reagents and the SPS-MS3 method. Basic pH reversed-phase chromatography (bRPLC) was used for off-line pre-fractionation; 12 fractions were analyzed for proteome mappings (PMID: 26700037) and 24 fractions sample for phosphoproteome mappings (PMID: 31606085). Phosphoproteome mappings were done using both HCD fragmentation with Orbitrap fragment ion detection and CID fragmentation with ion trap fragment ion detection (PMID: 29487189, PMID: 31606085).\n\nRAW files from the proteome mapping experiment are named HorwitzMaheswaranHaber_proteome_fraction01 to 12.\n\nRAW files from the phosphoproteome mapping experiment are named\n\nTMT labeling was the same for the proteomics and the phosphoproteomics experiments:\nBRx82_DTX-_#1 (129c)\nBRx82_DTX-_#2 (130n)\nBRx82_DTX+_#1 (127c)\nBRx82_DTX+_#2 (128n)\nBRx142_DTX-_#1 (126)\nBRx142_DTX-_#2 (127n)\nBRx142_DTX+_#1 (128c)\nBRx142_DTX+_#2 (129n)\n","fileCount":"44","fileSizeKB":"28039224","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion;Orbitrap Fusion Lumos","modification":"57.02146374 (IAA), cysteine, static;79.966331 (phosphorylation) serine, threonine, tyrosine, variable;15.9949146221 (oxidation), methionine, variable;229.162932 (TMT10), lysine, N-terminus, static","keywords":"Breast cancer, circulating tumor cells, chemotherapy, docetaxel, persister cells, proteomics, phosphoproteomics, TMT, TMT10, Orbitrap Fusion, Orbitrap Lumos Fusion, SPS MS3","pi":[{"name":"Daniel Haber","email":"dhaber@mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center and Harvard Medical School","country":"US"},{"name":"Shyamala Maheswaran","email":"smaheswaran@mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center and Harvard Medical School","country":"US"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital Cancer Center and Harvard Medical School","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"43993ff13d92454cb8a135c27c80a6a2","id":"2842"}, {"dataset":"MSV000094241","datasetNum":"94241","title":"Native top down proteomics reveals EGFR ER signaling crosstalk in breast cancer cells dissociates NUTF2 dimers to modulate ER signaling and cell growth ","user":"pereiragomf","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709687038000","created":"Mar. 5, 2024, 5:03 PM","description":"Native top-down characterization of complexoforms in breast cancer cells","fileCount":"44","fileSizeKB":"2494971","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"Acetylation","keywords":"Native top-down proteomics","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5cb03c82eb4348ed83ce60895cadce94","id":"2843"}, {"dataset":"MSV000094239","datasetNum":"94239","title":"An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709667978000","created":"Mar. 5, 2024, 11:46 AM","description":"Transcriptional coregulators and transcription factors (TFs) contain intrinsically disordered regions (IDRs) that are critical for their partitioning and function in gene regulation. Canonically, IDRs drive coregulator-TF association by directly promoting multivalent protein-protein interactions. Using a chemical genetic approach, we report an unexpected mechanism by which the IDR of the corepressor LSD1 excludes TF association, acting as a dynamic conformational switch that tunes repression of active cis-regulatory elements. Hydrogen-deuterium exchange shows that the LSD1 IDR interconverts between transient open and closed conformational states, the latter of which inhibits partitioning of the proteins structured domains with TF hubs. This autoinhibitory switch controls leukemic differentiation by modulating repression of active cis-regulatory elements bound by LSD1 and master hematopoietic TFs. Together, these studies unveil that the dynamic crosstalk between opposing structured and unstructured regions is an alternative paradigm by which disordered regions can shape coregulator-transcription factor interactions to control cis-regulatory landscapes and cell fate.","fileCount":"145","fileSizeKB":"39689717","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Q Exactive HF-X;Orbitrap Exploris 480","modification":"K-TMT10, n-term-TMT10, C-carbamidomethylation, M-oxidation, N-term acetylation, Pyroglutamic acid (N-termQ)","keywords":"N-terminus IDR, LSD1","pi":[{"name":"Steven A. 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Analysis was performed by Tiffany Cho, Laura McGary, Cassandra Wong, and Daniel Durocher. \nThe files are associated with a manuscript submitted for publication by Tiffany Cho et al. The main goal of this paper was to identify mechanisms required for the essential function of SUMO. This dataset showed no difference in differentially SUMOylated proteins upon knockout of NFATC2IP compared to WT. \nDaniel Durocher is the corresponding author of the manuscript (durocher@lunenfeld.ca); Karen Colwill should be contacted for questions on this dataset (colwill@lunenfeld.ca)\n\nThis submission is associated with 2 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence\n","fileCount":"170","fileSizeKB":"7556137","spectra":"0","psms":"44894","peptides":"4887","variants":"5699","proteins":"1233","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"UNIMOD:1 - \\\"Acetylation.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"NFATC2IP;SUMO","pi":[{"name":"Karen Colwill","email":"colwill@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050361","task":"13b693fa3b7441c4aa7a18954d38ed24","id":"2845"}, {"dataset":"MSV000094235","datasetNum":"94235","title":"The proteomics data of Aspergillus niger ATCC 1015 after spirolactone treatment","user":"yyds","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709625706000","created":"Mar. 5, 2024, 12:01 AM","description":"Fungal infections pose a great threat to public health and the existing four classes of antifungals have limitations due to high toxicity, drug-drug interactions, and emerging drug-resistance. Streptomyces spp. represent an important source of antimicrobial substances, notably including the antifungal agent amphotericin B. The rapamycin-producer Streptomyces iranensis displayed strong antifungal activities against Aspergillus. Revisiting its genome revealed several intriguing biosynthetic gene clusters, including one unparalleled Type I polyketide synthase, which codes for uncharacterized metabolites. The identification of a novel macrolide spirolactone was facilitated through CRISPR-based gene editing, HR-ESI-MS analysis, followed by fermentation and purification processes. Their structures and absolute configurations were confirmed by NMR, MS and X-ray crystallography. Spirolactone A harbors an undescribed carbon skeleton with 13 chiral centers, featuring a rare ?-lactone moiety, a [6,6]-spiroketal ring, and an unprecedented 7-oxo-octylmalonyl-CoA extender unit. Spirolactone displayed profound antifungal effects against numerous fungal pathogens, e.g. the genus Talaromyces and several sections of Aspergillus including clinically relevant species such as Aspergillus niger and A. tubingensis (section Nigri), A. terreus (section Terrei) and the azol-resistant A. calidoustus (section Usti). Proteomics analysis revealed spirolactone potentially disrupted the integrity of fungal cell walls and induced the expression of stress-response proteins in A. niger. Spirolactone A represents a new class of potential agents leading to combat fungal infections.","fileCount":"10","fileSizeKB":"12343266","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus niger ATCC 1015 (NCBITaxon:380704)","instrument":"LTQ Orbitrap Discovery","modification":"No","keywords":"Aspergillus niger ATCC 1015;Antifungal agent;Spirolactone","pi":[{"name":"Ling Ding","email":"lidi@dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"02862edfe92047c5b6c3e2a5b3d61dac","id":"2846"}, {"dataset":"MSV000094234","datasetNum":"94234","title":"Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap)","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709603592000","created":"Mar. 4, 2024, 5:53 PM","description":"Mouse brain and MLE-12 lysates were alkylated with N-ethylmaleimide, precipiated with methanol and trapped on a pyridyl disulfide quartx (PDQ) suspension trap. Protein were washed and incubated with -\/+hydroxylamine and trypsin, and unbound peptides were labeled with TMTPro reagents on C18 StageTips. Bound peptides were labeled with TMTPro reagents on PDQ traps, eluted with DTT and alkylated with iodoacetamide followed by StageTip cleanup. Peptides were analyzed by nanoLC-MS\/MS using a 90 min gradient in duplicate. MS\/MS used a SPS-MS3 (or FAIMS-SPS-MS3) method as indicated in metadata. Raw files were converted to .mzml and analyzed using FragPipe.","fileCount":"37","fileSizeKB":"9597872","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";MOD:00483 - \\\"A protein modification that is produced by reaction with N-ethylmaleimide.\\\";UNIMOD:1 - \\\"Acetylation.\\\";MOD:00068 - \\\"A protein modification that effectively converts a glycine residue to N-myristoylglycine.\\\"","keywords":"palmitoylation;S-acylation","pi":[{"name":"Matthew W. Foster","email":"mwfoster@duke.edu","institution":"Duke University","country":"USA"},{"name":"Michael T. Forrester","email":"michael.forrester@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD050341","task":"30bde115de68438a9b6413adfbf6ab13","id":"2847"}, {"dataset":"MSV000094231","datasetNum":"94231","title":"Emerging combination strategy: FANCI suppression induces PARP1 redistribution to enhance efficacy of PARP inhibitors in breast cancer ","user":"Nuonuonuo123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709548642000","created":"Mar. 4, 2024, 2:37 AM","description":"The data of co-immunoprecipitation (co-IP) followed by mass spectrometry (MS) analysis using FANCI antibody and non-specific IgG antibody in breast cancer cell lines SUM-1315 and ZR-75-1.","fileCount":"11","fileSizeKB":"6270814","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichuris sp. ex Homo sapiens JP-2011 (NCBITaxon:1035824)","instrument":"Q Exactive HF-X","modification":"no","keywords":"FANCI co-IP","pi":[{"name":"Ding Qiang","email":"dingqiang@njmu.edu.cn","institution":"Nanjing Medical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d6d53355d0d54dddb603119b2104375d","id":"2848"}, {"dataset":"MSV000094229","datasetNum":"94229","title":"DATASET - Top-Down - Snake venom proteomics of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Turkiye\/Turkey","user":"MDamm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709540419000","created":"Mar. 4, 2024, 12:20 AM","description":"This DATASET collection includes the mass spectrometry files for proteomics venom investigation of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Turkiye\/Turkey.\n\nSpecies list:\n\nVipera berus barani\nVipera darevskii\nMontivipera bulgardaghica bulgardaghica \nMontivipera bulgardaghica albizona\nMontivipera xanthina\nMacrovipera lebetinus obtusa\nDaboia palaestinae\n\nFolders - TOP-DOWN PROTEOMICS: The venom pools were investigated by the non-reduced and TCEP reduced top-down (labled as TD) approach and in short: untreated (non-reduced) or TCEP reduced samples submitted to HPLC-MS\/MS. Files are included as RAW and MZML format.\n\nUsed instrument: Q Exactive HF mass spectrometer (Thermo, Bremen, Germany) with a Vanquish ultra-high performance liquid chromatography (UHPLC) system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Supelco Discovery BIO wide C18 (2.0 x 150 mm; 3 um particle size; 300 A pore size).\n\nModifications: none (either red. or non-red. disulfide bridges)\n\n","fileCount":"29","fileSizeKB":"14614266","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vipera berus (NCBITaxon:31155);Vipera berus barani;Vipera barani (NCBITaxon:247077);Vipera darevskii (NCBITaxon:2493147);Montivipera bulgardaghica (NCBITaxon:1850566);montivipera bulgardaghica bulgardaghica;Montivipera bulgardaghica albizona;Montivipera albizona (NCBITaxon:110210);Montivipera xanthina (NCBITaxon:110207);Macrovipera lebetina (NCBITaxon:8709);Macrovipera lebetinus;Macrovipera lebetina obtusa (NCBITaxon:209528);Daboia palaestinae (NCBITaxon:1170828)","instrument":"Q Exactive HF","modification":"none (either red. or non-red. disulfide bridges)","keywords":"snake venomics;venom;snake;viper;snakebite;proteomics;peptidomics","pi":[{"name":"Maik Damm","email":"maik.damm@outlook.de","institution":"TU Berlin","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3f0b9caa960f47c4ab8d729ecc51efc2","id":"2849"}, {"dataset":"MSV000094228","datasetNum":"94228","title":"DATASET - Bottom-Up - Snake venom proteomics of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Turkiye\/Turkey","user":"MDamm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709540074000","created":"Mar. 4, 2024, 12:14 AM","description":"This DATASET collection includes the mass spectrometry files for proteomics venom investigation of seven taxa of the genera Vipera, Montivipera, Macrovipera and Daboia across Turkiye\/Turkey.\n\nSpecies list:\n\nVipera berus barani\nVipera darevskii\nMontivipera bulgardaghica bulgardaghica \nMontivipera bulgardaghica albizona\nMontivipera xanthina\nMacrovipera lebetinus obtusa\nDaboia palaestinae\n\nFolders 01-07 - BOTTOM-UP PROTEOMICS: The venom pools were investigated by the bottom-up \"snake venomics\" (labled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o\/n tryptic digested. Samples submitted to HPLC-MS\/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS\/MS analytic w\/o further gel procession. Folders 01 to 07 include the MS and MS\/MS spectra of the snake species 1-7, respectively. Files are included as RAW and MZML format.\n\nUsed instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 x 150 mm; 5 um particle size) column.\n\nModifications: UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","fileCount":"2001","fileSizeKB":"35282558","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vipera berus (NCBITaxon:31155);Vipera berus barani;Vipera barani (NCBITaxon:247077);Vipera darevskii (NCBITaxon:2493147);Montivipera bulgardaghica (NCBITaxon:1850566);montivipera bulgardaghica bulgardaghica;Montivipera bulgardaghica albizona;Montivipera albizona (NCBITaxon:110210);Montivipera xanthina (NCBITaxon:110207);Macrovipera lebetina (NCBITaxon:8709);Macrovipera lebetinus;Macrovipera lebetina obtusa (NCBITaxon:209528);Daboia palaestinae (NCBITaxon:1170828)","instrument":"LTQ Orbitrap XL","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"snake venomics;venom;snake;viper;snakebite;proteomics;peptidomics","pi":[{"name":"Maik Damm","email":"maik.damm@outlook.de","institution":"TU Berlin","country":"Deutschland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f8872b47554a4e588fc0580dd4bda293","id":"2850"}, {"dataset":"MSV000094226","datasetNum":"94226","title":"GNPS - Metabolomics data for Figure 1D-1F. Schofield et al, Cell Reports, ","user":"ryan_sheldon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709505081000","created":"Mar. 3, 2024, 2:31 PM","description":"Metabolomics raw LCMS files for Figure 1D-1F. Schofield et al, Cell Reports, \"Acod1 Expression in Cancer Cells Promotes Immune Evasion through the Generation of Inhibitory Peptides\". 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Acyl chlorides and amines were used to create these compounds. The following reactants are: Palmitoyl, Tetradecanoyl, Decanoyl, Octanoyl, Hexanoyl, Butyryl, Acetyl chlorides with Arg, Phe, Tyr, Trp, Ser, Met, Gly, Homoserine, Leu, GABA, 5-aminobutanoic acid, His, Lys, Thr.","fileCount":"15","fileSizeKB":"3194833","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"N-Acyl Lipids;Amino Acids;Carboxylic Acid","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9758fb19f32341cea76d8066a9f98156","id":"2852"}, {"dataset":"MSV000094219","datasetNum":"94219","title":"Diagnosing and staging epithelial ovarian cancer by serum glycoproteomic profiling","user":"GX_InterVenn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709342245000","created":"Mar. 1, 2024, 5:17 PM","description":"Background \nThere is a need for diagnostic tests for screening, triaging and staging of epithelial ovarian cancer (EOC). Glycoproteomics of blood samples has shown promise for biomarker discovery.\n\nMethods\nWe applied glycoproteomics to serum of people with EOC or benign pelvic masses and healthy controls. A total of 653 analytes were quantified and assessed in multivariable models, which were tested in an independent cohort. Additionally, we analyzed glycosylation patterns in serum markers and in tissues.\n\nResults\nWe identified a biomarker panel that distinguished benign lesions from EOC with sensitivity and specificity of 83.5% and 90.1% in the training set, and of 86.7 and 86.7% in the test set, respectively. ROC analysis demonstrated strong performance across a range of cutoffs. Fucosylated multi-antennary glycopeptide markers were higher in late-stage than in early-stage EOC. A comparable pattern was found in late-stage EOC tissues. \n\nConclusions\nBlood glycopeptide biomarkers have the potential to distinguish benign from malignant pelvic masses, and early- from late-stage EOC. Glycosylation of circulating and tumor tissue proteins may be related. This study supports the hypothesis that blood glycoproteomic profiling can be used for EOC diagnosis and staging and it warrants further clinical evaluation. \n","fileCount":"392","fileSizeKB":"164528","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Agilent 6495C Triple Quadrupole","modification":"Glycosylation","keywords":"Ovarian cancer;Glycoproteomics;Biomarker","pi":[{"name":"Gege Xu","email":"ggxu@venn.bio","institution":"InterVenn Biosciences","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ca5c86e3d11b485b8d77d5ee81ae2d32","id":"2853"}, {"dataset":"MSV000094218","datasetNum":"94218","title":"GNPS - Caffeine Inhibitory Effect on Catalase","user":"simonezuffa","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709335953000","created":"Mar. 1, 2024, 3:32 PM","description":"Investigation of possible inhibitory effect of caffeine on catalase for dopamine conversion into salsolinol. 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Data are composed of four Malpighiaceae plant samples (a subset of MSV000085119). Data were acquired in a Maxis Impact Q-TOF mass spectrometer (Bruker Daltonics) equipped with an ESI source (positive ionization mode).","fileCount":"5","fileSizeKB":"221483","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Amorimia andersonii (NCBITaxon:1816314);Niedenzuella multiglandulosa (NCBITaxon:1816324);Stigmaphyllon blanchetii (NCBITaxon:1804190);Stigmaphyllon paralias (NCBITaxon:151877)","instrument":"maXis","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"plants;Malpighiaceae","pi":[{"name":"Pieter C. 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The causes of delayed regeneration in the elderly remain unclear. Here, we used proteomic and metabolomic profiling of intestinal tissues together with functional assays to characterize the dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent. Comparison of regeneration dynamics in mice of different ages revealed emergence of a proteostasis stress signature and increased levels of polyamines following injury exclusively in old epithelia. Mechanistically, we show that delayed regeneration is a cell-intrinsic feature of old epithelial cells that display reduced protein synthesis and accumulation of ubiquitylated proteins. We demonstrate that an intervention based on dietary restriction followed by re-feeding prior to injury elevates intracellular polyamine levels, alleviates proteostasis stress and restores the regenerative capacity of the old intestines. Our work provides novel targets and strategies to improve intestinal regeneration in the elderly.","fileCount":"71","fileSizeKB":"500705522","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Intestinal regeneration Protein homeostasis Polyamine metabolism","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD050266","task":"cb3877fd31a947a9bd96429099e25cdf","id":"2858"}, {"dataset":"MSV000094211","datasetNum":"94211","title":"GNPS - MobiLipid: A Tool for Enhancing CCS Quality Control of IM-MS Lipidomics by Internal Standardization","user":"felinah","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709290390000","created":"Mar. 1, 2024, 2:53 AM","description":"Measurements of U13C labeled and unlabeled lipids of an ethanolic yeast (Komagataella phaffii) extract using both LC-DTIM-MS and LC-TIM-MS.","fileCount":"2373","fileSizeKB":"61409854","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Komagataella phaffii (NCBITaxon:460519)","instrument":"6560 Q-TOF LC\\\/MS;timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lipidomics;ion mobility mass spectrometry;LC-DTIM-MS;LC-TIM-MS;U13C labeling","pi":[{"name":"Gunda Koellensperger","email":"gunda.koellensperger@univie.ac.at","institution":"University of Vienna","country":"Austria"},{"name":"Tim Causon","email":"tim.causon@boku.ac.at","institution":"University of Natural Resources and Life Sciences Vienna","country":"Austria"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5f9520cddcbe44008a5d3ce097a2990f","id":"2859"}, {"dataset":"MSV000094210","datasetNum":"94210","title":"Deficiency in the SNARE protein SYNTAXIN-11 causes a secondary B cell defect","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709289406000","created":"Mar. 1, 2024, 2:36 AM","description":"CD4 T cell help requires functional SNARE protein SYNTAXIN-11 for successful interaction with B cells, CD40L mobilization and secretion of IL-2 and IL-10 to promote B cell differentiation, germinal centre formation and class switch. 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The GLUT1-deficient reticulocytes possess no tangible alterations to membrane composition or deformability in reticulocytes. Metabolomic analyses of GLUT1-deficient reticulocytes reveal hallmarks of reduced glucose import, downregulated metabolic processes and upregulated AMPK-signaling, alongside alterations in antioxidant metabolism, resulting in increased osmotic fragility and metabolic shifts indicative of higher oxidant stress. Despite detectable metabolic changes in GLUT1 deficient reticulocytes, the absence of developmental phenotype, detectable proteomic compensation or impaired deformability comprehensively alters our understanding of the role of GLUT1 in red blood cell structure, function and metabolism. It also provides cell biological evidence supporting clinical consensus that reduced GLUT1 expression does not cause anemia in GLUT1 deficiency syndrome.","fileCount":"199","fileSizeKB":"77711780","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:108 - \\\"N-ethylmaleimide on cysteines.\\\"","keywords":"GLUT1,reticulocyte ","pi":[{"name":"Tim J Satchwell","email":"T.Satchwell@bristol.ac.uk","institution":"University of Bristol ","country":"UK"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ab88082fec2b43b2952a16535b013127","id":"2864"}, {"dataset":"MSV000094203","datasetNum":"94203","title":"GNPS - 3D mapping of the International Space Station negative ionization","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709199382000","created":"Feb. 29, 2024, 1:36 AM","description":"Surface swab samples from the International Space Station. 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Samples were incubated for 2 hr at room temperature followed by addition of 1.47uL of DMTMM (20mg\/mL) for 45min at room temperature (shaking at 300 rpm). 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Samples were incubated at room temperature for 2 hr to allow formation of oligomeric assemblies. Final concentrations of 8 mM DMTMM (Sigma-Aldrich) were added to the protein samples and incubated at 23 C with shaking for 45 min. 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Final conditions for mass spectrometry analysis of multimeric species included 1.7 mM protein, 200 mM KCl and 2 hr incubation at 23 C. For DMTMM cross-linking, 8 mM 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (Sigma-Aldrich) was added to the protein samples and incubated at 23 C with shaking for 45 min. 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Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable DNA probes to deliver proximity-biotinylating enzymes to a target RNA, enabling molecules within that RNA's subcellular microcompartment to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its RNA-targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs, and enabled systematic discovery of nucleolar-chromatin interactions across multiple cell lines. O-MAP uses exclusively off-the-shelf parts requiring no genetic- or cell-line engineering and is easily portable across diverse specimen-types and target RNAs. 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The precipitates were transferred to E3filters and digestion was performed overnight with trypsin. The peptides were desalted with StageTips, and were analyzed on Eclipse Orbitrap with DIA mode. For MS1, the resolution was set to 120,000. Mass range was 380-980 m\/z. AGC target was standard. Max injection time was auto. For MS\/MS, the isolation window was 8 m\/z. Activation type was HCD with 30% NCE. The scan range was 145-1450 m\/z. The normalized AGC target was 800%. Max injection time was auto. For FAIMS, three CVs were used, -40v, -55v, and -75v.","fileCount":"39","fileSizeKB":"27444930","spectra":"986976","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Quantitative proteomics;Proteomics;E3technology;On-filter digestion;NAE1\/ULA1\/Appbp1;Data-independent acquisition;DIA","pi":[{"name":"Gang Xin","email":"Gang.Xin@osumc.edu","institution":"The Ohio State University College of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"82137ac3b42840ca9c9f83b33153e854","id":"2882"}, {"dataset":"MSV000094178","datasetNum":"94178","title":"Retinal cells derived from patients with DRAM2-dependent CORD21 dystrophy exhibit key lysosomal enzyme deficiency and lysosomal content accumulation","user":"NUPPA","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709042035000","created":"Feb. 27, 2024, 5:53 AM","description":"Biallelic DRAM2 mutations cause an autosomal recessive cone-rod dystrophy named CORD21 typically manifesting by the third decade of life. DRAM2 localises to the lysosomes of photoreceptor and retinal pigment epithelium (RPE) cells, however, it remains unclear how DRAM2 contributes to retinal degeneration. Herein, we have derived and characterised retinal organoids (ROs) and RPE cells from two CORD21 induced pluripotent stem cells (iPSCs) lines. CORD21 ROs and RPE manifested abnormal lipid metabolism, autophagic flux defects, aberrant lysosomal content accumulations and reduced lysosomal enzyme activity. A combined proteomics and western blot approach revealed the involvement of DRAM2 in vesicular trafficking that was further corroborated by the immunofluorescent co-localisation of DRAM2 with clathrin adaptor-related proteins AP-1 and AP-3 in ROs. Collectively, our data suggest an indispensable role for DRAM2 in the maintenance of photoreceptors and RPE cells by overseeing the transport of lysosomal enzymes.","fileCount":"70","fileSizeKB":"56677748","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"DRAM2;CORD21;cone-rod dystrophy;retina;lysosomal deficiency;PPT1;NPC2;CTSD;lysosome","pi":[{"name":"Majlinda Lako","email":"majlinda.lako@newcastle.ac.uk","institution":"Newcastle University","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050186","task":"ec9bb67fc8b34d3bbbc723001f7a6fb0","id":"2883"}, {"dataset":"MSV000094176","datasetNum":"94176","title":"mRNA-LNP HIV-1 trimer boosters elicit precursors to bnAbs","user":"sbaboo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1709006334000","created":"Feb. 26, 2024, 7:58 PM","description":"Germline-targeting (GT) HIV vaccine strategies are predicated on deriving broadly neutralizing antibodies (bnAbs) through multiple boost immunogens. However, as the recruitment of memory B cells (MBCs) to germinal centers (GCs) is inefficient and may be derailed by serum antibody-induced epitope masking, driving further B cell receptor (BCR) modification in GC-experienced B cells after boosting poses a challenge. Using humanized Ig knockin mice, we found that GT protein trimer immunogen N332-GT5 could prime inferred-germline precursors to the V3-glycan-targeted bnAb BG18, and that B cells primed by N332-GT5 were effectively boosted by either of two novel protein immunogens designed to have minimum cross-reactivity with the off target V1-binding responses. The delivery of the prime and boost immunogens as mRNA-LNPs generated long-lasting GCs, somatic hypermutation, and affinity maturation, and may, therefore, be an effective tool in HIV vaccine development.","fileCount":"31","fileSizeKB":"9407962","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Human immunodeficiency virus (NCBITaxon:12721)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";UNIMOD:43 - \\\"N-Acetylhexosamine.\\\";MOD:01293 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid with one (18)O.\\\"","keywords":"DeGlyPHER;N-glycans;HIV Env Trimer;mRNA vaccine;V3-glycan epitope;bNAb;germline targeting","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD050174","task":"f318ab82e9a244769ef4057e21dfe141","id":"2884"}, {"dataset":"MSV000094174","datasetNum":"94174","title":"Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates","user":"sbaboo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708993842000","created":"Feb. 26, 2024, 4:30 PM","description":"Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to human immunodeficiency virus (HIV) and other pathogens.\nHowever, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. We found that immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in 8 of 8 rhesus macaques to substantial frequencies, and with diverse lineages, in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo-electron microscopy. The results demonstrate proof of principle for priming of HCDR3-dominant bnAb precursors in outbred animals, suggest that N332-GT5 has promise to induce similar responses in humans, and encourage application of HCDR3-dominant germline-targeting for other bnAbs to HIV and additional pathogens.","fileCount":"115","fileSizeKB":"44576090","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Human immunodeficiency virus (NCBITaxon:12721)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:00040 - \\\"A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid.\\\";UNIMOD:43 - \\\"N-Acetylhexosamine.\\\";MOD:01293 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid with one (18)O.\\\"","keywords":"DeGlyPHER;N-glycans;HIV Env trimer;vaccine;germline targeting;V3-glycan epitope;bNAb","pi":[{"name":"John R. Yates III","email":"jyates@scripps.edu","institution":"The Scripps Research Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD050163","task":"d4f918e7e8d746579e5b11121adc825b","id":"2885"}, {"dataset":"MSV000094172","datasetNum":"94172","title":"GNPS - Targeted and non-targeted mass spectrometry to explore the chemical diversity of the genus Gambierdiscus in the Atlantic Ocean","user":"tyon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708972314000","created":"Feb. 26, 2024, 10:31 AM","description":"The 15 strains of Gambierdiscus were cultivated in four separate laboratories. Each laboratory grew their available strains (see sample metadata) in addition to the G. australes strain AUS S080911_1 isolated from Pacific Ocean.\r\n\r\nIrradiance (70-100 umol photons m-2 s-1) and light\/dark cycle (12h:12h) were standardized between the different laboratories, the other cultivation parameters were defined by each laboratory considering optimal growth parameters and technical requirements.\r\n\r\nSamples were extracted twice in methanol 90% from freeze-dried cell pellets (2mL per million of cells). The extraction cycle was as follows: vortex 30 s, ultrasonic bath (25 kHz on ice, 15 min), vortex 30 s and centrifugation (4 000 g, 2 min). The extracts resulting from the two extraction cycles were pooled into an amber glass vial and stored at -80 C (final concentration : 250,000 cells mL-1).\r\n\r\nMetabolomic profiles were acquired by Ultra-high-performance Liquid Chromatography-High Resolution Mass Spectrometry (UHPLC-HRMS). The instrumentation consisted of a UHPLC system (1290 Infinity II, Agilent) coupled to a quadrupole-time of flight mass spectrometer (QTOF 6550, Agilent) equipped with a Dual Jet Stream electrospray ionization (ESI) interface. The analytical column was a core-shell Kinetex C18 (100 x 2.1 mm, 1.7 um, Phenomenex) with a suited guard column. Mobile phases consisted of water (A) and acetonitrile\/water (95:5, V:V) (B), both containing 2 mM ammonium formate and 50 mM formic acid The flow rate was 0.4 mL min-1 and the injection volume was 5 uL. The following elution gradient was used: 5% B (0-1 min), 5-100% B (1-11 min), 100% B (11-13 min), 5% B (13-18 min).\r\n\r\nMass spectra were recorded in both positive and negative full-scan modes from m\/z 100 to 1700 at a mass resolving power of 25 000 full-width at half-maximum (fwhm, m\/z = 922.0099) and an acquisition rate of 2 spectra\/s.\r\n\r\nAuto-MS\/MS was performed iteratively: each sample was injected 5 times in ESI+ mode and the ions fragmented were manually excluded from the following analyses\r\n","fileCount":"13","fileSizeKB":"15575","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Gambierdiscus australes (NCBITaxon:439317);Gambierdiscus belizeanus (NCBITaxon:439316);Gambierdiscus caribaeus (NCBITaxon:864185);Gambierdiscus carolinianus (NCBITaxon:864182);Gambierdiscus excentricus (NCBITaxon:986170);Gambierdiscus silvae (NCBITaxon:1550089)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"marine toxins, ciguatera, gambierones, maitotoxins","pi":[{"name":"Thomas Yon","email":"thomas.yon@ifremer.fr","institution":"Laboratoire METALG, Ifremer","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ab8b81b407ce46759e61c9e70b62bdd2","id":"2886"}, {"dataset":"MSV000094171","datasetNum":"94171","title":"GNPS - Volatile and semivolatile compounds from the aqueous extract of Ilex guayusa leaves","user":"NPLIKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708969274000","created":"Feb. 26, 2024, 9:41 AM","description":"Volatilma of the aqueous extract of Ilex guayusa leaves under different light and age conditions.","fileCount":"104","fileSizeKB":"5663970","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ilex guayusa","instrument":"GC-MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"secondary metabolites, guayusa, GCMS","pi":[{"name":"Denice Mariela Arias Carrillo","email":"denice.arias@est.ikiam.edu.ec","institution":"Universidad Regional Amazonica IKIAM","country":"Ecuador"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"53e8586d433846e38613a45670c4e5ff","id":"2887"}, {"dataset":"MSV000094169","datasetNum":"94169","title":"GNPS - Hand-on Microbiome course","user":"oloap1_1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708962419000","created":"Feb. 26, 2024, 7:46 AM","description":"Non-target metabolomics data of leaves after bacterial treatment ","fileCount":"14","fileSizeKB":"673554","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plant;microbiome;Metabolome profile","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c8031d1ede4740f78f4b679af989d52d","id":"2888"}, {"dataset":"MSV000094168","datasetNum":"94168","title":"Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708958355000","created":"Feb. 26, 2024, 6:39 AM","description":"Authors: David R. Amici, Sammy Alhayek, Austin T. Klein, Yi-Zhi Wang, Anika P. Wilen, Weimin Song, Pei Zhu, Abhishek Thakkar, McKenzi A. King, Adam Steffeck, Milad J. Alasady, Clara Peek, Jeffrey N. Savas, Marc L. Mendillo*\r\n\r\nABSTRACT\r\nThe recently discovered HAPSTR1 protein broadly oversees cellular stress responses. This function requires HUWE1, a ubiquitin ligase which paradoxically marks HAPSTR1 for degradation, but much about this pathway remains unclear. Here, leveraging multiplexed proteomics, we find that HAPSTR1 enables nuclear localization of HUWE1 with implications for nuclear protein quality control. We show that HAPSTR1 is tightly regulated and identify ubiquitin ligase TRIP12 and deubiquitinase USP7 as upstream regulators titrating HAPSTR1 stability. Finally, we generate conditional Hapstr1 knockout mice, finding that Hapstr1-null mice are perinatal lethal, adult mice depleted of Hapstr1 have reduced fitness, and primary cells explanted from Hapstr1-null animals falter in culture coincident with HUWE1 mislocalization and broadly remodeled signaling. Notably, while HAPSTR1 potently suppresses p53, we find that Hapstr1 is essential for life even in mice lacking p53. Altogether, we identify novel components and functional insights into the conserved HAPSTR1-HUWE1 pathway and demonstrate its requirement for mammalian life.","fileCount":"31","fileSizeKB":"19771788","spectra":"0","psms":"63455","peptides":"14918","variants":"29507","proteins":"6482","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:6 - \\\"Iodoacetic acid derivative.\\\";312.2213 K","keywords":"HAPSTR1;HUWE1","pi":[{"name":"David R. Amici","email":"david.amici@northwestern.edu","institution":"Northwestern University","country":"United States of America"},{"name":"Marc L. Mendillo","email":"mendillo@northwestern.edu","institution":"Northwestern University","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050150","task":"7a7d560021064fd4b0e9e82c1d063260","id":"2889"}, {"dataset":"MSV000094166","datasetNum":"94166","title":"The dynamics and functional impact of transfer RNA repertoires during the maternal to zygotic transition in zebrafish","user":"klemens_froehlich","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708942631000","created":"Feb. 26, 2024, 2:17 AM","description":"Embryogenesis entails dramatic shifts in mRNA translation and turnover to account for gene expression differences during proliferation and cellular differentiation. Codon identity modulates mRNA stability during early vertebrate embryogenesis, but how the composition of tRNA pools adapts to the embryo s translational demand is unknown. By quantitatively profiling the tRNA repertoires of zebrafish embryos during the maternal-to-zygotic transition, here we find that maternal and zygotic tRNA pools are distinct. We show that translational activation during embryogenesis and tRNA gene derepression are temporally coordinated by TORC1 activity, which increases at gastrulation and inactivates the RNA polymerase III repressor Maf1a\/b in vivo. Reshaping of tRNA pools results in differential tRNA anticodon supply, but these changes do not alter decoding rates in zebrafish embryos. Instead, our data indicate that tRNA repertoires reflect the inherent codon bias of the zebrafish mRNA transcriptome, and tRNA levels are boosted at gastrulation to ensure efficient translation as embryos enter differentiation.\n","fileCount":"164","fileSizeKB":"29664327","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"tRNA, translation regulation, maternal-to-zygotic transition, TORC1, zebrafish, phosphoproteomics","pi":[{"name":"Madalena M. Reimao-Pinto","email":"madalena.pinto@unibas.ch","institution":"Biozentrum, University of Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8a90fce85ce14da4949896889b7d625d","id":"2890"}, {"dataset":"MSV000094160","datasetNum":"94160","title":"RNA quality control factors nucleate Clr4\/SUV39H and trigger constitutive heterochromatin assembly","user":"whaas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708876222000","created":"Feb. 25, 2024, 7:50 AM","description":"RNA surveillance (MTREC) and degradation (exosome) complexes nucleate Clr4\/SUV39H at a heterochromatic long noncoding RNA, at which the two deacetylases, Sir2 and Clr3, also amass by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4 from the nucleation center which with the help from RNAi establish heterochromatin. (this is like the abstract for the paper) To identify nuclear Sir2-interacting proteins, a protocol was adopted by which frozen intact nuclei suitable for biochemical purifications were released by low pressure, semi-automated cryogrinding of frozen yeast pellets after which the nuclei were isolated by differential centrifugation. From these nuclear extracts, FLAG-tagged Sir2 was purified and analyzed by nanoscale micro-capillary tandem mass spectrometry.","fileCount":"12","fileSizeKB":"1531115","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Schizosaccharomyces pombe (NCBITaxon:4896)","instrument":"LTQ Orbitrap Velos","modification":"57.02146374 (IAA), cysteine, static;15.9949146221 (oxidation), methionine, variable ","keywords":"RNA quality control, S pombe, deacetylases, Sir2, Clr3, affinity purification, spectral counting, Orbitrap Velos ","pi":[{"name":"Mo Motamedi","email":"mo_motamedi@hms.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f5433f7e25b8436a805b670d98c78a1f","id":"2891"}, {"dataset":"MSV000094158","datasetNum":"94158","title":"Active site remodeling of IDH1 by tumor_relevant mutations and potential resistance mechanisms","user":"ekomives","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708829914000","created":"Feb. 24, 2024, 6:58 PM","description":"HDXMS data on isocitrate dehydrogenase (IDH1) and variants of the enzyme bound to cofactors and substrates.","fileCount":"3390","fileSizeKB":"106905334","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Synapt G2 HDMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"isocitrate dehydrogenase, IDH1, HDXMS","pi":[{"name":"Christal Sohl","email":"csohl@sdsu.edu","institution":"SDSU","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD050109","task":"d24eb2fc5c0a4a2d9437dc1598212530","id":"2892"}, {"dataset":"MSV000094156","datasetNum":"94156","title":"PRMT9 interaction proteins (WT and G189R) Nature Communications 2024","user":"Yanzhong_Yang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708664014000","created":"Feb. 22, 2024, 8:53 PM","description":"In this study, we identified interaction proteins of WT human PRMT9 and a mutant PRMT9 (G189R) that was identified in patients with Intellectual Disability. We also included the Flag-vector as a negative control. The immunoprecipitation was performed in 293T cells. Each group has two biological repeats. Vector control 1 (70835), Vector control 2 (70834), PRMT9 WT1 (70833), PRMT9 WT2 (70832), PRMT9 GR1 (70827), PRMT9 GR2 (70826).","fileCount":"26","fileSizeKB":"2237794","spectra":"0","psms":"126839","peptides":"84980","variants":"88112","proteins":"42022","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"PRMT9, arginine methylation, RNA splicing","pi":[{"name":"Yanzhong Yang","email":"yyang@coh.org","institution":"Beckman Research Institute, City of Hope Cancer Center","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050058","task":"6474d0d6c4394d9f985da53614cf5a21","id":"2893"}, {"dataset":"MSV000094153","datasetNum":"94153","title":"A Protein Phosphatase 1 specific phosphatase targeting peptide (PhosTAP) to identify the PP1 phosphatome","user":"madamo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708616683000","created":"Feb. 22, 2024, 7:44 AM","description":"Most eukaryotic proteins are regulated by phosphorylation. Phosphoprotein phosphatases (PPPs) are the key serine\/threonine phosphatases that regulate all essential signaling cascades. In particular, Protein Phosphatase 1 (PP1) dephosphorylates a predicted ~80% of all ser\/thr phosphorylation sites. Here, we developed a phosphatase targeting peptide (PhosTAP) that binds all PP1 isoforms and does so with a stronger affinity than any other known cognate PP1 regulator. This PhosTAP can be used as a PP1 recruitment tool for PhosTAC-type recruitment in in vitro and cellular experiments, as well as in phosphoproteomics experiments to identify PP1-specific substrates and phosphosites. The latter is especially important to further our understanding of cellular signaling, as the identification of substrates and especially phosphosites that are targeted by specific phosphatases, like PP1, lags far behind that of their kinase counterparts. This is due to a lack of chemical\/biological tools that are specific for individual phosphatases and a lack of established active site recognition sequences. Using PhosTAP-based proteomics studies, we show that, counter to our current understanding, many PP1 regulators are also substrates; that the number of residues between regulator PP1-binding and phosphosites vary significantly; and that PP1 also counteracts the activities of mitotic kinases. Finally, we also discovered that Haspin kinase is a direct substrate of PP1 and that its PP1-dependent dephosphorylation modulates its activity during anaphase. Taken together, we show that PP1-specific PhosTAPs are a powerful tool for studying PP1 activity in vitro and in cells.","fileCount":"386","fileSizeKB":"48524987","spectra":"0","psms":"1702348","peptides":"763863","variants":"1025793","proteins":"20043","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phosphoprotein phosphatase;PPP;PP1;PhosTAP;Haspin","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"The Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050038","task":"3baa630c5f184f87bd23430c8a55e9ec","id":"2894"}, {"dataset":"MSV000094152","datasetNum":"94152","title":"Thiocarboxylation of Urm1 is regulated by tightly-controlled biochemical checkpoints","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708609983000","created":"Feb. 22, 2024, 5:53 AM","description":"Ubiquitin related modifier 1 (Urm1) is a highly conserved member of the Ubiquitin-like (UBL) family of proteins. Urm1 is a key component of the eukaryotic thiolation cascade, which is responsible for introducing sulfur at U34 in several eukaryotic tRNAs. Like other UBLs, Urm1 is also able to conjugate to target proteins under mild oxidative stress. In both cases, the C-terminus of Urm1 needs to be thiocarboxylated (Urm1-SH) by Ubiquitin-like protein activator 4 (Uba4). Uba4 first adenylates, and then thiocarboxylates the C-terminus of Urm1 using its AD and RHD domains. However, the detailed mechanisms of Uba4, the interplay between the two domains, and the release of Urm1 remain elusive. Here, we report a cryo-EM-based structural model of the Uba4\/Urm1 complex and a detailed biochemical analysis of its reaction cycle. Our results show how the chemical fate of Urm1s C-terminus depends on conserved cysteine residues of Uba4, how the complex avoids off-target reactions by the appearing volatile intermediates, and how the Urm1-SH product is released. Finally, we show that Urm1 only interacts with Ncs6, but not with Ncs2, of the downstream thioltransferase complex and Tum1 can functionally complement the RHD domain of Uba4.","fileCount":"166","fileSizeKB":"38768","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932);Chaetomium thermophilum (NCBITaxon:209285)","instrument":"micrOTOF-Q II","modification":"MOD:01778 - \\\"A protein modification that effectively converts a C-terminal glycine residue to N-(glycyl)-L-cysteine by forming a peptide bond with a free L-cysteine.\\\";UNIMOD:405 - \\\"AMP binding site.\\\"","keywords":"Urm1;thiocarboxylation","pi":[{"name":"Sebastian Glatt","email":"sebastian.glatt@uj.edu.pl","institution":"Malopolska Centre of Biotechnology (MCB), Jagiellonian University","country":"Poland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"09b78250db164920ba90ac90a293c510","id":"2895"}, {"dataset":"MSV000094151","datasetNum":"94151","title":"GNPS Aspergillus novoparasiticus NIPE-UNIFESP Diadema positive","user":"AugustoL","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708607331000","created":"Feb. 22, 2024, 5:08 AM","description":"Analysis of secondary metabolites during incubations of 7 to 28 days using Aspergillus novoparasiticus (strain Y174) in sugarcane juice, through LC-DAD-HRMS\/MS2 in the positive mode.","fileCount":"13","fileSizeKB":"158467","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus novoparasiticus (NCBITaxon:986946)","instrument":"micrOTOF-Q II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sugarcane;oxylipin;mycotoxin;microbial natural products","pi":[{"name":"Augusto Leonardo dos Santos","email":"augusto.leonardo@unifesp.br","institution":"ITAL","country":"Campinas, SP"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ad1d9701e17c469490c999c9d67a351c","id":"2896"}, {"dataset":"MSV000094150","datasetNum":"94150","title":"Data deposition for publication entitled 'Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem'","user":"CA_Curtin_University","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708559682000","created":"Feb. 21, 2024, 3:54 PM","description":"Mass spectrometry data for publication 'Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem.\nChristina E. Andronis, Silke Jacques, Francisco J. Lopez-Ruiz, Richard Lipscombe and Kar-Chun Tan.'\n","fileCount":"13","fileSizeKB":"110706364","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lupinus angustifolius (NCBITaxon:3871)","instrument":"Q Exactive","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:39 - \\\"Beta-methylthiolation.\\\"","keywords":"Phytophthora cinnamomi;dieback;phytopathogens","pi":[{"name":"Christina Andronis","email":"christina.andronis@curtin.edu.au","institution":"Curtin University","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e1cf16ae52b84a2a8f1e799f6e416b35","id":"2897"}, {"dataset":"MSV000094149","datasetNum":"94149","title":"Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control","user":"PatrickTreffon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708554345000","created":"Feb. 21, 2024, 2:25 PM","description":"Site-specific S-nitrosoproteome of hot5-2 inflorescences.","fileCount":"14","fileSizeKB":"12386110","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion","modification":"UNIMOD:345 - \\\"Cysteine oxidation to cysteic acid.\\\"","keywords":"gsnor\/hot5_2 site specific S-nitrosoproteome, AT5G43940","pi":[{"name":"Elizabeth Vierling","email":"vierling@umass.edu","institution":"University of Massachusetts Amherst","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2a9c444f2f9c41c2811def7cd77da48a","id":"2898"}, {"dataset":"MSV000094148","datasetNum":"94148","title":"Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control","user":"PatrickTreffon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708553947000","created":"Feb. 21, 2024, 2:19 PM","description":"The Organomercury-resin-assisted capture (MRC) of S-nitrosoproteins was done with modifications as described in (Doulias and Gould, 2018). Entire inflorescences pre-anthesis (corresponding to FD stages up to 12\/13) of soil grown WT and hot5-2 plants were harvested, shock frozen in lN2 and ground to a fine powder. 5 mL of plant material was used to extract proteins using a 1:1 ratio of extraction buffer (250 mM Hepes pH 7.7, 1 mM DTPA, 0.1 mM neocuproine, 40mM MMTS, 1% TritonX-100). After 5 min of vortexing, samples were centrifuged at 16.000 x g at 4 C for 15 min to separate cell debris from soluble protein. Centrifugation was repeated, protein concentration measured using the BCA assay (Thermo Scientific, USA) and 10 mg of total protein per sample used for the subsequent S-nitrosoprotein enrichment. For photolysis controls 0.1 M mannitol and 5 mM MMTS were added to 10 mg of protein homogenate, vortexed briefly and placed into borosilicate glass vials. The vial was placed on top of an ice bucket and proteins were illuminated under a UV lamp for 7 min in time mode using a UV-crosslinker with a 254 nm light source (Stratalinker Model 1800, Stratagene, USA). Each sample had a corresponding UV-treated negative control analyzed under identical conditions. Proteins were obtained after acetone precipitation and centrifugation at 4500 x g for 15 min at 4 C by resuspending in blocking buffer (250 mM Hepes pH 7.7, 1 mM DTPA, 0.1 mM neocuproine, 50 mM MMTS, 2.5 % SDS). All samples were alkylated for 35 min in the dark in a 50 C water bath with frequent vortexing, followed by another round of acetone precipitation to remove any non-reacted MMTS. Proteins were resuspended to 0.5 mg\/ ml using loading buffer (250 mM MES pH 6.0, 1 mM DTPA, 1 % SDS). Organo-mercury resin was synthesized as mention in (Doulias and Gould, 2018). After alkylation, proteins were loaded onto 15 ml of activated organo-mercury resin slurry (50 %) and incubated for 60 min at RT in the dark to allow binding of S-nitrosated proteins to the resin material. Following the incubation, columns were washed with 50 CV of 50 mM Tris-HCl pH 7.5, 0.3 M NaCl, 0.5 % SDS, 50 CV of 50 mM Tris-HCl pH 7.5, 0.3 M NaCl, 0.05 % SDS, 50 CV of 50 mM Tris-HCl pH 7.5, 0.3 M NaCl, 1 % Triton X-100, 50 CV of 50 mM Tris-HCl pH 7.5, 0.3 M NaCl, 0.1 % Triton X-100, 0.1 M Urea and 200 CV of H2O. For on-column trypsin digest, columns were pre-equilibrated with 5 CV of 0.1 M NH4CO3 and then loaded with 1 CV of 0.1 M NH4CO3 containing 1 ug\/ml trypsin gold (Promega V5280, Promega, USA). The flow-through containing the digested peptides of S-nitrosated proteins (elution 1) was collected in glass tubes after incubation overnight at RT in the dark. The remaining S-nitrosated peptides that were still bound to the organo-mercury resin were washed with 40 CV of 1 M NH4CO3, 0.3 M NaCl, 40 CV of 1 M NH4CO3, 40 CV of 0.1 M NH4CO3 and 200 CV of H2O. Bound peptides (elution 2) were then oxidatively released by incubation with 1 CV of 1 % performic acid for 45 min at RT and then collected in glass tubes. Following lyophilization of the samples and resuspension in 300 ul of 0.1 % formic acid, sample volume was reduced to 30 ul using a vacuum concentrator (Thermo Savant SPD111V, Thermo Scientific, USA) and then centrifuged for 20 min at 16,000 x g at 4C to remove any precipitate. Peptides were desalted using C18 tips as recommended by the manufacturer (Pierce C18 Tips, Thermo Scientific, USA) and resuspended into 15 ul of 1 % formic acid.\r\nFor the LC-MS\\MS run, a 5 uL injection was loaded by a Thermo Easy nLC 1000 UPLC on to a 2 cm trapping column and desalted with 12 uL mobile phase A (0.1% formic acid in water). Peptides were eluted at 300 nL\/min on to a 75 um x 15 cm RSLC column (Thermo) using a linear gradient of 5-35% mobile phase B (0.1% formic acid in acetonitrile) over 90 minutes. Ions were introduced by positive ESI using a stainless steel capillary at 2.1 kV into a Thermo Orbitrap Fusion tribrid mass spectrometer. Mass spectra were acquired over m\/z 350-2000 at 120,000 resolution (m\/z 200) and 1 second cycle time with an AGC target of 1e6, and data-dependent acquisition selected the top speed most abundant precursor ions for tandem mass spectrometry by HCD fragmentation using an isolation width of 2 Da, and automatic gain settings. Peptides were fragmented with a normalized collision energy of 27 %, and fragment spectra acquired in the linear ion trap. Targeted mass exclusion was activated to avoid MS\/MS of ions previously identified as Rubisco or keratin peptides \r\n","fileCount":"13","fileSizeKB":"19347642","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gsnor\/hot5_2 S-nitrosoproteome, AT5G43940","pi":[{"name":"Elizabeth Vierling","email":"vierling@umass.edu","institution":"University of Massachusetts Amherst","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2e6417fab8de4080a73524c6dd048da6","id":"2899"}, {"dataset":"MSV000094146","datasetNum":"94146","title":"Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control","user":"PatrickTreffon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708552228000","created":"Feb. 21, 2024, 1:50 PM","description":"Pooled sepals and petals (hereafter referred to as SePel) of hot5-2 and WT were harvested from the same plants of which pistils have been isolated. Material from around 50 flowers at stages before pollination (floral developmental stage, FD 12-13) were pooled and represent one biological replicate. A total of five biological replicates were further processed as mentioned for the pistil proteome. For the LC-MS\\MS run, a 3 uL injection was loaded by a Thermo Easy nLC 1000 UPLC on to a 2 cm trapping column and desalted with 8 uL mobile phase A (0.1% formic acid in water). Peptides were eluted at 300 nL\/min on to a 75 um x 15 cm RSLC column (Thermo) using a linear gradient of 5-35% mobile phase B (0.1% formic acid in acetonitrile) over 90 minutes. Ions were introduced by positive ESI using a stainless steel capillary at 2.1 kV into a Thermo Orbitrap Fusion tribrid mass spectrometer. Mass spectra were acquired over m\/z 300-1750 at 120,000 resolution (m\/z 200) with an AGC target of 1e6, and data-dependent acquisition selected the top 10 most abundant precursor ions for tandem mass spectrometry by HCD fragmentation using an isolation width of 1.6 Da, maximum fill time 110 ms and AGC target 1e5. Peptides were fragmented with a normalized collision energy 27, and fragment spectra acquired at a resolution of 15,000 (m\/z 200).","fileCount":"11","fileSizeKB":"38264463","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gsnor\/hot5_2 quantitative SePel proteome, AT5G43940","pi":[{"name":"Elizabeth Vierling","email":"vierling@umass.edu","institution":"University of Massachusetts Amherst","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c5157e7b2bc4cd0868ffb6c96056c6b","id":"2900"}, {"dataset":"MSV000094145","datasetNum":"94145","title":"Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control","user":"PatrickTreffon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708551787000","created":"Feb. 21, 2024, 1:43 PM","description":"Pistils of hot5-2 and WT at stages before pollination (FD 12-13) were harvested and immediately shock frozen in lN2. Around 50 pistils per genotype were pooled and represent one biological replicate with a total of three biological replicates per genotype. Proteins were extracted using diluted HENS buffer (25mM HEPES pH 7.7, 1mM EDTA, 2.5 % SDS, protease inhibitor cocktail (Pierce A32955), TCA precipitated and resuspended in the same buffer. After BCA protein determination, 50 ug of each whole cell lysate was run on a 4-20% SDS-PAGE for approx. 15 min to separate proteins from lower molecular weight contaminants. The entire protein region was excised of the gel and subjected to in-gel trypsin digestion after reduction with dithiothreitol and alkylation with iodoacetamide as described in (Treffon et al., 2021). Peptides eluted from the gel were lyophilized and re-suspended in 50uL of 5% acetonitrile (0.1% (v\/v) FA). For each biological replicate, three technical replicates were measured by LC-MS\/MS. A 2 uL injection was loaded by a Waters NanoAcquity UPLC in 5% acetonitrile (0.1% formic acid) at 4.0 uL\/min for 4.0 min onto a 100 um I.D. fused-silica pre-column packed with 2 cm of 5 um (200A) Magic C18AQ (Bruker-Michrom). Peptides were eluted at 300 nL\/min from a 75 um I.D. gravity-pulled analytical column packed with 25 cm of 3 um (100A) Magic C18AQ particles using a linear gradient from 5-35% of mobile phase B (acetonitrile + 0.1% formic acid) in mobile phase A (water + 0.1% formic acid) over 90 minutes. Ions were introduced by positive electrospray ionization via liquid junction at 1.4kV into a Thermo Scientific Q Exactive hybrid mass spectrometer. Mass spectra were acquired over m\/z 300-1750 at 70,000 resolution (m\/z 200) with an AGC target of 1e6, and data-dependent acquisition selected the top 10 most abundant precursor ions for tandem mass spectrometry by HCD fragmentation using an isolation width of 1.6 Da, max fill time of 110ms, and AGC target of 1e5. Peptides were fragmented by a normalized collisional energy of 27, and fragment spectra acquired at a resolution of 17,500 (m\/z 200).","fileCount":"19","fileSizeKB":"16713112","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"gsnor\/hot5_2 quantitative pistil proteome, AT5G43940","pi":[{"name":"Elizabeth Vierling","email":"vierling@umass.edu","institution":"University of Massachusetts Amherst","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b1771d9c0df34f498ef0ee77e10ee137","id":"2901"}, {"dataset":"MSV000094144","datasetNum":"94144","title":"Development and crystal structures of a more potent second-generation dual degrader of BCL-2 and BCL-xL","user":"stweintraub","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708545175000","created":"Feb. 21, 2024, 11:52 AM","description":"Overexpression of BCL-xL and BCL-2 play key roles in tumorigenesis and cancer drug resistance. Advances in PROTAC technology facilitated recent development of the first BCL-xL\/BCL-2 dual degrader, 753b, a VHL-based degrader with improved potency and reduced toxicity compared to previous small molecule inhibitors. Here, we determined crystal structures of VHL\/753b\/BCL-xL and VHL\/753b\/ BCL-2 ternary complexes. The two ternary complexes exhibit markedly different architectures that are accompanied by distinct networks of interactions at the VHL\/PZ753b-linker\/target interfaces. The importance of these interfacial contacts was validated via functional analysis and informed subsequent rational and structure-guided design focused on the 753b linker and BCL-2\/BCL-xL warhead. This resulted in the design of a novel degrader, WH244, with enhanced potency to degrade BCL-xL\/BCL-2 in cells. Using biophysical assays followed by in cell activities, we were able to explain the enhanced target degradation of BCL-2\/BCL-xL in cells. Most PROTACs are empirically designed and lack structural studies, making it challenging to understand their modes of action and specificity. Our work presents a streamlined approach that combines rational design and structure-based insights backed with cell-based studies to develop effective PROTAC-based cancer therapeutics.","fileCount":"17","fileSizeKB":"36239139","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PROTAC;ubiquitin;E3 ligase;ternary complex;BCL-xL\/BCL-2;crystal structure;degrader","pi":[{"name":"Daohong Zhou, M.D.","email":"zhoud@uthscsa.edu","institution":"The University of Texas Health Science Center at San Antonio","country":"U.S.A."}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050013","task":"8e26433df08f47d9bef1c44503a07ae4","id":"2902"}, {"dataset":"MSV000094142","datasetNum":"94142","title":"GNPS - Seven marine Actinomycetota from the South Pacific","user":"ACumsille","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708532852000","created":"Feb. 21, 2024, 8:27 AM","description":"Crude extracts from seven marine actinobacteria. Strains were cultured for seven days at 30 C in a shaker in three media: ISP2-ASW, R5A, and A1BFe+C. Extracts were prepared extracting twice with ethyl acetate 1:1. \r\n\r\nData was collected by Dr. Nestor Serna in Collaboration with Dr. Alesis Tietze at the Department of Chemistry and Molecular Biology at the University of Gothenburg, Sweden.","fileCount":"759","fileSizeKB":"24779422","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces (NCBITaxon:1883);Nocardiopsis (NCBITaxon:2013);Pseudonocardia (NCBITaxon:1847)","instrument":"IMS-qToF-MS (SynaptG2-Si, WatersCorporation)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces;Nocardiopsis;Pseudonocardia;Actinomycetotota;Actinobacteria;marine","pi":[{"name":"Beatriz Camara","email":"beatriz.camara@usm.cl","institution":"Universidad Tecnica Federico Santa Maria","country":"Chile"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"782ff4f103354f088caa8d431b2784eb","id":"2903"}, {"dataset":"MSV000094141","datasetNum":"94141","title":"Identification of NKG7-proximal proteins by TurboID","user":"KLJohnson218","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708530251000","created":"Feb. 21, 2024, 7:44 AM","description":"NKG7 is a lysosomal membrane protein whose expression is restricted to cytotoxic lymphocytes. Although the importance of NKG7 in anti-tumor immunity has been shown, little is known about the molecular function and regulation of NKG7. To elucidate NKG7 molecular function, we performed NKG7-proximity labeling using TurboID system in 293T cells, followed by mass-spectrometry. We identified vacuolar H+ ATPase (v-ATPase; lysosomal proton pump) subunit ATP6AP2 as a potential NKG7-interacting protein, and validated the interaction via exogenous coimmunoprecipitation. We further showed that NKG7 inhibits v-ATPase activity, thereby impacting lysosomal homeostasis and mTORC1 regulation at lysosomes.","fileCount":"29","fileSizeKB":"10247272","spectra":"216227","psms":"72489","peptides":"32281","variants":"41773","proteins":"6063","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Human","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:3 - \\\"Biotinylation.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"TurboID, proximity labeling, NKG7, cytotoxic lymphocytes, lysosome","pi":[{"name":"Daniel Billadeau, Ph.D.","email":"Billadeau.Daniel@mayo.edu","institution":"Mayo Clinic, Rochester, MN","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050004","task":"768764fa2bff4a3cbfcc403fe3fd1b44","id":"2904"}, {"dataset":"MSV000094140","datasetNum":"94140","title":"Human pancreatic cancer EV proteome","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708518094000","created":"Feb. 21, 2024, 4:21 AM","description":"Human plasma proteome profiling of pancreatic cancer patients and non-disease healthy controls. EVs isolated (Nova), characterized, and DIA-based proteomics performed. Comparative analyses on oncofactors in EVs, Pancreatic Cancer Markers and various other signaling factors as cargo in cancer EVs\n","fileCount":"33","fileSizeKB":"84832645","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"pancreatic;cancer;biomarker;extracellular vesicle;plasma;proteomics","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"465f03461d494bde8c9f9bbc7fcf0456","id":"2905"}, {"dataset":"MSV000094138","datasetNum":"94138","title":"Granzyme B cleaves Tenascin-C to release its C-terminal FBG-like domain into the synovial fluid of patients with rheumatoid arthritis","user":"LangeLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708493496000","created":"Feb. 20, 2024, 9:31 PM","description":"Raw files and search engine files for the proteomics data resulting from the digestion of Tenascin-C by Granzyme B ","fileCount":"36","fileSizeKB":"3231285","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"granzyme B;Tenascin-C;rheumatoid arthritis;synovial fluid","pi":[{"name":"Dr. Philipp Lange","email":"philipp.lange@ubc.ca","institution":"The University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049980","task":"7ee129453d68456a9125968e80c262ac","id":"2906"}, {"dataset":"MSV000094137","datasetNum":"94137","title":"Proteome Profiling - Quality and Quantifiability using the Orbitrap Astral MS (IBD)","user":"vegesnam","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708486799000","created":"Feb. 20, 2024, 7:39 PM","description":"Biomarker development has two key challenges; the high rate of false positives in discovery and the slow validation phase. To address these challenges we have developed and rigorously tested the Targeted Evaluation and Assessment of Quality (TEAQ) software package. This innovative tool for identifying and selecting precursors, peptides, and proteins that meet the stringent criteria of targeted assays, thus overcoming the limitations faced in the current biomarker development landscape. We implemented the TEAQ to evaluate the performance of the Orbitrap Astral MS using Data-Independent Acquisition Mass Spectrometry (DIA-MS) on plasma samples. This assessment focused on crucial parameters such as proteome linearity, specificity, repeatability, reproducibility, and others essential for substituting dedicated targeted techniques in the more rigorous discovery phase of biomarker development. Through the application of TEAQ on a clinical cohort comprising individuals with inflammation bowel disease (n=493) and an 11-point loading curve, our software successfully identified the signature precursors of quantifiable proteins. A signature peptide or precursor, as per our definition, is a unique peptide or precursor sequence specific to the target protein, exhibiting no miss-cleavages, a linearity R2 value exceeding 0.8, and a coefficient of variation (CV) below 20%. Furthermore, deviations should be less than 20% at low limited quantification concentrations. In instances where multiple peptides or precursors originate from the same protein, it is imperative that all peptides demonstrate a correlation coefficient within the same proteins (>0.7) in the study. Our data set has been made available to as a resource for targeted assay development. This comprehensive approach ensures the reliability and accuracy of our biomarker identification process, paving the way for advancements in clinical practice.","fileCount":"495","fileSizeKB":"3122279186","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Biomarker Identification;DIA;Orbitrap Astral;Quality Control;Proteome Profiling;IBD","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049979","task":"66acb4de356e4ad697afc72f51b13f75","id":"2907"}, {"dataset":"MSV000094136","datasetNum":"94136","title":"Proteome Profiling - Quality and Quantifiability using the Orbitrap Astral MS (LoadingCurve: 24min5ms, 14min3p5ms, 8min3p5ms)","user":"vegesnam","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708485963000","created":"Feb. 20, 2024, 7:26 PM","description":"Biomarker development has two key challenges; the high rate of false positives in discovery and the slow validation phase. To address these challenges we have developed and rigorously tested the Targeted Evaluation and Assessment of Quality (TEAQ) software package. This innovative tool for identifying and selecting precursors, peptides, and proteins that meet the stringent criteria of targeted assays, thus overcoming the limitations faced in the current biomarker development landscape. We implemented the TEAQ to evaluate the performance of the Orbitrap Astral MS using Data-Independent Acquisition Mass Spectrometry (DIA-MS) on plasma samples. This assessment focused on crucial parameters such as proteome linearity, specificity, repeatability, reproducibility, and others essential for substituting dedicated targeted techniques in the more rigorous discovery phase of biomarker development. Through the application of TEAQ on a clinical cohort comprising individuals with inflammation bowel disease (n=493) and an 11-point loading curve, our software successfully identified the signature precursors of quantifiable proteins. A signature peptide or precursor, as per our definition, is a unique peptide or precursor sequence specific to the target protein, exhibiting no miss-cleavages, a linearity R2 value exceeding 0.8, and a coefficient of variation (CV) below 20%. Furthermore, deviations should be less than 20% at low limited quantification concentrations. In instances where multiple peptides or precursors originate from the same protein, it is imperative that all peptides demonstrate a correlation coefficient within the same proteins (>0.7) in the study. Our data set has been made available to as a resource for targeted assay development. This comprehensive approach ensures the reliability and accuracy of our biomarker identification process, paving the way for advancements in clinical practice.","fileCount":"163","fileSizeKB":"427118414","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Astral","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Loading Curve;Orbitrap Astral;Quality Control;Proteome Profiling;DIA","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049978","task":"995f732b7d1e4a8cb904356f4a5209cb","id":"2908"}, {"dataset":"MSV000094135","datasetNum":"94135","title":"GNPS - Lee_feline_fecal_12min_gradient","user":"ipmohanty","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708468119000","created":"Feb. 20, 2024, 2:28 PM","description":"Fecal samples from 14 different species of felines were extracted using 50:50 MeOH: H2O and chromatographed using a Phenomenex polar C18 column. MS\/MS data was acquired on Orbitrap in positive ionization mode on 12 min LC gradient. ","fileCount":"70","fileSizeKB":"9948415","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Felidae (NCBITaxon:9681)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acids;Feline;Fecal","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"ef4d84c627c442cdb27ab72794ea0af0","id":"2909"}, {"dataset":"MSV000094134","datasetNum":"94134","title":"Extracellular Glutathione Peroxidase 3 GPx3 Levels are Markedly Reduced in Children Affected with Konzo an Irreversible Spastic Paralysis Associated with Food Poisoning","user":"VictorProteoCHUL","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708459899000","created":"Feb. 20, 2024, 12:11 PM","description":"Konzo, a neglected paralytic neurological disease associated with food (cassava) poisoning, affects the world poorest children and women of childbearing ages across regions of sub Saharan Africa, with the Democratic Republic of the Congo having the largest case burden. The primary risk factors for development include a dietary reliance on cyanogenic rich cassava and malnutrition, factors which are exacerbated by environmental stressors such as drought and famine. Despite understanding the dietary risks that lead to konzo, the molecular markers and mechanisms that trigger this disease remain unknown. \nPlasma, collected from two large independent cohorts 10 years apart, were subjected to multiple high throughput mass spectrometry in search of disease biomarkers and proteins that were differentially expressed in children affected with konzo relative to those unaffected, including their siblings. DDA experiment was performed on the first cohort with a validation by SRM analysis. For the second cohort, DIA experiment was performed with a validation by PRM.","fileCount":"576","fileSizeKB":"405381994","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion;TSQ Altis;Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Konzo disease;GPx3;Oxidative stress;Plasma proteomics","pi":[{"name":"Arnaud Droit","email":"arnaud.droit@crchuq.ulaval.ca","institution":"CHU de Quebec Universite Laval","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049973","task":"e6757f9945b9440082263f89bb3528a1","id":"2910"}, {"dataset":"MSV000094133","datasetNum":"94133","title":"HPK-1 Citron Homology Domain interactions with Kinase Domain","user":"btwalters","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708457526000","created":"Feb. 20, 2024, 11:32 AM","description":"The files uploaded here are converted into a standard mzxml format, and utilize processing procedures described in 10.1021\/acs.analchem.9b01682 \n \nBriefly, HXMS data processing consists of \n\n1. MSMS experiment to identify peptides and their associated retention times. These files have *MSMS* in the filename. They are searched using HPK.fasta.\n2. Unlabeled peptide pool file is used to refine the exact RT range of the peptide in the experiment (MSMS experiment may be conducted at a different time).\n3. Labeling experiments are then searched using ExMS2 (see manuscript linked above) to produce carried deuterium at each time point for peptides included in the pool.\n\nComparing uptake patterns between \"FullLength\" files and \"Kinase\" files produces the map of differences on the kinase domain induced by the citron homology domain.\n\nThere are two CSV files, these contain the peptides identified in each MSMS run. These are found in Search Engine Files. \n\nThere are also finaltables produced by the ExMS program containing all raw and unfiltered results. There is a pdf file associated that shows the final peptides used for the analyses after discarding noisy peptides upon manual inspection.\n\nAll protection factors extracted from this data along with a summary table can be found in \"File_HX_TABLES.xlsx\".","fileCount":"84","fileSizeKB":"56620351","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Citron Homology Domain","pi":[{"name":"Benjamin Walters","email":"walters.benjamin@gene.com","institution":"Genentech","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"22799ea7f0d54fffb92e86edfa225368","id":"2911"}, {"dataset":"MSV000094131","datasetNum":"94131","title":"Thylakoid Protein FPB1 Synergistically Cooperates with PAM68 to Promote CP47 Biogenesis and Photosystem II Assembly","user":"zhanglin2017","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708454538000","created":"Feb. 20, 2024, 10:42 AM","description":"LC-MS\/MS analysis was used for protein identification of immunoprecipitation. 20 uL eluted samples of immunoprecipitation were separated by 12.5% SDS-PAGE and each gel lane was cut in consecutive gel slices followed by destaining twice using NH4HCO3\/ACN. Proteins were digested in-gel with DTT, IAA and trypsin. Digested peptides in the gel slices were then desalted using StageTips with C18 Cartridge (Sigma). Peptides extracts for each gel slice were analyzed by High Performance Liquid Chromatography (HPLC) using EASY column (Fisher Scientific, USA) coupled with a Q-Exactive mass spectrometer (Thermo Finnigan). Resulting MS\/MS spectra were searched against the predicted Arabidopsis proteome (35386 entries, 20191018) with maxquant software (version 2.3).","fileCount":"6","fileSizeKB":"2343954","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"High Performance Liquid Chromatography (HPLC)","modification":"No PTMs are included in the dataset","keywords":"FPB1, Shortgun, coIP","pi":[{"name":"Lin Zhang","email":"zhanglin2017@shnu.edu.cn","institution":"Shanghai Normal University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049968","task":"c74dd58b934141f6a87b92f496983664","id":"2912"}, {"dataset":"MSV000094130","datasetNum":"94130","title":"Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques.","user":"jess_conforti1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708445505000","created":"Feb. 20, 2024, 8:11 AM","description":"The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identifications. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. Recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. We hypothesize that differences in capture mechanisms of SP3 and SP4 affect which proteins are identified by each clean-up technique. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. Ultimately, we demonstrate that protein-capture mechanisms are distinct, and selection of a clean-up technique that yields high proteome coverage is dependent on protein-sample hydrophobicity. Data has been deposited into MassIVE (MSV000094130) and ProteomeXchange (PXD049965).","fileCount":"6682","fileSizeKB":"4524433444","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Synapt G2-S HDMS;nanoACQUITY UPLC","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:00046 - \\\"A protein modification that effectively converts an L-serine residue to O-phospho-L-serine.\\\";MOD:00047 - \\\"A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine.\\\";MOD:00048 - \\\"A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"Proteomics;Sample Preparation;Mass Spectrometry;Single-Pot, Solid-Phase-Enhanced Sample Preparation (SP3);Solvent-Precipitation, Single-Pot, Solid-Phase-Enhanced Sample Preparation (SP4);Sodium Deoxycholate;Detergent-Assisted Digestion","pi":[{"name":"Elyssia Gallagher","email":"elyssia_gallagher@baylor.edu","institution":"Baylor University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049965","task":"f9190f49a4d84163b0eb49afb9706a3b","id":"2913"}, {"dataset":"MSV000094128","datasetNum":"94128","title":"CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote","user":"aad100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708439773000","created":"Feb. 20, 2024, 6:36 AM","description":"Mass spectrometry data and DIA-NN search results pertaining to the paper: CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote","fileCount":"231","fileSizeKB":"163443794","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"timsTOF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Synechococcus elongatus PCC7942;cyanobacteria;high-throughput tagging;protein localisation;interactome;prk;gap2;cp12;photosynthesis","pi":[{"name":"Luke Mackinder","email":"luke.mackinder@york.ac.uk","institution":"University of York","country":"UK"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049961","task":"bd2c6f028ac84108917afb75c108ff2d","id":"2914"}, {"dataset":"MSV000094125","datasetNum":"94125","title":"Honey bee arginine kinase is involved in Deformed Wing Virus infection","user":"Marialuisa_PX","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708419524000","created":"Feb. 20, 2024, 12:58 AM","description":"Deformed wing virus (DWV) is a major bee pathogen that is actively transmitted by the parasitic mite Varroa destructor and plays a primary role in overwinter colony losses of Apis mellifera. Despite of the intense investigation driven by the unique environmental and economic importance of this essential pollinator species, the mechanisms underlying honeybee-DWV interactions are still poorly understood. Here we report on a group of honeybee proteins that were selectively immunoprecipitated by an antibody directed against DWV particles and present a functional analysis of a major component of this set of potential DWV interactors, which was identified as an arginine kinase (ArgK). ArgK RNA levels positively correlated with DWV load in field collected larvae and honeybees and significantly increased upon DWV injection in controlled laboratory conditions, indicating that the ArgK gene was upregulated by DWV infection. RNAi experiments performed in vitro to target ArgK gene expression resulted in reduced DWV viral load, thus demonstrating that ArgK function is required for DWV replication. Taken together, these data indicate that successful DWV infection relies on transcriptional regulation and active recruitment of host ArgK by this viral pathogen. Therefore, our findings open novel perspectives on the potential control of DWV pathogenicity by targeting its interaction with specific host proteins. \nImmunoprecipitated samples in quadruplicate were separated in a precast polyacrylamide gradient gel,run in MES buffer for 25 min at 200 V and the proteins were stained with the Imperial Coomassie stain. Each lane was divided into 6 bands, 48 bands in total, which where destained with 50mM ammonium bicarbonate and acetonitrile (ACN) 1:1 treated for cysteine reduction (10mM dithiothreitol at 56C for 45min) and alkylation (55mM iodoacetamide at RT for 30min in the dark), and for enzymatic digestion with 12.5ng ul trypsin at 37C overnight. The resulting peptide mixture was analyzed by LC MS MS using an Ultimate 3000 HPLC coupled with an Orbitrap Fusion Tribrid (Thermo Fisher Scientific, CA, United States). Peptides were desalted on a trap column and separated on a 19 cm long silica capillary, packed in house with a C18, 1.9um, 100 A resin. The analytical column was encased by a column oven (Sonation; 40C during data acquisition) and attached to a nanospray flex ion source. Peptides were separated on the analytical column by running a 95min gradient of buffer A (5 percent ACN, and 0.1 percent formic acid) and buffer B (95 percent acetonitrile and 0.1 percent formic acid), at a flow rate of 250nl min. The mass spectrometer operated in positive ion mode and full MS was acquired in the Orbitrap in the mass over charge 350 1550 scan range at 120K resolution. Data dependent acquisition was performed in top speed mode (3 s long maximum total cycle): the most intense precursors were selected through a monoisotopic precursor selection (MIPS) filter and with charge greater than 1, quadrupole isolated (1.6 mass over charge width) and fragmented by 30 percent higher energy collision dissociation. Product ion spectra were acquired in the ion trap with a rapid scan rate. \nPeptide spectra were analyzed with Proteome Discoverer 2.4 by the search engine Sequest HT using a mixed database containing Apis mellifera (reviewed and unreviewed 20.818 sequences; release 26 01 2022), homo sapiens (42.253 sequences, v2017 10 25) and Oryctolagus cuniculus (892 sequences, release 07 03 2022), and Deformed wing virus (1067 sequences, release 26 01 2022), all downloaded from Uniprot.\nPrecursor and fragment mass tolerance were set to 15 ppm and 0.6 Da, respectively. Cysteine carbamydomethylation was set as static modification, while methionine oxidation and N-acetylation on protein terminus were set as variable modifications. Specific trypsin cleavages with maximum two miscleavages were admitted. Spectral matches were filtered at 1 percent false discovery rate (FDR), based on q values, and target decoy approach, using the Percolator node. Only master proteins were taken into account. \nQuantification was based on precursor intensity of unique and razor peptides.\nThe Perseus software (1.6.15) was used to perform statistical analyses and evaluate differential protein expression. After contaminant removal (rabbit and human proteins), the abundance values were log2 transformed and filtered for containing at least four valid values in at least one group. Missing values were imputed with the constant value 13. A Students t-test was performed applying 250 randomizations, setting S0=2 and 0.01 FDR, and used to draw a Volcano plot to evaluate significantly different IP over IgG ratios.\n","fileCount":"97","fileSizeKB":"103963014","spectra":"5186300","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460);Varroa destructor (NCBITaxon:109461)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Honeybees, apis mellifera, varroa destructor, deforming wing virus, proteomics, interactomics","pi":[{"name":"Marialuisa Casella","email":"marialuisa.casella@iss.it","institution":"Istituto Superiore Sanita","country":"Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049721","task":"46dcab1ed8694c84a7aa466e9ee70c87","id":"2915"}, {"dataset":"MSV000094124","datasetNum":"94124","title":"20240219 drug analog library mgf","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708389011000","created":"Feb. 19, 2024, 4:30 PM","description":"mgf file for drug analog library. Under development not final release.","fileCount":"2","fileSizeKB":"9928","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"NA","modification":"NA","keywords":"drug;analogMASST","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f99934f5682a4f3e977a12844fdbc0cb","id":"2916"}, {"dataset":"MSV000094122","datasetNum":"94122","title":"GNPS - FVLGNPS2-Final-project-combinedfraction","user":"baldem","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708383519000","created":"Feb. 19, 2024, 2:58 PM","description":"Characterization and comparison study of foeniculum vulgare for BS and BP products.","fileCount":"9","fileSizeKB":"3570061","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Foeniculum vulgare (NCBITaxon:48038);Final-P","instrument":"Orbitrap ID-X","modification":"none","keywords":"Foeniculum, metabolites","pi":[{"name":"Mamadou Aliou BALDE","email":"mamadou.balde@rothamsted.ac.uk","institution":"Rothamsted","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b4bc6e67cd8545fb81aac9b2cc17c364","id":"2917"}, {"dataset":"MSV000094121","datasetNum":"94121","title":"Effects of cadherin mediated contact normalization on oncogenic Src kinase mediated gene expression and protein phosphorylation","user":"haiyanzheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708375744000","created":"Feb. 19, 2024, 12:49 PM","description":"Nontransformed cells form heterotypic cadherin junctions with adjacent transformed cells to inhibit tumor cell growth and motility. Transformed cells must override this form of growth control, called contact normalization, to invade and metastasize during cancer progression. Heterocellular cadherin junctions between transformed and nontransformed cells are needed for this process. However, specific mechanisms downstream of cadherin signaling have not been clearly elucidated. Here, we utilized a b-catenin reporter construct to determine if contact normalization affects Wnt signaling in transformed cells. b-catenin driven GFP expression in Src transformed mouse embryonic cells was decreased when cultured with cadherin competent nontransformed cells compared to transformed cells cultured with themselves, but not when cultured with cadherin deficient nontransformed cells. We also utilized a layered culture system to investigate the effects of oncogenic transformation and contact normalization on gene expression and oncogenic Src kinase mediated phosphorylation events. RNA-Seq analysis found that the cadherin dependent contact normalization inhibited the expression of 22 transcripts that were induced by Src transformation, and increased the expression of 78 transcripts that were suppressed by Src transformation. Phosphoproteomic analysis of cells expressing a temperature sensitive Src kinase construct found that contact normalization decreased phosphorylation of 10 proteins on tyrosine residues that were phosphorylated within 1 hour of Src kinase activation in transformed cells. Taken together, these results indicate that cadherin dependent contact normalization inhibits Wnt signaling to regulate oncogenic kinase activity and gene expression, particularly PDPN expression, in transformed cells in order to control tumor progression.","fileCount":"70","fileSizeKB":"53072249","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Src kinase;PDPN;podoplanin;contact normalization;cell transformation","pi":[{"name":"Gary S. Goldberg","email":"goldbega@rowan.edu","institution":"Science Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5eceb0eab48248e297ea4fd3220b471a","id":"2918"}, {"dataset":"MSV000094120","datasetNum":"94120","title":"Major facilitator family transporters specifically enhance caffeyl alcohol uptake during C-lignin biosynthesis in Cleome hassleriana","user":"pabraham_ornl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708372424000","created":"Feb. 19, 2024, 11:53 AM","description":"Here we address whether monolignol transporters are involved in the process of C-lignin production in the seed coat of Cleome. By interrogating expression data from transcriptome and proteome analyses of seed coat material during development, coupled with uptake and efflux assays using a yeast expression system, we identified two major facilitators of caffeyl alcohol transport, annotated as a polyol and a sucrose transporter respectively. Gain of function studies support the ability of these transporters to facilitate caffeyl alcohol transport in planta. These results are discussed in relation to the balance between G and C-lignin accumulation in the Cleome seed coat, and the evolution of C-lignin formation across the plant kingdom.","fileCount":"15","fileSizeKB":"7466702","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cleome (NCBITaxon:25782)","instrument":"Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"C-lignin;caffeyl alcohol;monolignol;proteome","pi":[{"name":"Paul Abraham","email":"abrahampe@ornl.gov","institution":"ORNL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a0040e581ea248cd9630cea22c6d9d3a","id":"2919"}, {"dataset":"MSV000094118","datasetNum":"94118","title":"GNPS - Chevrette et al. 2022 Microbiome composition modulates secondary metabolism in a multispecies bacterial community","user":"ACumsille","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708364322000","created":"Feb. 19, 2024, 9:38 AM","description":"Dataset from Chevrette MG, Thomas CS, Hurley A, Rosario-Melendez N, Sankaran K, Tu Y, Hall A, Magesh S, Handelsman J. Microbiome composition modulates secondary metabolism in a multispecies bacterial community. Proc Natl Acad Sci U S A. 2022 Oct 18;119(42):e2212930119. doi: 10.1073\/pnas.2212930119. Epub 2022 Oct 10. PMID: 36215464; PMCID: PMC9586298.\r\n\r\nCultures of a simplified model of the rhizosphere, composed of Bacillus cereus (Bc), Flavobacterium johnsoniae (Fj), and Pseudomonas koreensis (Pk). In addition, a Pseudomonas koreensis mutant with the koreenceine BGC deletion (D) was used for cultures.\r\nData were collected using monocultures, as well as two- and three-member cocultures. ","fileCount":"263","fileSizeKB":"33508171","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas koreensis (NCBITaxon:198620);Bacillus cereus (NCBITaxon:1396);Flavobacterium johnsoniae (NCBITaxon:986)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"THOR;Pseudomonas;Flavobacterium;Bacillus;coculture","pi":[{"name":"Jo Handelsman","email":"jo.handelsman@wisc.edu","institution":"UW-Madison","country":"US"},{"name":"Marc Chevrette","email":"mchevrette@ufl.edu","institution":"University of Florida","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"670c153e0bfc488ebecddb7480b7a338","id":"2920"}, {"dataset":"MSV000094116","datasetNum":"94116","title":"GNPS-mirror plot of new secondary bile acids","user":"qixingnie","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708329031000","created":"Feb. 18, 2024, 11:50 PM","description":"Comparison of LC\/MS data of 3-acetylated CAs from synthetic standards and\nbacteria cultured samples ","fileCount":"9","fileSizeKB":"1184124","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria","instrument":"Q Extractive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acids","pi":[{"name":"Changtao Jiang","email":"jiangchangtao@bjmu.edu.cn","institution":"Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China., China ","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1121a2a89173435a95b4abedc580650f","id":"2921"}, {"dataset":"MSV000094115","datasetNum":"94115","title":"GNPS-alkyne probe of CA for the identification of new secondary bile acids","user":"qixingnie","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708327139000","created":"Feb. 18, 2024, 11:18 PM","description":"Alkyne probe of CA (alkCA) was synthesized and incubated in human stool-derived ex vivo communities. The alkCA is transformed into CA-linker (CA-LNK) after the click reaction, and then analyzed by LC-MS\/MS","fileCount":"21","fileSizeKB":"2692779","spectra":"218598","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteria","instrument":"QE Extractive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Bile acids","pi":[{"name":"Changtao Jiang","email":"jiangchangtao@bjmu.edu.cn","institution":"Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China.","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"502b72d7f5794fc4ba19d05c7ed2fcc5","id":"2922"}, {"dataset":"MSV000094114","datasetNum":"94114","title":"Experimental viral infections in honey bee queens in queen monitoring cages","user":"abbichapman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708307816000","created":"Feb. 18, 2024, 5:56 PM","description":"We injected honey bee queens with a combination of BQCV&DWV-B, the same combination of virus that was inactivated with UV, or saline and monitored them in queen monitoring cages for 7 days before sacrificing them and performing proteomics on the hemolymph, ovaries, and eggs that were collected from the cages. ","fileCount":"7","fileSizeKB":"148311801","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"timsTOF Pro","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";N-terminal acetylation","keywords":"honey bee;queen;hemolymph;ovary;eggs;immunity","pi":[{"name":"Leonard Foster","email":"foster@msl.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4ea979e0c4194e629eec6c0a7e02a4cd","id":"2923"}, {"dataset":"MSV000094113","datasetNum":"94113","title":"Experimental viral infections in honey bee queens in the field ","user":"abbichapman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708307570000","created":"Feb. 18, 2024, 5:52 PM","description":"We injected honey bee queens with a either a combination of BQCV & DWV-B or saline and assessed them weekly in colonies for 7 weeks before sacrificing them and performing proteomics on the hemolymph and ovaries. 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Conversely, depalmitoylation detaches palmitic acid from modified proteins in the cytosol or endolysosome to regulate their recycling and degradation. The balance between these two opposing mechanisms controls proteostasis. While the role of palmitoylation is well-established in neuronal differentiation and synaptic plasticity, depalmitoylation is far less understood. Here, we study a lysosomal depalmitoylating enzyme, palmitoyl-protein thioesterase 1 (PPT1), which is associated with the devastating neurodegenerative disease infantile neuronal ceroid lipofuscinosis (CLN1).","fileCount":"25","fileSizeKB":"47614793","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Palmitoylation;depalmitoylation;PPT1;synaptic proteomic analysis;CLN1","pi":[{"name":"Akira Yoshii","email":"ayoshii@uic.edu","institution":"University of Illinois Chicago","country":"USA"},{"name":"Stephanie Cologna","email":"cologna@uic.edu","institution":"University of Illinois at Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e9c851fbf5214e1d8f257a9f390614e3","id":"2925"}, {"dataset":"MSV000094101","datasetNum":"94101","title":"Structural basis for Retriever-SNX17 assembly and endosomal sorting","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708110525000","created":"Feb. 16, 2024, 11:08 AM","description":"Protein-protein interaction analysis by label-free quantitation.\n\nLUM2_1153149, LUM2_1153150, LUM2_1153151: EV\nLUM2_1153152, LUM2_1153153, LUM2_1153154: WT\nLUM2_1153155, LUM2_1153156, LUM2_1153157: V205D-R248M","fileCount":"19","fileSizeKB":"37050804","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Endosomal sorting;SNX17;Retriever","pi":[{"name":"Ezra Burstein","email":"ezra.burstein@utsouthwestern.edu","institution":"UT Southwestern Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1520ac3af3d044769e6eb3a5ce86faec","id":"2926"}, {"dataset":"MSV000094098","datasetNum":"94098","title":"Mannose-6-phosphate isomerase functional status shapes a rearrangement in the proteome and degradome of mannose-treated melanoma cells","user":"azelanis","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708093491000","created":"Feb. 16, 2024, 6:24 AM","description":"Metabolic reprogramming is a ubiquitous feature of transformed cells, comprising one of the hallmarks of cancer and enabling neoplastic cells to adapt to new environments. Accumulated evidence reports on the failure of some neoplastic cells to convert mannose-6-phosphate into fructose-6-phosphate, thereby impairing tumor growth in cells displaying low levels of the enzyme mannose-6-phosphate isomerase (MPI). Thus, we performed functional analyses and profiled the proteome landscape and the repertoire of substrates of proteases (degradome) of melanoma cell lines with distinct mutational backgrounds submitted to the treatment with mannose. Our results suggest a significant rearrangement in the proteome and degradome of melanoma cells lines upon mannose treatment, including the activation of catabolic pathways (such as protein turnover) and differences in protein N-terminal acetylation. Such biological implications might reflect the metabolic rewiring caused by the functional status of MPI enzyme and may help target specific molecular players from affected signaling circuits in melanoma. ","fileCount":"82","fileSizeKB":"115157521","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Melanoma; phosphomannose isomerase; degradomics; metabolic rewiring; proteomics","pi":[{"name":"Andre Zelanis","email":"andre.zelanis@unifesp.br","institution":"Functional Proteomics Laboratory, Department of Science and Technology, Federal University of Sao Paulo, Sao Jose dos Campos, SP, Brazil","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e420854927554488b8da2b5137b62ab8","id":"2927"}, {"dataset":"MSV000094097","datasetNum":"94097","title":"GNPS - Osteoarthritis diet study","user":"helenamrusso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708067469000","created":"Feb. 15, 2024, 11:11 PM","description":"Untargeted LC-MS\/MS data for plasma, serum, fecal, and saliva samples from patients with osteoarthritis before and after diet intervention.","fileCount":"270","fileSizeKB":"13832976","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"osteoarthritis;diet;fecal;serum;plasma;saliva","pi":[{"name":"Monica Guma","email":"mguma@ucsd.edu","institution":"UCSD","country":"USA"},{"name":"Pieter C. 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An LC-MS\/MS based analysis focusing on the post-translational modifications (PTMs) of mAb X was conducted on samples that had undergone accelerated aging at 40 degree. Along with PTMs that are known to affect mAbs structure function and stability (such as deamidation and oxidation), a novel mAb PTM was discovered, the esterification of glutamic acid by sorbitol. Incubation of mAb X with a 1to 1 ratio of unlabeled sorbitol and isotopically labeled sorbitol (13C6) further corroborated that the modification was the consequence of the esterification of glutamic acid by sorbitol. Levels of esterification varied across glutamic acid residues and correlated with incubation time and sorbitol concentration. After 4 weeks of accelerated stability with isotopically labeled sorbitol, it was found that 16 percent of the total mAb possesses an esterified glutamic acid. No esterification was observed at aspartic acid sites despite the free carboxylic acid side chain. This study unveils a unique modification of mAbs, emphasizing its potential significance for formulation and drug development.","fileCount":"27","fileSizeKB":"11140561","spectra":"0","psms":"198","peptides":"6","variants":"21","proteins":"6","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Scientific Orbitrap Fusion Lumos Mass Spectrometer ","modification":"Esterification","keywords":"Esterification, sorbitol, glutamic acid","pi":[{"name":"Bin Yu","email":"byu@coherus.com","institution":"Coherus BioSciences","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"","task":"f4c41201d6b645d3a1b01c04d64b8c0e","id":"2929"}, {"dataset":"MSV000094094","datasetNum":"94094","title":"MolPsy2024_YZWang_Neuron type-specific proteomics","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1708017530000","created":"Feb. 15, 2024, 9:18 AM","description":"Combinatorial expression of postsynaptic proteins underlies synapse diversity within and between neuron types. Thus, characterization of neuron-type-specific postsynaptic proteomes is key to obtaining a deeper understanding of discrete synaptic properties and how selective dysfunction manifests in synaptopathies. To overcome the limitations associated with bulk measures of synaptic protein abundance, we developed a biotin proximity protein tagging probe to characterize neuron-type-specific postsynaptic proteomes in vivo. We found Shank3 protein isoforms are differentially expressed by direct and indirect pathway spiny projection neurons (dSPNs and iSPNs). Investigation of Shank3B-\/- mice lacking exons 13-16 within the Shank3 gene, reveal distinct Shank3 protein isoform expression in iSPNs and dSPNs. In Shank3B-\/- striatum, Shank3E and Shank3NT are expressed by dSPNs but are undetectable in iSPNs. Proteomic analysis indicates significant and selective alterations in the postsynaptic proteome of Shank3B-\/- iSPNs. Correspondingly, the deletion of exons 13-16 diminishes dendritic spine density, reduces spine head diameter, and hampers corticostriatal synaptic transmission in iSPNs. Remarkably, reintroducing Shank3E in adult Shank3B-\/- iSPNs significantly rectifies the observed dendritic spine morphological and corticostriatal synaptic transmission deficits. We report unexpected cell-type specific synaptic protein isoform expression which could play a key causal role in specifying synapse diversity and selective synapse dysfunction in synaptopathies.","fileCount":"825","fileSizeKB":"380483163","spectra":"0","psms":"1492006","peptides":"148580","variants":"148580","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Shank3, ASD, Isoform;iSPN, dSPN, Striatum","pi":[{"name":"Jeffrey N. Savas, PhD","email":"jeffrey.savas@northwestern.edu","institution":"Department of Neurology Northwestern University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD049408","task":"058c0dbbcc764de6b3fa46ff28f06e3d","id":"2930"}, {"dataset":"MSV000094092","datasetNum":"94092","title":"Anaerobic gut fungi are an untapped reservoir of natural products.","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707960805000","created":"Feb. 14, 2024, 5:33 PM","description":"Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and have not been extensively mined for the biosynthetic enzymes of natural products such as antibiotics. Here, we investigate the potential of anaerobic gut fungi to synthesize natural products that could regulate membership within the gut microbiome. Complementary 'omics' approaches were combined to catalog the natural products of anaerobic gut fungi from four different representative species: Anaeromyces robustus (A. robustus), Caecomyces churrovis (C. churrovis), Neocallimastix californiae (N. californiae), and Piromyces finnis (P. finnis). In total, 146 genes were identified that encode biosynthetic enzymes for diverse types of natural products, including nonribosomal peptide synthetases and polyketide synthases. In addition, N. californiae and C. churrovis genomes encoded seven putative bacteriocins, a class of antimicrobial peptides typically produced by bacteria. During standard laboratory growth on plant biomass or soluble substrates, 26% of total core biosynthetic genes in all four strains were transcribed. Across all four fungal strains, 30% of total biosynthetic gene products were detected via proteomics when grown on cellobiose. Liquid chromatography-tandem mass spectrometry (LC-MS\/MS) characterization of fungal supernatants detected 72 likely natural products from A. robustus alone. A compound produced by all four strains of anaerobic fungi was putatively identified as the polyketide-related styrylpyrone baumin. Molecular networking quantified similarities between tandem mass spectrometry (MS\/MS) spectra among these fungi, enabling three groups of natural products to be identified that are unique to anaerobic fungi. Overall, these results support the finding that anaerobic gut fungi synthesize natural products, which could be harnessed as a source of antimicrobials, therapeutics, and other bioactive compounds. See publication: https:\/\/www.doi.org\/10.1073\/pnas.2019855118.\n\nThis research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:https:\/\/doi.org\/10.46936\/fics.proj.2018.50386\/60000039) and used resources at the DOE Joint Genome Institute (https:\/\/ror.org\/04xm1d337) and the Environmental Molecular Sciences Laboratory (https:\/\/ror.org\/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).","fileCount":"1409","fileSizeKB":"99181032","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Anaeromyces robustus; Caecomyces churrovis; Neocallimastix californiae; Piromyces finnis","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"anaerobic gut fungi;natural products;biosynthetic genes;antimicrobial peptides","pi":[{"name":"Michelle O'Malley","email":"momalley@engineering.ucsb.edu","institution":"University of California Santa Barbara","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f040f0b4839b469da4cf74aa7668560a","id":"2931"}, {"dataset":"MSV000094091","datasetNum":"94091","title":"GNPS - Elucidation of the Gene Regulatory Networks Governing Terpenoid-Mediated Plant-Environment Interactions to Enable Advanced Bioenergy Crops","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707960775000","created":"Feb. 14, 2024, 5:32 PM","description":"The proposed project aims to elucidate the gene-regulatory networks (GRNs) underlying terpenoid metabolism in three major bioenergy crops, switchgrass (Panicum virgatum), maize (Zea mays), and sorghum (Sorghum bicolor), to aid crop development for enhanced stress resilience and biofuel production from biomass feedstock. Prior studies identified more than 50 terpene synthases (TPS) and cytochrome P450 monooxygenases (P450), as key enzymes in generating bioactive terpenoids, in several bioenergy plants including switchgrass and maize. This knowledge now enables a precise investigation of the GRNs that govern common and species-specific terpenoid pathways. We will integrate transcription factor (TF) functional studies, TF binding site mapping, transcript and metabolite profiling, and terpenoid pathway engineering to identify the terpenoid-metabolic TF networks mediating stress responses in switchgrass, maize and sorghum.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001378) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"683","fileSizeKB":"41305311","spectra":"805443","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Panicum virgatum","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"terpenoid metabolism;bioenergy crops","pi":[{"name":"Philipp Zerbe","email":"pzerbe@ucdavis.edu","institution":"UC Davis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fda2273804f1494aa00cc6eb3abd88d3","id":"2932"}, {"dataset":"MSV000094090","datasetNum":"94090","title":"GNPS - Microbial regulation of soil water repellency to control soil degradation","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707960712000","created":"Feb. 14, 2024, 5:31 PM","description":"Soil water repellency (SWR) (i.e. soil hydrophobicity or decreased soil wettability) is a major cause of global soil degradation and a key agricultural concern. This metabolomics data will support the larger effort measuring soil water repellency and soil aggregate formation caused by microbial community composition through a combination of the standard drop penetration test, transmission electron microscopy characterization and physico-chemical analyses of soil aggregates at 6 timepoints. Model soils created from clay\/sand mixtures as described in Kallenbach et al. (2016, Nature Communications) with sterile, ground pine litter as a carbon\/nitrogen source were inoculated with 15 different microbial communities known to have significantly different compositions based on 16S rRNA sequencing. This data will allow assessment of the direct influence of microbial community composition on soil water repellency and soil aggregate stability, which are main causes of soil degradation.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001346) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"1215","fileSizeKB":"72369903","spectra":"67547","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"soil water repellency;soil degradation","pi":[{"name":"Marie Kroeger","email":"mkroeger@lanl.gov","institution":"Los Alamos National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fcefa3de833e4b77997d8fb1e0f5cad7","id":"2933"}, {"dataset":"MSV000094089","datasetNum":"94089","title":"GNPS - Determination of metabolic changes occurring in engineered low-lignin poplar","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707960712000","created":"Feb. 14, 2024, 5:31 PM","description":"Hybrid poplar (Populus alba?×?grandidentata; p39) wild type (WT) and QsuB transgenic low-lignin lines were previously described (Unda et al., 2022). WT and lines QsuB1, QsuB5, and QsuB15 were grown in a greenhouse as described in Lin et al., 2022. Samples for metabolomic analyses were collected after a growth period of six months. Stems were cut 5 cm above the root collar and segments of 5 cm were collected above the 1st (bottom), 20th (middle), and 40th (top) internodes. The bark was peeled and developing xylem tissue was collected by scraping the surface of the debarked segments using a razor blade. This approach generated developing xylem samples from the mature (bottom segment), intermediate (middle segment), and immature (top segment) parts of the stem. All the samples were immediately placed in liquid nitrogen, and stored at ?80 °C until time of use. Frozen samples were pulverized with a ball mill (Retsch) using stainless steel jars and grinding balls. Four biological replicates from each transgenic poplar line and WT control were used for metabolomic analyses. The data showed that some changes in metabolite abundance occur only in a specific tissue such as the xylem, phloem, or periderm. In the poplar line that exhibits the strongest reduction of lignin, we found that ~19% of the detected metabolite ions had different abundances in the xylem from mature stems. Changes affect predominantly the shikimate and phenylpropanoid pathways, secondary cell wall metabolism, and result in significant accumulation of hydroxybenzoates that derive from protocatechuate and salicylate.\r\nUnda et al., 2022: https:\/\/doi.org\/10.1111\/nph.18136\r\nLin et al., 2022: https:\/\/doi.org\/10.1186\/s13068-022-02245-4.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000514) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"566","fileSizeKB":"43795250","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Populus","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"poplar;lignin","pi":[{"name":"Aymerick Eudes","email":"ageudes@lbl.gov","institution":"JBEI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a31f2ec180514a4baf0039954cb890cb","id":"2934"}, {"dataset":"MSV000094088","datasetNum":"94088","title":"GNPS - Microbial environmental feedbacks and the evolution of soil organic matter","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707960681000","created":"Feb. 14, 2024, 5:31 PM","description":"More than two thirds of organic carbon stored in terrestrial ecosystems is contained in soil organic matter (SOM). The residence time of SOM is strongly dictated by the physical and biological properties of soil, including the formation of soil aggregates and the binding of OM to the surface of soil minerals. Both mechanisms protect otherwise available C from microbial (fungal, bacterial and archaeal) catabolism. However, our emerging conceptual understanding of SOM stabilization highlights the role anabolic metabolisms play in the formation of SOM from microbial necromass and metabolic byproducts, and the propensity of certain functional groups to bind to the surface of minerals. Notably, microbially derived SOM containing phosphoric or nitrogenous (e.g., aliphatic or amine) functional groups, showed preferential binding to mineral surfaces, and hence, enhanced stabilization of OM compounds in soils. Stabilizing the C cycle remains a social imperative. Bridging this critical knowledge gap is dependent on our elucidating the traits, mechanisms and drivers dictating the production of diverse biochemical compounds and the factors determining the residence time of these compounds under perturbation. This dataset aims to improve mechanistic understanding of the pathways and processes leading to the production of microbial SOM, which currently limits our capability to predict how these complex ecosystems will respond to pulse or press disturbances anticipated under a changing climate.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001233) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"501","fileSizeKB":"37115281","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"soil microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"drought stress;soil organic matter","pi":[{"name":"Nicholas Bouskill","email":"njbouskill@lbl.gov","institution":"Lawrence Berkeley National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e5672074ef7c41c99a9347f4ae1d2999","id":"2935"}, {"dataset":"MSV000094087","datasetNum":"94087","title":"Fibroblast Growth Factor (FGF) 23 and FGF Receptor 4 promote cardiac metabolic remodeling in CKD","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707947407000","created":"Feb. 14, 2024, 1:50 PM","description":"Frozen mitochondrial pellets were sonicated in SDS followed by centrifugation. 18 micrograms of protein was reduced and alkylated and digested with 1.5 ugs trypsin using an S-Trap micro device (Protifi) and lyophilized. A study pool QC (SPQC) was made from equal volumes of reconstituted samples. 0.75 ug of each sample and replicates of the SPQC (see metadata for run order) were analyzed by LC-MS\/MS using a nanoACQUITY UPLC system (Waters) operating in trap-elute configuration with a 90 min analytica gradient of 5-30% MeCN and a 75 um x 25 cm HSS-T3 column. The LC was coupled to a Q-Exactive HF-X high resolution accurate mass tandem mass spectrometer (Thermo) via a nanoFlex ionization source. MS was performed in data-dependent acquisition (DDA) mode with a 120,000 resolution (@ m\/z 200) full MS scan\nfrom m\/z 375 to 1600 followed by a with a target AGC value of 3e6 ions and 50 ms maximum injection time (IT). MS\/MS used a Top30 method at 15,000 resolution and with an AGC targeted of 5e4 and max IT of 45 ms, and isolation window of 1.2 m\/z and normalized collision energy of 27. Peptides were selected for MS\/MS using a minimum AGC target of 2.25e3, charge state filtering (2-5), an apex trigger of 5 to 40 s, and a dynamic exclusion of 20 s.","fileCount":"28","fileSizeKB":"27674447","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"cardiac mitochondria","pi":[{"name":"Alexander Grabner","email":"a.grabner@uke.de","institution":"University Hospital Hamburg-Eppendorf","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0e698025e4204a7f84a7667d2b1d2292","id":"2936"}, {"dataset":"MSV000094086","datasetNum":"94086","title":"Lacritin N-104 affinity purification of P. aeruginosa surface proteins","user":"anwaruddin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707937052000","created":"Feb. 14, 2024, 10:57 AM","description":"The precleared whole cell P. aeruginosa PA14 lysates underwent an overnight incubation with bead-immobilized N-104 peptide (or C-95 as a negative control peptide) under physiological conditions. Subsequent steps included washes and a gradual step-gradient elution ranging from 50 to 500 mM KCl. The eluate obtained at 500 mM KCl was then analyzed using tandem mass spectrometry to identify PA14 proteins that bind to N-104.","fileCount":"5","fileSizeKB":"2784659","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa PA14 (NCBITaxon:652611)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lacritin;N-104;P. aeruginosa;PA14;YaiW","pi":[{"name":"Gordon W. Laurie","email":"glaurie@virginia.edu","institution":"Department of Cell Biology, University of Virginia","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"72147a3716e34e7eb2c24f084ee08436","id":"2937"}, {"dataset":"MSV000094085","datasetNum":"94085","title":"Screen for proteins or peptides in human tears that are synergistic with N-104","user":"anwaruddin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707933113000","created":"Feb. 14, 2024, 9:51 AM","description":"It is evident that the effectiveness of N-104 decreases with increasing osmolarity. To investigate potential synergies, we exposed pre-cleared human tears in PBS to N-104 and a negative control, C-95, using affinity columns. After thorough PBS washing, eluants with 500 mM KCl were analyzed using tandem mass spectrometry. Specificity was examined by subtracting proteins interacting with C-95 from those bound to N-104. We identified affinity with 10 proteins known for antimicrobial activity, with the GKY20 (GKYGFYTHVFRLKKWIQKVI) peptide of thrombin being particularly supported by the literature.","fileCount":"5","fileSizeKB":"2876851","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa PA14 (NCBITaxon:652611)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lacritin;N-104;human basal tears;thrombin","pi":[{"name":"Gordon W. Laurie","email":"glaurie@virginia.edu","institution":"Department of Cell Biology, University of Virginia","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"27f1ca8b86734a2bad287e523e2103ee","id":"2938"}, {"dataset":"MSV000094084","datasetNum":"94084","title":"GNPS - Data files for manuscript - Selected ion monitoring for orbitrap-based metabolomics","user":"wenyunlu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707931563000","created":"Feb. 14, 2024, 9:26 AM","description":"Please open README-data-for-SIM-paper-20240210.doc for details. \r\n \r\n","fileCount":"222","fileSizeKB":"60453927","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"selected ion monitoring, SIM, full scan, orbitrap, metabolomics","pi":[{"name":"Joshua Rabinowitz","email":"joshr@exchange.Princeton.EDU","institution":"Princeton University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0dcbec28212240128d680fbba847aa7e","id":"2939"}, {"dataset":"MSV000094082","datasetNum":"94082","title":"Development of an Efficient, Effective, and Economical Technology for Proteome Analysis_part II","user":"yayu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707928430000","created":"Feb. 14, 2024, 8:33 AM","description":"Proteomics experiments often have unreasonably high economic and technical barriers to broad biomedical scientists, which not only result in costly supplies, but also the difficulties to standardize and the reluctance to adopt new techniques. We present an efficient and effective, yet economical approach (named E3technology), for proteomics sample preparation. We developed a novel Empore membrane, which could be used as a robust and low-cost medium to generate LCMS-friendly samples in a rapid and reliable fashion. Using different formats of E3technology, we explored a variety of sample types in varied complexity, quantity, volume, and size. We benchmarked their performance against several established approaches, and our data suggest that E3technology provides equivalent or better performance in terms of proteome-wide identification and quantitation. Moreover, we developed an enhanced yet simplified single vessel approach, E4technology, which opens new avenues for low-input or low-cell proteomics analysis. To further demonstrate their practical applicability, we applied the E3 and E4 technologies to investigate RNA-binding proteins derived from affinity purification, and to profile the intact bacterial cell proteome. Overall, our data suggest that these technologies are highly reliable, widely applicable, easily scalable, and much affordable and feasible to non-expert proteomics laboratories. They represent a breakthrough innovation in biomedical science, and we anticipate their widespread adoption by the proteomics community.\n","fileCount":"25","fileSizeKB":"36765381","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090);Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Proteomics;on-filter digestion;in-cell digestion;E3technology;E4technology","pi":[{"name":"Yanbao Yu","email":"yybyu@udel.edu","institution":"Department of Chemistry and Biochemistry, University of Delaware, USA","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4d0846f803d94930a12da5849fd170c2","id":"2940"}, {"dataset":"MSV000094081","datasetNum":"94081","title":"LC-MS analysis of Streptomyces globisporus extract","user":"unverkurt_05","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707919184000","created":"Feb. 14, 2024, 5:59 AM","description":"The microorganism was cultivated in M1 medium for 10 days, 28 centigrade degrees and 150 rpm followed by obtaining microbial extract with liquid-liquid extraction using ethyl acetate.","fileCount":"2","fileSizeKB":"127459","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces globisporus (NCBITaxon:1908)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"marine pharmacognosy;natural products;depsipeptides;LC-MS","pi":[{"name":"Erdal Bedir","email":"erdalbedir@iyte.edu.tr","institution":"Izmir Institute of Technology","country":"Turkey"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3965c4807641432d879a3871873fce5b","id":"2941"}, {"dataset":"MSV000094080","datasetNum":"94080","title":"Species-specific variation in mental gland secretions of turtles revealed by proteomic and lipidomic profiling","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707910716000","created":"Feb. 14, 2024, 3:38 AM","description":"Chemical signaling through pheromones is an ancient and widespread mode of communication. Turtles and tortoises (chelonians) secrete pheromones via mental (chin) glands and have superior olfactory capacities rendering them a promising group to study the evolution and function of chemical communication in vertebrates. Here, we use state-of-the art proteomics and lipidomics techniques to identify and explore the possible functions of proteins and lipids secreted by mental glands in turtles. We examined four turtle species all from the family Geoemydidae, to understand among-species as well as sexual variation in the composition of mental gland secretions. Differential expression of a relatively small number (ca. 65) of proteins explained a large portion of the proteome variation across species, highlighting the existence of specific signals evolving even in closely related species. Lipidomic analysis revealed high inter-individual variation but species differences could be attributed to five differing lipid classes. The lipids found in mental glands could have a dietary origin or be related to individual condition but may nonetheless be used in communication. We also examined sex-specific differences in the proteome of a single species (Mauremys leprosa) and found that males expressed a much larger array of proteins than females. Our findings establish a group of candidate proteins potentially involved in chemical signaling freshwater geoemydid turtles. Alternatively, differently expressed proteins in mental glands could have an indirect link to chemical communication, being involved in pheromone transport and\/or antioxidant protection. 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At any given moment, only a subset of the proteome has physical access to the DNA and organizes its structure, transcription, replication, repair, and other essential molecular functions. We have developed a \u2018zero-distance\u2019 photo-crosslinking approach to quantify proteins in direct contact with DNA in living cells. Collecting DNA interactomes from human breast cancer cells, we present an atlas of over one thousand proteins with physical access to DNA, and hundreds of peptide-nucleotide crosslinks pinpointing protein-DNA interfaces with single-amino-acid resolution. Quantitative comparisons of DNA interactomes from differentially treated cells recapitulate the recruitment of key transcription factors as well as DNA repair proteins, and uncover fast-acting restrictors of chromatin accessibility on a timescale of minutes. This opens a direct way to explore genomic regulation in a hypothesis-free manner, applicable to many organisms and systems.","fileCount":"1883","fileSizeKB":"471132166","spectra":"14749498","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse;Orbitrap Fusion Lumos","modification":"4-thiothymidine (4ST) crosslinks, 321 Dalton","keywords":"human DNA interactome, protein-DNA interaction, peptide-nucleotide crosslinks, photo-crosslinking, UVEN, XDNAX, estrogen, genotoxic drugs","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, Technical University Munich (TUM)","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f5d5d65667a14f2a817c4ce7bb77edf5","id":"2943"}, {"dataset":"MSV000094076","datasetNum":"94076","title":"GNPS - Dataset Creation from GNPS Molcular Networking - ","user":"MoustafaZohair","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707892934000","created":"Feb. 13, 2024, 10:42 PM","description":"Micorbial interaction of microbial communities in medicinal plant rhizosphere","fileCount":"9","fileSizeKB":"362672","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspergillus, Trichoderma, Bacillus ","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Microbial interaction ","pi":[{"name":"Moustafa Zohair","email":"moustafazohair@yahoo.com","institution":"Kyushu University , Japan","country":"Japan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"926ea080811e40c1a24f1e561f6690af","id":"2944"}, {"dataset":"MSV000094075","datasetNum":"94075","title":"Phosphoproteomic analysis of DYRK1A-knockin mice","user":"yangyj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707885586000","created":"Feb. 13, 2024, 8:39 PM","description":"Dyrk1A deficiency is linked to various neurodevelopmental disorders, including developmental delays and autism spectrum disorders (ASD). Haploinsufficiency of Dyrk1a in mice leads to ASD-related phenotypes, although key pathological mechanisms remain unclear. In addition, human DYRK1A mutations have not been characterized in mice. Here we report Dyrk1a-knockin mice carrying a human mutation (Ile48LysfsX2; Dyrk1a-I48K mice). These mice display severe microcephaly, social and cognitive deficits, dendritic shrinkage, excitatory synaptic deficits, and altered phospho-proteome patterns enriched for multiple signaling pathways and synaptic proteins. Early chronic lithium treatment of newborn mutant mice rescues brain volume, behavior, dendrite, synapse, and signaling\/synapse phospho-proteome phenotypes at juvenile and adult stages. These results suggest that signaling\/synaptic alterations contribute to phenotypic alterations in Dyrk1a-I48K mice, and that early correction of these alterations by lithium treatment has long-lasting effects of preventing juvenile and adult-stage phenotypes.","fileCount":"36","fileSizeKB":"21578288","spectra":"0","psms":"26732","peptides":"8233","variants":"14627","proteins":"2348","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"dyrk1a;phosphoproteomics;lithium;autism","pi":[{"name":"Jin Young Kim","email":"jinyoung@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep. of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD049357","task":"718591a2247648a0a38a784faa66e412","id":"2945"}, {"dataset":"MSV000094073","datasetNum":"94073","title":"Proteomic analysis of DYRK1A-knockin mice","user":"yangyj","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707877390000","created":"Feb. 13, 2024, 6:23 PM","description":"Dyrk1A deficiency is linked to various neurodevelopmental disorders, including developmental delays and autism spectrum disorders (ASD). Haploinsufficiency of Dyrk1a in mice leads to ASD-related phenotypes, although key pathological mechanisms remain unclear. In addition, human DYRK1A mutations have not been characterized in mice. Here we report Dyrk1a-knockin mice carrying a human mutation (Ile48LysfsX2; Dyrk1a-I48K mice). These mice display severe microcephaly, social and cognitive deficits, dendritic shrinkage, excitatory synaptic deficits, and altered phospho-proteome patterns enriched for multiple signaling pathways and synaptic proteins. Early chronic lithium treatment of newborn mutant mice rescues brain volume, behavior, dendrite, synapse, and signaling\/synapse phospho-proteome phenotypes at juvenile and adult stages. These results suggest that signaling\/synaptic alterations contribute to phenotypic alterations in Dyrk1a-I48K mice, and that early correction of these alterations by lithium treatment has long-lasting effects of preventing juvenile and adult-stage phenotypes. ","fileCount":"66","fileSizeKB":"48244088","spectra":"0","psms":"166983","peptides":"87590","variants":"119532","proteins":"7797","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Dyrk1a;proteomics;PTM;phosphoproteomics;ASD;lithium","pi":[{"name":"Jin Young Kim","email":"jinyoung@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep. of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD049356","task":"d769b12089a74d91aa8ad9fa78f8a12e","id":"2946"}, {"dataset":"MSV000094072","datasetNum":"94072","title":"GNPS - Decoding the chemical language of Suillus fungi: genome mining and untargeted metabolomics uncover terpene chemical diversity","user":"pabraham_ornl","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707865723000","created":"Feb. 13, 2024, 3:08 PM","description":"This research highlights the importance of combining genomics and metabolomics to advance our understanding of the chemical diversity underpinning fungal signaling and communication.","fileCount":"18549","fileSizeKB":"29086198","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Suillus (NCBITaxon:5379)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fungi;Ectomycorrhizae;Metabolomics;Terpene","pi":[{"name":"Paul Abraham","email":"abrahampe@ornl.gov","institution":"ORNL","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3d9f8a5ee4f34f5c896797c64a38f83a","id":"2947"}, {"dataset":"MSV000094069","datasetNum":"94069","title":"Senescence of endothelial cells promotes phenotypic changes in adventitial fibroblasts: possible implications for vascular aging","user":"Urszula","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707837082000","created":"Feb. 13, 2024, 7:11 AM","description":"Aging is the most important risk factor for the development of cardiovascular diseases. Senescent cells release plethora of factors commonly known as the senescence-associated secretory phenotype (SASP), which can modulate the normal function of the vascular wall. It is currently not well understood if and how endothelial cell senescence can affect adventitial niche. The aim of this study was to characterize oxidative stress-induced endothelial cells senescence and identify their paracrine effects on the primary cell type of the adventitia, the fibroblasts. Human aortic endothelial cells (HAEC) were treated with hydrogen peroxide to induce premature senescence. Mass spectrometry analysis identified several proteomic changes in senescent HAEC with top upregulated secretory protein growth differentiation factor 15 (GDF-15). Treatment of the human adventitial fibroblast cell line (hAdv cells) with conditioned medium (CM) from senescent HAEC resulted in alterations in the proteome of hAdv cells identified in mass spectrometry analysis. Majority of differentially expressed proteins in hAdv cells treated with CM from senescent HAEC were involved in the uptake and metabolism of lipoproteins, mitophagy and ferroptosis. We next analyzed if some of these changes and pathways might be regulated by GDF-15. We found that recombinant GDF-15 affected some ferroptosis-related factors (e.g. ferritin) and decreased oxidative stress in the analyzed adventitial fibroblast cell line, but it had no effect on erastin-induced cell death. Contrary, silencing of GDF-15 in hAdv cells was protective against this ferroptotic stimuli. Our findings provide a better understanding of the biology of senescent cells and can be of importance for potential therapeutic strategies targeting cell senescence or ferroptosis to alleviate vascular diseases.\r\n\r\nThis work was supported by grant ERA-CVD\/MEND-AGE\/6\/2019 from the National Centre for Research and Development in the frame of ERA-CVD (JTC2018) and project No. 2021\/43\/B\/NZ5\/03336 financed from the funds of the National Science Center, Poland.","fileCount":"20","fileSizeKB":"72787140","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"adventitial fibroblasts;endothelial cell senescence;ferroptosis;GDF-15;oxidative stress","pi":[{"name":"Agnieszka Jazwa-Kusior","email":"agnieszka.jazwa@uj.edu.pl","institution":"Jagiellonian University","country":"Poland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049353","task":"12a4487b03f048d98ce7f04791a31411","id":"2948"}, {"dataset":"MSV000094068","datasetNum":"94068","title":"Characterization of Complex Proteoform Mixtures by Online Nanoflow Ion-Exchange Chromatography - Native Mass Spectrometry ","user":"ZiranZhai","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707836959000","created":"Feb. 13, 2024, 7:09 AM","description":"This dataset was used to support the project \"Characterization of Complex Proteoform Mixtures by Online Nanoflow Ion-Exchange Chromatography - Native Mass Spectrometry\".","fileCount":"15","fileSizeKB":"630451","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Proteins;Antibodies;E.coli cell lysate","instrument":"QE","modification":"Not suitable","keywords":"Ion-exchange chromatography;Native MS;Intact analysis","pi":[{"name":"Ziran Zhai","email":"z.zhai@uva.nl","institution":"University of Amsterdam","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7f190059bfbe40d39954473f9056bf84","id":"2949"}, {"dataset":"MSV000094067","datasetNum":"94067","title":"Biomphalaria Snail Hemolymph Lipidomics Upon Exposure to Schistosomes","user":"rqkidner01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707775548000","created":"Feb. 12, 2024, 2:05 PM","description":"Raw lipidomics mass spectrometry data from Biomphalaria glabrata hemolymph samples. Hemolymph was collected by the foot-retraction method from: naive NMRI strains, naive M-line strains, or M-line strains infected and shedding PR1 Schistosoma mansoni. Lipidomics analysis completed by the Beth Israel Deaconess Medical Center (BIDMC) Metabolomics Core in Boston, MA.","fileCount":"25","fileSizeKB":"2159483","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Biomphalaria glabrata (NCBITaxon:6526)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Chemical signaling;Animal Microbiomes;Schistosomiasis;Snails","pi":[{"name":"J.P. Gerdt","email":"jpgerdt@iu.edu","institution":"Indiana University Bloomington","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b1a2ec7ca7ba48edb8011553867b5f96","id":"2950"}, {"dataset":"MSV000094063","datasetNum":"94063","title":"GNPS - seq2pks data - Streptomyces polyketides","user":"Rolandoo1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707676316000","created":"Feb. 11, 2024, 10:31 AM","description":"Streptomyces cinnamoneus NRRL B-24434 and Streptomyces aureoverticillatus NRRL B-3326 were cultivated in ISP2 liquid medium for 7 days at 28C. This was followed by n-butanol liquid:liquid extraction of the growth medium, rotovaporation, resuspension in 80% methanol, filtration with Whatman 0.2 micron syringeless filters followed by LC-MS\/MS analysis. LC-MS data was collected on a Thermo QExactive Orbitrap connected to a Vanquish LC system. LC settings were as follows: injection volume 5 microliter, Phenomenex Kinetex 2.6 micrometer C18 reverse phase 100 A 150x3 mm LC column, LC gradient, solvent A, 0.1% formic acid, solvent B, acetonitrile (0.1% formic acid), 0 min, 10% B, 5 min, 60% B, 5.1 min, 95% B, 6 min, 95% B, 6.1 min, 10% B, 9.9 min, 10% B, 0.5 ml\/min. 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For all 'home', 'away' and control conditions for each species we also had high or low oxygen treatments. 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How PP2A-B55 selects its substrates presents a severe knowledge gap in our understanding of phospho-dependent signaling. By integrating AlphaFold modelling with comprehensive experimental high-resolution mutational scanning, we show that alpha-helices in interactors bind a conserved platform on the B55 regulatory subunit. Despite limited sequence similarity, these alpha-helices share key amino acid determinants that engage hydrophobic and electrostatic patches on B55 in a remarkably similar way. We characterize a total of 15 instances in yeast, humans, and viruses, suggesting an evolutionarily conserved mechanism. Using this insight and deep learning protein design, we generate a specific and highly potent competitive peptide inhibitor that binds to B55 with low nanomolar affinity. With this inhibitor, we uncover that PP2A-B55 regulates the nuclear exosome targeting (NEXT) complex by binding to an alpha-helical recruitment module in one of its core components, RBM7. Collectively, our findings provide a framework for the understanding and interrogation of PP2A-B55 in health and disease.","fileCount":"398","fileSizeKB":"34276486","spectra":"0","psms":"1479623","peptides":"388431","variants":"440701","proteins":"19322","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion;Orbitrap Fusion Lumos;Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"PP2A-B55;B55;alpha-helix;NEXT;RBM7","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"The Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD049307","task":"c9f532aa287f431cbad3d16e73d301c0","id":"2956"}, {"dataset":"MSV000094052","datasetNum":"94052","title":"DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707506480000","created":"Feb. 9, 2024, 11:21 AM","description":"DNAJB8 + Tau XL-MS:\nDNAJB8 + tau Mi: LUM2_1026062_inj1; LUM2_1026062_inj2; LUM2_1026062_inj3\nDNAJB8 + Ms: LUM2_931918; LUM2_931946; LUM2_931956\n\nDNAJB8S3 mutant + Tau XL-MS:\nDNAJB8S3 + Mi: LUM2_1026063_inj1; LUM2_1026063_inj2; LUM2_1026063_inj3\nDNAJB8S3 + Ms: LUM2_935402; LUM2_935444; LUM2_935466\n","fileCount":"37","fileSizeKB":"60482362","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"DNAJB8, tau Mi, and tau Ms samples of recombinant protein purified from E. coli.","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"J-domain proteins;chaperone;DNAJB8;DNAJB6;tau;polyQ;LARKS;neurodegeneration;proteostasis;Alzheimers disease","pi":[{"name":"Lukasz A. Joachimiak","email":"lukasz.joachimiak@utsouthwestern.edu","institution":"UT Southwestern","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049306","task":"13128d01e6cc4deba6cdd68330304376","id":"2957"}, {"dataset":"MSV000094051","datasetNum":"94051","title":"Host lipids regulate multicellular behavior of a predator of a human pathogen","user":"Jon_Trinidad","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707496855000","created":"Feb. 9, 2024, 8:40 AM","description":"Raw proteomics and lipidomics mass spectrometry data from Biomphalaria glabrata hemolymph samples. Hemolymph was collected by the foot-retraction method from: naive NMRI strains, naive M-line strains, or M-line strains infected and shedding PR1 Schistosoma mansoni. Untargeted proteomics analysis completed by the Laboratory for Biological Mass Spectrometry at Indiana University. Lipidomics analysis completed by the Beth Israel Deaconess Medical Center (BIDMC) Metabolomics Core in Boston, MA.","fileCount":"17","fileSizeKB":"11142076","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Biomphalaria glabrata (NCBITaxon:6526);Schistosoma mansoni (NCBITaxon:6183)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Chemical Signaling;Animal Microbiome;Microeukaryote Symbiont;Schistosomiasis;Protective Symbiosis;Evolution of Multicellularity;Lipid Mediated Signaling;Hemolymph Composition;Snails;Protists","pi":[{"name":"J.P. Gerdt","email":"jpgerdt@iu.edu","institution":"Indiana University Bloomington","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049305","task":"4bb78b60d482451f8a38a60faf208dff","id":"2958"}, {"dataset":"MSV000094049","datasetNum":"94049","title":"Regulation of Glycogen Synthase kinase 3beta by phosphorylation and O-beta-linked N-acetylglucosaminylation: implications on tau protein phosphorylation ","user":"Adeline","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707485802000","created":"Feb. 9, 2024, 5:36 AM","description":"Glycogen synthase kinase 3 (GSK3) plays a pivotal role in signaling pathways related to insulin metabolism and in the pathogenesis of Alzheimer s disease (AD) and other neurodegenerative disorders. More particularly, the GSK3beta isoform is involved in AD-associated tau pathology as one of the major kinases involved in the hyperphosphorylation of the microtubule-associated tau protein, one of the neuropathological hallmarks of AD. As a constitutively active serine\/threonine proline-directed kinase, GSK3 is inactivated by Akt\/PKB-mediated phosphorylation of Ser9 at the N-terminal disordered domain. Furthermore, GSK3 activity requires for most of its substrates a priming (pre-phosphorylation) by another kinase that allows binding of the substrate in a phosphate-specific pocket near to the active site. It has been shown that GSK3 is also post-translationally modified by O-linked beta-N-acetylglucosaminylation (O-GlcNAcylation) with still unknown functional implications. We have found that binding of the phosphorylated, active form of Akt inhibits GSK3beta kinase activity on both primed and unprimed tau substrates, and Akt-mediated Ser9 phosphorylation restores the GSK3beta kinase activity on primed tau only. Therefore, Ser9 phosphorylation only inactivates GSK3 kinase activity on an unprimed substrate. Additionally, we have shown that GSK3beta is O-GlcNAcylated at multiple sites in both its disordered N- and C-terminal domains including Ser9, but O-GlcNAcylation does not alter kinase activity nor the Akt-mediated regulation of GSK3.","fileCount":"88","fileSizeKB":"18553930","spectra":"765507","psms":"56821","peptides":"1118","variants":"2025","proteins":"54","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:43 - \\\"N-Acetylhexosamine.\\\"","keywords":"Glycogen Synthase kinase 3 beta ;phosphorylation;O-beta-linked N-acetylglucosaminylation;microtubule-associated tau protein","pi":[{"name":"Caroline Smet-Nocca","email":"caroline.smet-nocca@univ-lille.fr","institution":"Universite de Lille","country":"France"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"45048fc4d22244d4bd0acb8ccd720c9c","id":"2959"}, {"dataset":"MSV000094044","datasetNum":"94044","title":"Evaluation of the carrier proteome limit on a ZenoTOF instrument","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707419955000","created":"Feb. 8, 2024, 11:19 AM","description":"This analysis sought to evaluate the carrier proteome limits on a SCIEX 7600 ZenoTOF mass spectrometer. A 9 channel TMTPro digest standard previously described in Orsburn, et al., Nature Communcations 2022 was used. . Briefly, a K562 human peptide digest standard (Promega) and E.coli peptide standard (Waters) were resuspended in 100mM TEAB (SimpliFi) and aliquots of 10 micrograms of each were labeled with the TMTPro reagents, 126, 127n, 128n, 129n, 130n, 131n, 132n, 133n and 134 and the reactions quenched with hydroxylamine according to vendor instructions. Labeled peptides were combined to maintain and equal concentration of K562 digest in each lane by combining 2 micrograms of each. E.coli peptides were diluted to 10to5to1 in TEAB and combined with the respective lanes to result in a repeating E.coli concentration of 20% and 10% of the first channel. The combined peptides were diluted to 100ng\/uL total concentration and analyzed on a SCIEX 7600 ZenoTOF instrument coupled to a Waters H Class microflow UHPLC. A 60 minute gradient was used at a flow rate of 5 uL\/min using a Phenomenex column. A top 10 data dependent method was used for all analysis. The resulting output files were converted to MGF using the ProteoWizard software and the MGF files were processed in Proteome Discoverer 2.4SP1 using a 15ppm MS1 and 0.03 Da MS\/MS tolerance window. Static carbamidomethylation of cysteine and TMTPro tags on lysine and peptide N-termini were used as well as dynamic modifications of methionine oxidation to search against a combination of the SwissProt Human and E.coli FASTA. The cRAP database was used for contaminant identification. ","fileCount":"64","fileSizeKB":"6709902","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Escherichia coli (NCBITaxon:562)","instrument":"ZenoTOF 7600","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Carrier proteome limit;SCoPE-MS","pi":[{"name":"Benjamin C Orsburn","email":"borsbur1@jhmi.edu","institution":"Johns Hopkins","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049286","task":"d8431493ab3a4c06ac8324b9553e2b40","id":"2960"}, {"dataset":"MSV000094039","datasetNum":"94039","title":"LC-MS test dataset of 32 substances","user":"SteffenHeu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707382619000","created":"Feb. 8, 2024, 12:56 AM","description":"LC MS dataset of 32 standard compounds. Compounds were prepared in acn\/water 1:1 and analysed using a ultimate 3000 and a waters acquity c18 beh column. Gradient elution started at 5% B and was increased to 95% B at 10 min, held until 14min, decreased to 5% at 14.01 min and held until 17.5 min. The flow rate was 0.4 mL\/min.","fileCount":"1016","fileSizeKB":"7028484","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"standards","pi":[{"name":"Robin Schmid","email":"rschmid1789@gmail.com","institution":"IOCB Prague","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4bbcfb24c6dc4e699f981fdeac84927a","id":"2961"}, {"dataset":"MSV000094038","datasetNum":"94038","title":"LC-IMS-MS test dataset of 32 substances","user":"SteffenHeu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707382589000","created":"Feb. 8, 2024, 12:56 AM","description":"LC IMS MS dataset of 32 standard compounds. Compounds were prepared in acn\/water 1:1 and analysed using a ultimate 3000 and a waters acquity c18 beh column. Gradient elution started at 5% B and was increased to 95% B at 10 min, held until 14min, decreased to 5% at 14.01 min and held until 17.5 min. The flow rate was 0.4 mL\/min.","fileCount":"963","fileSizeKB":"5049286","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"timsTOF fleX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"standards;tims","pi":[{"name":"Robin Schmid","email":"rschmid1789@gmail.com","institution":"IOCB Prague","country":"Czech Republic"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"008e5bb8c520479a911e8cbafe1b57a5","id":"2962"}, {"dataset":"MSV000094037","datasetNum":"94037","title":"WVSU_MitragynaSpeciosaProjectBBRL020824","user":"Djaedy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707373986000","created":"Feb. 7, 2024, 10:33 PM","description":"Mitragyna Speciosa leaves were soaked in Methanol and subjected for further analysis.","fileCount":"257","fileSizeKB":"5090669","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mitragyna speciosa (NCBITaxon:170351)","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Kratom","pi":[{"name":"Maria Karmella Apaya","email":"makarmella.apaya@wvsu.edu.ph","institution":"West Visayas State University","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"91492abb27024ae7963d6326310b5674","id":"2963"}, {"dataset":"MSV000094034","datasetNum":"94034","title":"2H-Thiopyran-2-Thione Sulfine, a Compound For Converting H2S to HSOH\/H2S2 and Increasing Intracellular Sulfane Sulfur Levels","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707357258000","created":"Feb. 7, 2024, 5:54 PM","description":"Reactive sulfane sulfur species such as persulfides (RSSH) and H2S2 are important redox regulators and closely linked to H2S signaling. However, the study of these species is still challenging due to their instability, high reactivity, and the lack of suitable donors to produce these species. Herein we report a unique compound, 2H-thiopyran-2-thione sulfine (TTS), which can specifically convert H2S to HSOH, and then to H2S2 in the presence of excess H2S. Meanwhile, the reaction product 2H-thiopyran-2-thione (TT) can be oxidized to reform TTS by biological oxidants. TTS can be conjugated to proteins to achieve specific delivery, and the combination of TTS and H2S leads to highly efficient protein persulfidation. When TTS is applied in conjunction with established H2S donors, the corresponding donors of H2S2 (or its equivalents) are obtained. Cell-based studies reveal that TTS can effectively increase intracellular sulfane sulfur levels and compensate for certain aspects of sulfide:quinone oxidoreductase (SQR) deficiency. Sample 1: GAPDH-SH + TTS + HPE-IAM; Sample 2: GAPDH-SH + TTS + Na2S + HPE-IAM; Sample 3: GAPDH-SH + TTS + Na2S + HPE-IAM","fileCount":"16","fileSizeKB":"4145180","spectra":"0","psms":"106240","peptides":"61830","variants":"74946","proteins":"53212","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Oryctolagus cuniculus (NCBITaxon:9986)","instrument":"Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";N-Iodoacetyltyramine;N-Iodoacetyltyramine_plus_S;N-Iodoacetyltyramine_plus_S2","keywords":"GAPDH;persulfidation","pi":[{"name":"Wei-Jun Qian","email":"Weijun.Qian@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD049256","task":"9f05e81dedc743ff8c5fa50e63e3a03e","id":"2964"}, {"dataset":"MSV000094033","datasetNum":"94033","title":"Deep Proteome Turnover of Human iPSC-derived Neurons","user":"haolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707352323000","created":"Feb. 7, 2024, 4:32 PM","description":"Proteostasis involves a dynamic network of biological pathways that regulate protein synthesis, maintenance, and degradation. As postmitotic cells, neurons are particularly sensitive to environmental changes, and dysfunction in cellular proteostasis can lead to an accumulation of aggregated and misfolded proteins. However, how proteins turnover on a global scale in human neurons is not well understood. In this study, we systematically improved a dynamic SILAC proteomic approach to enable a deep and accurate measurement of protein turnover in human induced pluripotent stem cell (iPSC)-derived cholinergic spinal motor and glutamatergic cortical neurons. Furthermore, we applied this deep proteome turnover method to evaluate how inhibiting the ubiquitin-proteasome and lysosome-autophagy pathway impacts proteostasis in iPSC-derived neurons. Using these datasets, we developed a freely available resource called Neuron Profile, an interactive website for visualizing and querying protein turnover in subcellular locations in human neurons. 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Kidneys were perfused with Dulbeccos Phosphate Buffered Saline, dissected, decapsulated and weighted. Kidneys were decellularized using 3 freeze-thaw cycles (freezing at -80C, 30 minute long thawing at 4C) and a 3-day long incubation in 2% SDS at 4C under gentle rotation. Ten to twenty milligram tissue net weight of each sample was homogenised. Protein concentration was determined using Bradford Assay. Ten micrograms of total protein was loaded in SDS-PAGE and migrated for 25min and prepared using the GeLC-MS method (doi: 10.1007\/7651_2017_76). \r\nFor LC-MS\/MS analysis a Dionex Ultimate 3000 HPLC nanoflow system was used in combination with a Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer. Samples were reconstituted in 25 microliters mobile phase A (98% water, 2% acetonitrile, 0.1% formic acid) and 10 microliters were loaded onto the LC column configured with a Dionex 0.1 x 20 mm, 5 micrometres, 100 A C18 nano trap column with a 5 microliters\/min flow rate. An Acclaim PepMapTM C18 100 nanoViper column 75 micrometres x 50cm, 2 micrometres 100 A was used with a flow rate of 300nL\/min. Peptides were eluted under a 250min gradient from 2% mobile phase B (0.1% formic acid in 80% acetonitrile) to 95% mobile phase B. Voltage of the positive ion electrospray ionization was set to 2.1kV. The mass spectrometer parameters were set as follows: 1) full MS: resolution of 70,000, automatic gain control (AGC) target at 1e6, maximum injection time (IT) of 100ms, scan range of 380 - 1,200m\/z; 2) dd-MS2: resolution of 17,500, AGC target at 1e5, maximum IT of 50ms, TopN of 20, normalized collision energy of 30; 3) dd settings: intensity threshold 1.6e5, Minimum AGC target 8.00e3, dynamic exclusion for 15s. Raw files were processed with Thermo Proteome Discoverer 2.4 software, utilizing the Sequest search engine and the UniProt Mus musculus fasta database containing only canonical sequences (downloaded on 31\/05\/2023, including 17,155 reviewed entries). Carbamidomethylation of cysteine was set as a static modification, and oxidation of methionine and oxidation of proline were set as dynamic modifications. Two missed cleavage sites, a precursor mass tolerance of 5ppm, and fragment mass tolerance of 0.05Da were allowed. 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The available data were converted in .mzML format using the Waters2mzML software, available on Github. \r\n\r\nDetailed information about data acquisition: For MSe, data acquisition was performed in a UPLC system coupled to an ESI source and a QTOF XevoTM G2 instrument (Waters Corp., Milford, MA, USA). Chromatographic separation was achieved using a C18 column (100 x 2.1 mm and 1.8 microm particle diameter, ACQUITY UPLC HSS T3), and a mobile phase gradient with a flow rate of 0.5 mL\/min, composed of ACN\/water, both phases acidified with 0.1% formic acid. The runtime was 10 minutes, with an injected sample volume of 5 microL, and the oven and shelf temperatures 40 C and 10 C, respectively. The chromatographic gradient began with an initial composition of 1 percent ACN and, was followed by a transition to 15 percent ACN at 0.1 min. Further changes in solvent composition occurred at 7.5 min (80 percent ACN), 8.5 min (99 percent ACN), and 8.6 min (1 percent ACN) until 10 min. The mass spectrometer was operated in MSe acquisition mode with alternating high and low-energy scans, for positive and negative ionization modes. The ionization energy was set at 3 eV for low-energy scans and 25-40 eV for high-energy scans. ESI-MS at a resolution up to 40.000 with a full mass scan range set from 50 to 1000 m\/z for functions 1 and 2 was applied. Instrument parameters, including cone voltage (40 V), capillary voltage (3.0 kV), cone gas flow (30 L\/h), auxiliary gas flow rate (10 L\/h); desolvation temperature (300 C), source temperature (120 C), and desolvation gas flow (600 L\/h), were carefully optimized. High-purity nitrogen was employed for desolvation, collision, and cone gas. To ensure accuracy and reproducibility, a solution of leucine-encephalin was used as a lock mass with m\/z 554.2622 (ESI-) and m\/z 556.2768 (ESI+) for identification. MS data were continuously collected, and lock spray calibration was performed every 10 seconds.","fileCount":"15","fileSizeKB":"689777","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ocotea guianensis (NCBITaxon:128661);Ocotea odorifera (NCBITaxon:128668);Ocotea diospyrifolia (NCBITaxon:881600);Ocotea notata;Ocotea porosa (NCBITaxon:1365881);Ocotea lancifolia (NCBITaxon:881603)","instrument":"Xevo G2 Q-Tof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Data-independent acquisition;MSe;Ocotea;Glycosylated flavonoid","pi":[{"name":"Daniela Aparecida Chagas-Paula","email":"daniela.chagas@unifal-mg.edu.br","institution":"Federal University of Alfenas-MG","country":"Brazil "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b12b5053ae38415d9986c24f7231d118","id":"2968"}, {"dataset":"MSV000094028","datasetNum":"94028","title":"LC-MS based Proteomics Analysis of aneuploid cells","user":"trendsetter","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707258189000","created":"Feb. 6, 2024, 2:23 PM","description":"\nDescription\n\nCells were cultured as described above and synchronized in G2\/M phase by incubating them for 24 hours with 2mM thymidine and, subsequently, for 12 hours with STLC 10uM. From each culture, 106 cells were collected by mitotic shake off, centrifuged and pellets were washed twice with PBS. Cells were lysed in 200 ul lysis buffer (2% sodium deoxycholate (SDC), 0.1 M ammoniumbicarbonate) using strong ultra-sonication (two cycles of sonication S3 for 10 seconds, Hielscher Ultrasonicator). Protein concentration was determined by BCA assay (Thermo Fisher Scientific) using a small sample aliquot. 50ug of proteins were digested as described previously (Ahrne et al., 2016), reduced with 5 mM TCEP for 15 min at 95 C and alkylated with 10 mM iodoacetamide for 30 min in the dark at 25 C. After diluting samples with 100 mM ammonium bicarbonate buffer to a final DOC concentration of 1%, proteins were digested by incubation with sequencing-grade modified trypsin (1\/50, w\/w; Promega, Madison, Wisconsin) overnight at 37C. Then, the samples were acidified with 2 M HCl to a final concentration of 50 mM, incubated for 15 min at 37 C and the precipitated detergent removed by centrifugation at 10,000xg for 15 min. Subsequently, peptides were desalted on C18 reversed-phase spin columns according to the manufacturers instructions (Microspin, Harvard Apparatus) and dried under vacuum. The dried peptide samples were subsequently labeled with isobaric tags (TMT 10plex, Thermo Fisher Scientific) according to the manufacturers instructions. To control for ratio distortion during quantification, a peptide calibration mixture consisting of six digested standard proteins mixed in different amounts was added to each sample before TMT labeling as recently described (Ahrne et al., 2016). After pooling the TMT labeled peptide samples, peptides were again desalted on C18 reversed-phase spin columns according to the manufacturers instructions (Macrospin, Harvard Apparatus) and dried under vacuum. TMT-labeled peptides were fractionated by high-pH reversed phase separation using a XBridge Peptide BEH C18 column (3,5 um, 130 A, 1 mm x 150 mm, Waters) on an Agilent 1260 Infinity HPLC system. Peptides were loaded onto the column in buffer A (ammonium formate (20 mM, pH 10) in water) and eluted using a two-step linear gradient starting from 2% to 10% in 5 minutes and then to 50% (v\/v) buffer B (90% acetonitrile \/ 10% ammonium formate (20 mM, pH 10) over 55 minutes at a flow rate of 42 ul\/min. Elution of peptides was monitored with a UV detector (215 nm, 254 nm). A total of 36 fractions were collected, pooled into 12 fractions using a post-concatenation strategy as previously described (Wang et al., 2011), dried under vacuum and subjected to LC-MS\/MS analysis. [doi:10.25345\/C5NC5SP9X] [dataset license: CC0 1.0 Universal (CC0 1.0)]\n","fileCount":"34","fileSizeKB":"23573340","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"aneuploid cells;TMT","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049216","task":"cbcb4aee69e8443286b3ec4ef0aec7cd","id":"2969"}, {"dataset":"MSV000094027","datasetNum":"94027","title":"HDX-MS of murine urokinase plasminogen activator and variants","user":"ekomives","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707254504000","created":"Feb. 6, 2024, 1:21 PM","description":"HDX-MS data revealing long-range allostery that affects the catalytic activity of the serine protease, murine urokinase plasminogen activator. The allostery is mediated by the disordered region connecting the N-terminal EGF and kringle domains to the protease domain.","fileCount":"1129","fileSizeKB":"42274867","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Synapt G2-S HDMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"allostery;protease;plasminogen activator;intrinsically disordered region","pi":[{"name":"Elizabeth Komives","email":"ekomives@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049214","task":"8bcf9e2eccf2493aa05fe4130e81adc5","id":"2970"}, {"dataset":"MSV000094026","datasetNum":"94026","title":"Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry","user":"jymbcrc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707252442000","created":"Feb. 6, 2024, 12:47 PM","description":"a new hybrid method, which integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein coronas enrichment for high throughput and efficient plasma proteomic profiling. ","fileCount":"129","fileSizeKB":"11793077","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human plasma","instrument":"Orbitrap Fusion Lumos","modification":"no","keywords":"direct infusion; plasma proteomics, nanoparticles","pi":[{"name":"Jesse G. Meyer","email":"jessegmeyer@gmail.com","institution":"UW-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8116cb168b2145c299a93426bbd49d4d","id":"2971"}, {"dataset":"MSV000094024","datasetNum":"94024","title":"A Salmonella subset subverts SLC11A1-imposed iron restriction by targeting red blood cell-degrading macrophages","user":"antelominia_2020","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707221840000","created":"Feb. 6, 2024, 4:17 AM","description":"This dataset comprises the raw data, metadata, the databases searched against in the analysis of this dataset, and the output file generated from the used search engine (SpectroNaut). \n","fileCount":"25","fileSizeKB":"22792328","spectra":"1413530","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Salmonella typhimurium (strain SL1344);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Salmonella infection;Nutritional immunity;Iron","pi":[{"name":"Dirk Bumann","email":"dirk.bumann@unibas.ch","institution":"Biozentrum University of Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD049197","task":"feaa989f168047a892cc59940085dad7","id":"2972"}, {"dataset":"MSV000094020","datasetNum":"94020","title":"Ubiquitin remnant motif profiling (Ubiquitomics) in VACV infected HeLa cells","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707183104000","created":"Feb. 5, 2024, 5:31 PM","description":"HeLa cells were pretreated with MG132, inoculated with VACV-Cop at an MOI of 3 for 1 h, and posttreated with MG132 again. Cells were lysed and extracted proteins were digested to peptides using trypsin, and desalted peptides were subjected to automated diGly enrichment\nusing the PTMScan ubiquitin remnant motif kit (Cell signaling) according to manufactuer's instructions.","fileCount":"7","fileSizeKB":"7735479","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Vaccinia virus Copenhagen (NCBITaxon:10249)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\"","keywords":"ubiquitomics;VACV;ubiquitin;ubiquitin remnant motif","pi":[{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"},{"name":"Robert Ingham","email":"ringham@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3c49e02023614556bf025e77c9b0b9ca","id":"2973"}, {"dataset":"MSV000094019","datasetNum":"94019","title":"GNPS - nanoRAPIDS, an analytical pipeline for the discovery of novel bioactive metabolites in complex culture extracts at nanoscale","user":"machushynets","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707172596000","created":"Feb. 5, 2024, 2:36 PM","description":"Here we present an analytical platform for the efficient identification and prioritization of low abundance bioactive compounds at nanoliter scale, called nanoRAPIDS. NanoRAPIDS encompasses analytical scale separation and nanofractionation of natural extracts, followed by the bioassay of interest, automated mass spectrometry identification, and Global Natural Products Social molecular networking (GNPS) for dereplication. As little as 10 microliters crude extract is thereby fractionated into 384 fractions. First, bioactive congeners of iturins and surfactins were identified in Bacillus, based on their activity against Gram-positive bacteria, Gram-negative bacteria and\/or fungi. Subsequently, bioactive molecules were identified in an extensive network of angucyclines elicited by catechol in cultures of Streptomyces sp. This allowed the discovery of a highly unusual N-acetylcysteine conjugate of saquayamycin, despite low production levels in an otherwise abundant molecular family. These data underline the utility and broad application of the technology for the prioritization of minor bioactive compounds in complex extracts.","fileCount":"11","fileSizeKB":"176021","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces sp. MBT84, Bacillus sp. 90A-23","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Nanofractionation, nanoRAPIDS, GNPS, bioactivity","pi":[{"name":"Gilles van Wezel","email":"g.wezel@biology.leidenuniv.nl","institution":"Institute of Biology, Leiden University","country":"The Netherlands"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c0601d0451174231974a32556086a1ec","id":"2974"}, {"dataset":"MSV000094018","datasetNum":"94018","title":"NIOZ DOM analysis - SEALINK 2021 Subset","user":"lschellenberg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707168831000","created":"Feb. 5, 2024, 1:33 PM","description":"DOM analysis of coral reef & coastal water metabolites at NIOZ Texel","fileCount":"45","fileSizeKB":"2119341","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Environmental samples","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DOM, coral reef, coastal waters","pi":[{"name":"Andreas Haas","email":"andi.haas@nioz.nl","institution":"NIOZ","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"240bbbcace1643a89eac6c92aba1ce0c","id":"2975"}, {"dataset":"MSV000094015","datasetNum":"94015","title":"NIOZ DOM analysis - Resilience Project 2022","user":"lschellenberg","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707165855000","created":"Feb. 5, 2024, 12:44 PM","description":"DOM analysis of coral reef & coastal water metabolites at NIOZ Texel","fileCount":"85","fileSizeKB":"5212296","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Environmental samples","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DOM, coral reef, coastal waters","pi":[{"name":"Andreas Haas","email":"andi.haas@nioz.nl","institution":"NIOZ","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"63230f76cfda4aeca293dce72535c7b0","id":"2976"}, {"dataset":"MSV000094014","datasetNum":"94014","title":"Casanovo non-enzymatic fine-tuning set","user":"melihyilmaz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707162144000","created":"Feb. 5, 2024, 11:42 AM","description":"To create a dataset of PSMs that does not exhibit tryptic bias, we selected PSMs with a uniform distribution of amino acids at the C-terminal peptide positions from two datasets: MassIVE-KB [Wang2018] and PROSPECT [Shouman2022]. The MassIVE-KB dataset contains 30 million PSMs and consists entirely of data generated using trypsin; hence, only a small proportion of the MassIVE-KB peptides do not end in K or R, corresponding to those that appear at the C-terminus of the corresponding protein. The PROSPECT dataset is a collection of 61 million PSMs generated from synthetic peptides. To avoid overrepresentation of some peptides in this dataset, we randomly selected at most 100 PSMs per unique peptide, similar to the processing that was done during the creation of the MassIVE-KB dataset. This pre-selection step reduced the size of the PROSPECT dataset to 12.6 million PSMs. Finally, to create a non-enzymatic dataset containing 1 million peptides, we selected 50,000 PSMs for each canonical amino acid. These PSMs were selected at random from MassIVE-KB, then supplemented as necessary from PROSPECT to obtain the desired count (see Yilmaz et al. [Yilmaz2023] Supplementary Table S1). This dataset contained PSMs from 247,859 unique peptides, which were randomly split into training, validation and test sets in the ratio 80\/10\/10. FTP directory contains the mgf files corresponding to train, validation and test splits.\n\n[Wang2018] M. Wang, J. Wang, J. Carver, B. Pullman, S. Won Cha, N. Bandeira, \"Assembling the Community-Scale Discoverable Human Proteome\", Cell Systems, Volume 7, Issue 4, 2018.\n\n[Shouman2022] O. Shouman, W. Gabriel, V. Giurcoiu, V. Sternlicht, M. Wilhelm, \"PROSPECT: Labeled Tandem Mass Spectrometry Dataset for Machine Learning in Proteomics\", NeurIPS Datasets and Benchmarks, 2022\n\n[Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux, R. Nelson, V. Ananth, S. Oh, and W. Noble,\"Sequence-to-sequence translation from mass spectra to peptides with a transformer model\", bioRxiv, 2023\n","fileCount":"4","fileSizeKB":"3651132","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:1 - \\\\\\\"Acetylation.\\\\\\\";UNIMOD:4 - \\\\\\\\\\\\\\\"Iodoacetamide derivative.\\\\\\\\\\\\\\\";UNIMOD:5 - \\\\\\\\\\\\\\\"Carbamylation.\\\\\\\\\\\\\\\"; UNIMOD:7 - \\\\\\\\\\\\\\\"Deamidation.\\\\\\\\\\\\\\\";UNIMOD:35 - \\\\\\\\\\\\\\\"Oxidation or Hydroxylation.\\\\\\\\\\\\\\\";UNIMOD:385 - \\\\\\\\\\\\\\\"Loss of ammonia.\\\\\\\\\\\\\\\"","keywords":"de novo;non-enzymatic","pi":[{"name":"William Noble","email":"wnoble@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"73b8074734104372bc5a441e8dc4447e","id":"2977"}, {"dataset":"MSV000094012","datasetNum":"94012","title":"Application of Predictive Modeling Tools for the Identification of Ocimum spp. Herbal Products","user":"kellogglab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707153222000","created":"Feb. 5, 2024, 9:13 AM","description":"LC-MS files for three species of Ocimum, to evaluate the potential of controlled growth studies to predict classification of consumer-based samples. ","fileCount":"117","fileSizeKB":"20531964","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ocimum basilicum (NCBITaxon:39350);Ocimum tenuiflorum (NCBITaxon:204149);Ocimum gratissimum (NCBITaxon:204144)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"basil;authentication;greenhouse;commercial ;untargeted metabolomics;botanicals","pi":[{"name":"Josh J Kellogg","email":"jjk6146@psu.edu","institution":"Pennsylvania State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4e18d5ef56614b629957435ac84f917e","id":"2978"}, {"dataset":"MSV000094010","datasetNum":"94010","title":"Molecular and Cellular Mechanisms of Teneurin Signaling in Synaptic Partner Matching","user":"malpap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707150439000","created":"Feb. 5, 2024, 8:27 AM","description":"In the developing brain, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Teneurins are evolutionarily conserved transmembrane proteins that instruct synaptic partner matching via matched expression and homophilic attraction between synaptic partners. Little is known how intracellular signaling pathways execute this and diverse other functions triggered by extracellular interactions of teneurins. Here, we use in situ proximity labeling to identify Ten-ms intracellular interactome in the Drosophila brain. Genetic interaction using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) suggest a common pathway Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution further reveal that ORN axons initially extend exuberant branches along their trajectory, and those that contact partner PN dendrites are selectively stabilized, accompanied by an increase of local F-actin accumulation. 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A total of 10 control and 10 Varroa-treated bees were used for label-free nano-liquid chromatography (LC)MS\/MS proteomic analysis. 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(OD600 0.6 or 0.750 0.5). 50 mL of cells were harvested before and after treatment. Cell pellets were extracted with 20% or 80% MeOH. n=5. \r\nColumn: Kinetex C18, 1.7 um EVO C18 100A, 50x2.1 mm. 500uL, 10min, 5-99%, DDA, Top5 ","fileCount":"93","fileSizeKB":"21598943","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"E.coli;Synechococcus elongatus;heat shock;LC-MSMS;Untargeted","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"024e4ed2f00d4afc86d7c0d5af393e45","id":"2983"}, {"dataset":"MSV000094003","datasetNum":"94003","title":"Integrating mutliple datasets to identify protein ligand interactions in E.coliset4","user":"VenkateshKumar","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707077225000","created":"Feb. 4, 2024, 12:07 PM","description":"DIA sec files from denmark, SECR1 files 1 to 40 analysed via spectronaut","fileCount":"41","fileSizeKB":"140922764","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"chromotography, sizeexclusion","pi":[{"name":"venkatesh kumar","email":"vpthirum@purdue.edu","institution":"purdue university","country":"usa"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cab9915e85834ccc9de3b82912f7c5e7","id":"2984"}, {"dataset":"MSV000094002","datasetNum":"94002","title":"GNPS - KratomMitragynaSpeciosa_WVSUBBRL","user":"Djaedy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1707054358000","created":"Feb. 4, 2024, 5:45 AM","description":"Mitragyna speciosa leaves were extracted with Methanol and subjected to further analysis. ","fileCount":"256","fileSizeKB":"5021825","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mitragyna speciosa (NCBITaxon:170351)","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Kratom, Mitragyna Speciosa","pi":[{"name":"Maria Karmella Apaya","email":"makarmella.apaya@wvsu.edu.ph","institution":"West Visayas State University","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5edde08aec95482b97f671279c9195dc","id":"2985"}, {"dataset":"MSV000093996","datasetNum":"93996","title":"Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706971234000","created":"Feb. 3, 2024, 6:40 AM","description":"Absolute quantification of ubiquitin chains and total ubiquitin changes using AQUA-PRM in mouse brain aging.","fileCount":"19","fileSizeKB":"3676086","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PRM-AQUA;Ubiquitin;chains;brain;mouse;aging","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD049135","task":"fbfdeb394e254b0684955b6fc53d2c52","id":"2986"}, {"dataset":"MSV000093995","datasetNum":"93995","title":"All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity proteomics","user":"MaoYiheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706942971000","created":"Feb. 2, 2024, 10:49 PM","description":"Spatial proteomics enables in-depth mapping of cellular components and tissue architectures, mostly achieved by laser microdissection-mass spectrometry (LMD-MS) and antibody-based imaging. However, the trade-offs among sampling resolution, throughput, and proteome coverage still limit the applicability of these strategies, especially toward deep proteome profiling with high spatial resolution. Here, we propose PSPro (Proximity labeling for Spatial Proteomics) by leveraging precise antibody-targeted biotinylation at three-dimension scale and efficient affinity purification for MS-based cell-type-specific proteome profiling from single tissue slice. With fine-tuned labeling parameters, PSPro achieves all-at-once cell-type proteome capture with sub-micrometer resolution and shows comparable performance to flow cytometry- and LMD-based proteomic workflows. We apply PSPro to fixed tumor and spleen slices, enriching thousands of proteins containing known markers from ten cell types. For tissue microenvironments with high heterogeneity, we further incorporate region-resolved LMD into PSPro to facilitate direct comparison of cell subpopulations from the same tissue slice, revealing spatial proteome heterogeneity of cancer cells and immune cells in pancreatic tumor. Collectively, PSPro converts traditional \u201Cantibody-epitope\u201D paradigm to \u201Cantibody-cell type proteome\u201D for spatial biology in a user-friendly manner.","fileCount":"148","fileSizeKB":"423582675","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X;timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"spatial proteomics, proximity labeling","pi":[{"name":"Ruijun Tian","email":"tian.rj@sustc.edu.cn","institution":"SUSTech","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"87bf720303b2481b88ce24f6f9b86a1a","id":"2987"}, {"dataset":"MSV000093994","datasetNum":"93994","title":"Single Cell Proteoform Analysis Using scPiMS","user":"mikehollas123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706917312000","created":"Feb. 2, 2024, 3:41 PM","description":"We introduce single-cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells drop casted onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enables a scalable approach to single-cell proteomics. This new scPiMS platform addresses the throughput bottleneck in single cell proteomics and boosts cell processing rate by several fold while accessing protein composition with higher coverage.","fileCount":"210","fileSizeKB":"10477471","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"LTQ Orbitrap","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"single cell;Proteomics ","pi":[{"name":"Neil Kelleher","email":"n-kelleher@northwestern.edu","institution":"Northwestern University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0f0a27ee924b4041bb7a5420daf06049","id":"2988"}, {"dataset":"MSV000093990","datasetNum":"93990","title":"EDC-3 and EDC-4 Regulate Embryonic mRNA Clearance and Biomolecular Condensate Specialization","user":"adarshmayank","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706899945000","created":"Feb. 2, 2024, 10:52 AM","description":"Animal development is dictated by the selective and timely decay of mRNAs in developmental transitions. The implication of mRNA decapping scaffold proteins in these processes was unknown. This study delineates the roles and interactions of the DCAP-2 decapping scaffolds EDC-3 and EDC-4 in the embryonic development of C. elegans. EDC-3 facilitates the timely removal of specific embryonic mRNAs, including ifet-1, car-1, and cgh-1, reducing their expression, and preventing excessive accumulation of DCAP-2 condensates in somatic cells. We further uncover a novel role for EDC-3 in defining the biochemical boundaries between P-bodies, P-granules, and stress granules. Lastly, we show that EDC-4 counteracts EDC-3 and mediates the assembly of DCAP-2 with the GID (CTLH) complex, a ubiquitin ligase involved in maternal-to-zygotic transition (MZT). Our findings refine a model wherein multiple RNA decay mechanisms temporally partake in the clearance of maternal and zygotic mRNAs throughout embryonic development.","fileCount":"19","fileSizeKB":"14811302","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Decapping, P bodies, DCAP-2, EDC-3, EDC-4","pi":[{"name":"Thomas F Duchaine","email":"thomas.duchaine@mcgill.ca","institution":"Department of Biochemistry, McGill University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"90001e5a1d0a4451af02433c1dd2c3aa","id":"2989"}, {"dataset":"MSV000093982","datasetNum":"93982","title":"Delineating Bovine Milk Derived Microvesicles from Exosomes Using Proteomics","user":"AndrewCouse","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706886902000","created":"Feb. 2, 2024, 7:15 AM","description":"This is a dataset for a publication in revision for the Journal of Proteome Research titled \"Delineating Bovine Milk Derived Microvesicles from Exosomes Using Proteomics\". The paper explores the extracellular vesicle proteomics of bovine milk treated with a serial ultracentrifugation method that partially separates differently sized particles. We used a clustering method to group proteins with corresponding categories of particles.","fileCount":"90","fileSizeKB":"34378446","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bos taurus (NCBITaxon:9913)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"exosome;microvesicle;extracellular vesicle;bovine;milk;proteomics;ultracentrifugation","pi":[{"name":"David Clemmer","email":"clemmer@indiana.edu","institution":"IU Bloomington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049121","task":"690313bdc3cb484d9634a736f51cc658","id":"2990"}, {"dataset":"MSV000093980","datasetNum":"93980","title":"Casanovo de novo peptide sequencing immunopeptidomics, metaproteomics and dark proteome","user":"melihyilmaz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706860734000","created":"Feb. 1, 2024, 11:58 PM","description":"Predicted peptides for the immunopeptidomics, metaproteomics and dark proteome samples described in Yilmaz et al. [Yilmaz2023]. FTP directory contains mzTab outputs for Casanovo for these 3 datasets. [Yilmaz2023] M. Yilmaz*, W. Fondrie*, W. Bittremieux*, R. Nelson, V. Ananth, S. Oh, and W. Noble,\"Sequence-to-sequence translation from mass spectra to peptides with a transformer model\", bioRxiv, 2023","fileCount":"10","fileSizeKB":"1756636","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Various species in metaproteomics samples","instrument":"various instruments","modification":"UNIMOD:1 - \\\\\\\"Acetylation.\\\\\\\" | UNIMOD:4 - \\\\\\\"Iodoacetamide derivative.\\\\\\\" | UNIMOD:5 - \\\\\\\"Carbamylation.\\\\\\\" | UNIMOD:7 - \\\\\\\"Deamidation.\\\\\\\" | UNIMOD:35 - \\\\\\\"Oxidation or Hydroxylation.\\\\\\\" | UNIMOD:385 - \\\\\\\"Loss of ammonia.\\\\\\\"","keywords":"de novo;immunopeptidomics;metaproteomics;dark proteome","pi":[{"name":"William Noble","email":"wnoble@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f32b15e0be7e4fd38f5ee4e2eda80572","id":"2991"}, {"dataset":"MSV000093975","datasetNum":"93975","title":"Metaproteomic study about diet-induced effects on the gut microbiota of patients affected by Crohn's disease","user":"slevimo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706784533000","created":"Feb. 1, 2024, 2:48 AM","description":"Metaproteomic study on fecal samples collected from Crohn's Disease (CD) patients and some Household Healthy Controls (HHC) during an eight week Lof Fat\/High fiber diet intervention. Stoo sampling was performed at baseline (V1), week 8 (V2) and week 36 (V3). Protein Identification and quantitation was performed by MetaLab 2.3 (MaxQuant).","fileCount":"377","fileSizeKB":"806849537","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"bacteria;Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"Metaproteomics;Crohn's Disease","pi":[{"name":"Stefano Levi Mortera","email":"stefano.levimortera@opbg.net","institution":"Bambino Gesu Children Hospital","country":"Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD049076","task":"3c3c2ff0472d45d8aabd86337650336a","id":"2992"}, {"dataset":"MSV000093974","datasetNum":"93974","title":"GNPS - WVSU_MitragynaSpeciosaProjectBBRL","user":"Djaedy","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706766758000","created":"Jan. 31, 2024, 9:52 PM","description":"Mitragyna speciosa leaves were extracted with Methanol and subjected to further analysis.","fileCount":"256","fileSizeKB":"7693819","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mitragyna speciosa (NCBITaxon:170351)","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Kratom, Mitragyna","pi":[{"name":"Maria Karmella Apaya","email":"makarmella.apaya@wvsu.edu.ph","institution":"West Visayas State University","country":"Philippines"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9377a2524b494221a5aa63a01d180ae5","id":"2993"}, {"dataset":"MSV000093973","datasetNum":"93973","title":"GnRH Induces Citrullination of the Cytoskeleton in Murine Gonadotrope Cells","user":"equigle2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706753018000","created":"Jan. 31, 2024, 6:03 PM","description":"Abstract: Peptidylarginine deiminases (PADs or PADIs) catalyze the conversion of positively charged arginine to neutral citrulline, which alters target protein structure and function. It is well established that a gonadotropin releasing hormone agonist (GnRHa) stimulates PAD2-catalyzed histone citrullination to epigenetically regulate gonadotropin gene expression in the gonadotrope derived LBT2 cell line. However, PADs are also found in the cytoplasm. Given this, we used mass spectrometry to identify additional non-histone proteins that are citrullinated following GnRHa stimulation and characterize the temporal dynamics of this modification. Our results show that actin and tubulin are rapidly citrullinated, which led us to hypothesize that GnRHa might induce their citrullination to modulate cytoskeletal dynamics and architecture. Data shows that 10 nM GnRHa induces citrullination of beta-actin with maximal levels occurring at 10 minutes. The level of beta-actin citrullination is reduced in the presence of the pan-PAD inhibitor bi-phenyl-benzimidazole-Cl-amidine (BB-ClA), which also prevents GnRHa induced actin reorganization in dispersed mouse gonadotrope cells. GnRHa induces citrullination of beta-tubulin with elevated levels occurring at 30 minutes; similarly to beta-actin, this response is attenuated in the presence of BB-ClA. To examine the functional consequence of beta-tubulin citrullination, we utilized fluorescently tagged end binding protein 1 (EB1-GFP) to track the growing plus end of microtubules (MT) in real time in transfected LBT2 cells. Time-lapse confocal microscopy of EB1-GFP reveals that MT average lifetime increases following 30 minutes of GnRHa treatment, but this increase is attenuated by PAD inhibition. Taken together, our data suggest that GnRHa induced citrullination alters actin reorganization and MT lifetime in gonadotrope cells. \nKeywords: gonadotrope, peptidylarginine deiminase, citrullination, cytoskeleton, beta tubulin, beta actin, microtubules\n","fileCount":"28","fileSizeKB":"6754188","spectra":"0","psms":"128742","peptides":"26060","variants":"30450","proteins":"3630","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"MOD:00219 - \\\"A protein modification that effectively converts an L-arginine residue to L-citrulline.\\\"","keywords":"gonadotrope, peptidylarginine deiminase, citrullination, cytoskeleton, beta tubulin, beta actin, microtubules","pi":[{"name":"Brian D Cherrington","email":"bdcherrin@uwyo.edu","institution":"University of Wyoming","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD049056","task":"9423c22e55314eeb8c1887ca542f249a","id":"2994"}, {"dataset":"MSV000093959","datasetNum":"93959","title":"ASK1 and CUL1 proximity labelling","user":"chrisfm","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706725121000","created":"Jan. 31, 2024, 10:18 AM","description":"Arabidopsis thaliana ASK1 (SKP1) and CUL1 interactome, using plants expressing ASK1-TurboID and CUL1-NTD-TurboID for proximity labeling. 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For detailed information on data acquisition, please refer to the original publication by Fossati et al. (PXD025671). In brief, for spectral library generation 500 ng for each fraction were acquired using DDA PASEF on the timsTOF Pro (Bruker Daltonik, Germany).\n\nIndividual spectrum peak files were searched against a combined human-Mtb database encompassing the *Mycobacterium Tuberculosis* proteome (4,081 entries, downloaded from Uniprot on 12\/02\/2021) and Homo Sapiens proteome (20,397 entries, downloaded on 07\/01\/2021). The number of missed cleavages was fixed to 2, using cysteine carbamidomethylation as fixed modification, and N-terminal acetylation and methionine oxidation as variable modifications. The search results were rescored by integrating Prosit's fragment ion intensity predictions, using Oktoberfest version 0.5.3 (https:\/\/github.com\/wilhelm-lab\/oktoberfest).\n\nPSM rescoring of the samples cleaved with AspN, GluC, and trypsin resulted in 1.5-fold, 1.7-fold, and 1.4-fold increases in unique identified peptides, respectively.","fileCount":"53","fileSizeKB":"1082126","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mycobacterium tuberculosis (NCBITaxon:1773)","instrument":"timsTOF Pro","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"timsTOF;Prosit;Multiple proteases","pi":[{"name":"Kurt Boonen","email":"kurt.boonen@uantwerpen.be","institution":"University of Antwerp","country":"Belgium"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD049004","task":"06e103c793aa4faeb467efa59d2200c1","id":"2996"}, {"dataset":"MSV000093951","datasetNum":"93951","title":"GNPS - AH metabolites\/zinc chelators associated with POAG identified by GC-MS-based metabolomic analysis","user":"chistyakof","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706605482000","created":"Jan. 30, 2024, 1:04 AM","description":"AH metabolites\/zinc chelators associated with POAG identified by GC-MS-based metabolomic analysis.\r\nMethanol\/chloroform extraction, derivatization - methoxylamine hydrochloride and of N,O-Bis(trimethylsilyl)trifluoroacetamide \r\n","fileCount":"61","fileSizeKB":"1036147","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"GCMS-QP2020","modification":"-","keywords":"GCMS;Aqueous humor;human;Primary open-angle glaucoma","pi":[{"name":"Dmitry Chistyakov","email":"chistyakof@gmail.com","institution":"MSU","country":"Russia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f519ac63bd794e289970fd1afb556217","id":"2997"}, {"dataset":"MSV000093950","datasetNum":"93950","title":"Wu Myocarditis iPSC label-free proteomics","user":"acaudal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706605135000","created":"Jan. 30, 2024, 12:58 AM","description":"Shotgun proteomics from human iPSC with specified treatment groups. 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However, the specific identity and health impact of LGG-dependent metabolites remain poorly understood. This study aims to investigate the host-LGG-tryptophan interaction by analyzing feces and serum from LGG mono-associated GF mice fed trp-sufficient or trp-free diets.","fileCount":"161","fileSizeKB":"31306971","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"germ-free mice;serum;feces;metabolites;Lactobacillus rhamnosus GG;Tryptophan","pi":[{"name":"Nan Gao","email":"ngao@newark.rutgers.edu","institution":"Rutgers University, Newark","country":"USA"},{"name":"Ronaldo Ferraris ","email":"ferraris@njms.rutgers.edu","institution":"New Jersey Medical School, Rutgers University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e09494c29aff4107aed17a94431ff2c5","id":"2999"}, {"dataset":"MSV000093930","datasetNum":"93930","title":"GNPS - The effet of siderophore on plant microbiome","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706282766000","created":"Jan. 26, 2024, 7:26 AM","description":"Plant extracts, with Syncom members and Pseudomonas mutant","fileCount":"27","fileSizeKB":"3905413","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Plant Microbiome;siderophore","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4d1c03fae6e143cbb66aee601df1e4c9","id":"3000"}, {"dataset":"MSV000093928","datasetNum":"93928","title":"Acetamiprid effect on queens and emerging bees","user":"arachnid","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706272141000","created":"Jan. 26, 2024, 4:29 AM","description":"We continuously exposed honey bee colonies to sublethal acetamiprid doses (20 ug\/L) under isolated conditions. After one month of exposure, the emerging bees and queens were collected and analyzed via high-throughput proteomics. The following treatment groups were established: i) a control without acetamiprid and ii) an acetamiprid-exposed group, in which the sugar solution was supplemented with acetamiprid to a final concentration of 20 ug\/L. Six emerging bees were analyzed per colony. Each queen homogenate was processed three times for proteomic analysis. The data were acquired using the Data Independent Acquisition (DIA) method with an MS1 scan covering the range 390-1000 m\/z at 120 K resolution (at 200 m\/z), and the AGC target was set to 250%. and maximum injection time in Auto mode. DIA windows covered the range 390-1000 m\/z in a total of 19 scans with 1 Da overlap and variable window width , Orbitrap resolution set to 30000, AGC target set to 1000% and maximum injection time in auto mode. Fragmentation was performed by HCD with a normalized collision energy of 30. ","fileCount":"56","fileSizeKB":"59046864","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";Oxidation (M);acetylation (N-term)","keywords":"honey bee;acetamiprid","pi":[{"name":"Tomas Erban","email":"arachnid@centrum.cz","institution":"Crop Research Institute","country":"Czechia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4fb11e802f2d43fc88dd2e0881a7b56e","id":"3001"}, {"dataset":"MSV000093927","datasetNum":"93927","title":"GNPS Mara1 Heterologous expression in S. albidoflavus J1074","user":"matmal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706271093000","created":"Jan. 26, 2024, 4:11 AM","description":"Heterologous expression of Mara1 in S. ablidoflavus J1074. Mara1 is from S. mirabilis P8-A2","fileCount":"88","fileSizeKB":"36890","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces albidoflavus (NCBITaxon:1886)","instrument":"6545 Q-TOF LC\\\/MS","modification":"n.a.","keywords":"Heterologous expression;Mara1;isoquinolinequinone terpenoid","pi":[{"name":"Karl Tilmann Weber","email":"tiwe@bioustain.dtu.dk","institution":"DTU","country":"Denmark"},{"name":"Ling Ding","email":"lidi@dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"9e4ce9102ce9466c9cceb9d587614ec1","id":"3002"}, {"dataset":"MSV000093926","datasetNum":"93926","title":"GNPS - A metabolomics perspective on clorobiocin biosynthesis: discovery of bromobiocin and novel derivatives through LC-MSE-based molecular networking","user":"NiklasJanzing","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706257307000","created":"Jan. 26, 2024, 12:21 AM","description":"Streptomyces roseochromogenes DS 12.976 was cultivated in DSMZ 65 medium. Clorobiocin and structural analogs were extracted from the supernatant and analyzed via LC-MSE. RAW Files were used to generate Figures 2 and 7.","fileCount":"54","fileSizeKB":"513062","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces roseochromogenes (NCBITaxon:67357)","instrument":"Vion IMS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Clorobiocin;metabolomics;specialized metabolites","pi":[{"name":"Julia Bandow","email":"julia.bandow@rub.de","institution":"Ruhr University Bochum - Applied Microbiology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ad1cbbf68574430db45540fc15b5636e","id":"3003"}, {"dataset":"MSV000093925","datasetNum":"93925","title":"Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706250859000","created":"Jan. 25, 2024, 10:34 PM","description":"Existing spatially-resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (Microdroplet Processing in One pot for Trace Samples), multiplexed isobaric labelling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram level of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5,000 unique proteins from a small-sized human pancreatic tissue pixel (~60,000 um2) and differentiate unique protein abundance patterns in pancreas. Further, the use of microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.","fileCount":"128","fileSizeKB":"57100074","spectra":"1067092","psms":"1174663","peptides":"760960","variants":"835590","proteins":"101020","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"spatial proteomics;pancreas;islet","pi":[{"name":"Paul D. Piehowski","email":"paul.piehowski@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048911","task":"7f8aaee7a96b410eabe00c3bbf3ec35b","id":"3004"}, {"dataset":"MSV000093924","datasetNum":"93924","title":"Deep peatland microbial community dynamics and organic matter priming in response to labile carbon additions","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706221851000","created":"Jan. 25, 2024, 2:30 PM","description":"Soil samples incubated with and without labeled\/unlabeled glucose. Samples were run by LC MS\/MS (21T), GC MS and 12T FTICR MS.","fileCount":"293","fileSizeKB":"48130737","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:48479)","instrument":"LTQ Orbitrap Velos Pro;Q Exactive GC Orbitrap;Agilent 7890A GC coupled to a 5975C inert XL MSD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"glucose;labile;metabolomics","pi":[{"name":"Malak Tfaily","email":"tfaily@arizona.edu","institution":"University of Arizona","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3328e63f2bb5475b8d73c9b02064a253","id":"3005"}, {"dataset":"MSV000093919","datasetNum":"93919","title":"GNPS - Variation of terpene alkaloids in Daphniphyllum macropodum across plants and tissues","user":"trl1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706171943000","created":"Jan. 25, 2024, 12:39 AM","description":"Daphniphyllum macropodum produces alkaloids that are structurally complex with polycyclic, stereochemically rich carbon skeletons. Understanding these compounds are formed by the plant may enable exploration of their biological function and bioactivities.We employed multiple metabolomics techniques, including a workflow to annotate compounds in the absence of standards, to compare alkaloid content across plants and tissues. Different alkaloid structural types were found to have distinct distributions between genotypes, between tissues and within tissues. Alkaloid structural types also showed different isotope labelling enrichments that matched their biosynthetic relationships. The work suggests that mevalonate derived 30-carbon alkaloids are formed in the phloem region prior to their conversion to 22-carbon alkaloids which accumulate in the epidermis, and sets the stage for further investigation into the biosynthetic pathway.\r\n","fileCount":"15","fileSizeKB":"52412258","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Daphniphyllum macropodum (NCBITaxon:276776)","instrument":"MALDI SYNAPT G2-Si","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Daphniphyllum;Alkaloids","pi":[{"name":"Benjamin Lichman","email":"benjamin.lichman@york.ac.uk","institution":"University of York","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"429e254911d7462da26f068105df2162","id":"3006"}, {"dataset":"MSV000093917","datasetNum":"93917","title":"Cardiac Hypertensive-Cmpd17b (therapeutic) - Cell treatment proteomics","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706146120000","created":"Jan. 24, 2024, 5:28 PM","description":"Formyl peptide receptors (FPR) play a critical role in the regulation of resolution of inflammation, an important mediator of hypertension-induced cardiac damage. We have previously discovered an FPR small-molecule prototype Cmpd17b exhibit cardioprotective effects against acute and severe cardiac inflammatory insults, but its impact on chronic cardiac inflammatory insult, such as hypertension, has not been explored. To investigate the therapeutic potential of our FPR agonist on mean arterial pressure (MAP), cardiac remodelling and function in hypertensive mice. This dataset relates to cardiac fibroblasts (human) and smooth muscle aortic cells (SMAC) cell proteome remodelling following Ang-II and Cmp17b treatment","fileCount":"22","fileSizeKB":"17560022","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Cardiac Hypertension, angiotensin, Cmpd17b, therapeutic, proteomics","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"03b864da9a754f8b84ad98f6f8da4cd6","id":"3007"}, {"dataset":"MSV000093916","datasetNum":"93916","title":"FGFR inhibition blocks NF-kappaB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma","user":"whaas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706135012000","created":"Jan. 24, 2024, 2:23 PM","description":"This study explored the response to FGFR inhibition in FGFR2-fusion+ intrahepatic cholangiocarcinoma. We conducted phosphoproteomics experiments in a patient-derived FGFR2-driven ICC cell line model upon FGFR inhibition. Samples were treated with the FGFR inhibitor, Futibatinib\/TAS120 (75 nM) for 4 or 24 hours or with DMSO vehicle.\n\nThe experiments were done using an Orbitrap Fusion Lumos mass spectrometer. Multiplexing was achieved using either TMT10\/11 reagents and the SPS-MS3 method. Basic pH reversed-phase chromatography (bRPLC) was used for off-line pre-fractionation; 12 fractions were analyzed for proteome mappings (PMID: 26700037) and 24 fractions plus a phosphotyrosine-enriched sample for phosphoproteome mappings (PMID: 31606085). Phosphoproteome mappings were done using both HCD fragmentation with Orbitrap fragment ion detection and CID fragmentation with ion trap fragment ion detection (PMID: 29487189, PMID: 31606085).\n\nLabeling scheme:\n126: DMSO-1, ICC13-7 cells were treated with DMSO, replicate 1\n127n: Futibatinib(TAS120)-4h-1, ICC13-7 cells were treated with Futibatinib (TAS120) for 4h, replicate 1\n127c: Futibatinib(TAS120)-24h-1, ICC13-7 cells were treated with Futibatinib (TAS120) for 24h, replicate 1\n128n: DMSO-2, ICC13-7 cells were treated with DMSO, replicate 2\n128c: Futibatinib(TAS120)-4h-2, ICC13-7 cells were treated with Futibatinib (TAS120) for 4h, replicate 2\n129n: Futibatinib(TAS120)-24h-2, ICC13-7 cells were treated with Futibatinib (TAS120) for 24h, replicate 2\n","fileCount":"26","fileSizeKB":"26107029","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"229.162932 (TMT10\\\/11), lysine, N-terminus, static;57.02146374 (IAA), cysteine, static;79.966331 (phosphorylation) serine, threonine, tyrosine, variable;15.9949146221 (oxidation), methionine, variable","keywords":"phosphoproteomics, cancer, cholangiocarcinoma, metabolism, FGFR, FGFR2 inhibitor, TMT11, Orbitrap Fusion Lumos","pi":[{"name":"Nabeel Bardeesy","email":"bardeesy.nabeel@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School, Boston","country":"USA"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"598187e239be46e3bfd7a26dc64a7a49","id":"3008"}, {"dataset":"MSV000093915","datasetNum":"93915","title":"Large-scale map of RNA binding protein interactomes across the mRNA life-cycle","user":"mj2794","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706134355000","created":"Jan. 24, 2024, 2:12 PM","description":"mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map across the mRNA life cycle in human cells by immunopurification-mass spectrometry (IP-MS) of ?100 endogenous RBPs with and without RNase, augmented by size exclusion chromatography-mass spectrometry (SEC-MS). We identify 8,742 known and 20,802 unreported interactions between 1,125 proteins and determine that 73% of the IP-MS-identified interactions are RNA regulated. Our interactome links many proteins, some with unknown functions, to specific mRNA life-cycle stages, with nearly half associated with multiple stages. We demonstrate the value of this resource by characterizing the splicing and export functions of enhancer of rudimentary homolog (ERH), and by showing that small nuclear ribonucleoprotein U5 subunit 200 (SNRNP200) interacts with stress granule proteins and binds cytoplasmic RNA differently during stress.","fileCount":"747","fileSizeKB":"479517949","spectra":"8835721","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RNA binding protein;interactome;RNA-dependent;IP-MS;SEC-MS","pi":[{"name":"Marko Jovanovic","email":"mj2794@columbia.edu","institution":"Columbia University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"66dc6dc681d54a56b030fcd95fbdb975","id":"3009"}, {"dataset":"MSV000093914","datasetNum":"93914","title":"Inhibition of RNA splicing triggers CHMP7 nuclear entry, impacting TDP-43 function and leading to the onset of ALS cellular phenotypes","user":"mj2794","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706129821000","created":"Jan. 24, 2024, 12:57 PM","description":"Amyotrophic lateral sclerosis (ALS) is linked to the reduction of certain nucleoporins in neurons. Increased nuclear localization of charged multivesicular body protein 7 (CHMP7), a protein involved in nuclear pore surveillance, has been identified as a key factor damaging nuclear pores and disrupting transport. Using CRISPR-based microRaft, followed by gRNA identification (CRaft-ID), we discovered 55 RNA-binding proteins (RBPs) that influence CHMP7 localization, including SmD1, a survival of motor neuron (SMN) complex component. Immunoprecipitation-mass spectrometry (IP-MS) and enhanced crosslinking and immunoprecipitation (CLIP) analyses revealed CHMP7\u2019s interactions with SmD1, small nuclear RNAs, and splicing factor mRNAs in motor neurons (MNs). ALS induced pluripotent stem cell (iPSC)-MNs show reduced SmD1 expression, and inhibiting SmD1\/SMN complex increased CHMP7 nuclear localization. Crucially, overexpressing SmD1 in ALS iPSC-MNs restored CHMP7\u2019s cytoplasmic localization and corrected STMN2 splicing. Our findings suggest that early ALS pathogenesis is driven by SMN complex dysregulation.","fileCount":"12","fileSizeKB":"4600170","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"CHMP7;IP-MS;neurons","pi":[{"name":"Gene Yeo","email":"geneyeo@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"de66d0402b1340448d5e3f2ad5448667","id":"3010"}, {"dataset":"MSV000093913","datasetNum":"93913","title":"GNPS - Understanding the molecular mechanisms of drought tolerance in wild soybean (Glycine soja) through multi-omics-based alternative splicing predictions","user":"tilldawn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706118812000","created":"Jan. 24, 2024, 9:53 AM","description":"This work is managed by Pf Jae Yoon Kim from Kongju National University of South Korea.","fileCount":"35","fileSizeKB":"57225393","spectra":"0","psms":"36518","peptides":"22168","variants":"25692","proteins":"10905","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Glycine soja (NCBITaxon:3848)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"soy bean;drought","pi":[{"name":"Heeyoun Hwang","email":"heeyounh@kbsi.re.kr","institution":"Korea Basic Science Institute","country":"Rep of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048845","task":"c3abf66b0cf0439f80f171fe8a47810c","id":"3011"}, {"dataset":"MSV000093912","datasetNum":"93912","title":"Proteogenomics analysis to identify acquired resistance-specific alterations in melanoma PDXs on MAPKi therapy","user":"sbyrum","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706116807000","created":"Jan. 24, 2024, 9:20 AM","description":"Therapeutic approaches to treat melanoma include small molecule drugs that target activating protein mutations in pro-growth signaling pathways like the MAPK pathway. While beneficial to the approximately 50% of patients with activating BRAFV600 mutation, mono- and combination therapy with MAPK inhibitors is ultimately associated with acquired resistance. To better characterize the mechanisms of MAPK inhibitor resistance in melanoma, we utilize patient-derived xenografts and apply proteogenomic approaches leveraging genomic, transcriptomic, and proteomic technologies that permit the identification of resistance-specific alterations and therapeutic vulnerabilities. A specific challenge for proteogenomic applications comes at the level of data curation to enable multi-omics data integration. Here, we present a proteogenomic approach that uses custom curated databases to identify unique resistance-specific alternations in melanoma PDX models of acquired MAPK inhibitor resistance. We demonstrate this approach with a NRASQ61L melanoma PDX model from which resistant tumors were developed following treatment with a MEK inhibitor. Our multi-omics strategy addresses current challenges in bioinformatics by leveraging development of custom curated proteogenomics databases derived from individual resistant melanoma that evolves following MEK inhibitor treatment and is scalable to comprehensively characterize acquired MAPK inhibitor resistance across patient-specific models and genomic subtypes of melanoma. ","fileCount":"32","fileSizeKB":"26206318","spectra":"0","psms":"208886","peptides":"76926","variants":"109868","proteins":"25059","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"proteogenomics;melanoma;patient-derived xenograft","pi":[{"name":"Stephanie Byrum","email":"sbyrum@uams.edu","institution":"University of Arkansas for Medical Sciences","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD048843","task":"e0a24b0ba01d4ca2bf4e259133685272","id":"3012"}, {"dataset":"MSV000093910","datasetNum":"93910","title":"GNPS - Variation of terpene alkaloids in Daphniphyllum macropodum across plants and tissues","user":"trl1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706107959000","created":"Jan. 24, 2024, 6:52 AM","description":"Daphniphyllum macropodum produces alkaloids that are structurally complex with polycyclic, stereochemically rich carbon skeletons. Understanding these compounds are formed by the plant may enable exploration of their biological function and bioactivities. We employed multiple metabolomics techniques, including a workflow to annotate compounds in the absence of standards, to compare alkaloid content across plants and tissues. Different alkaloid structural types were found to have distinct distributions between genotypes, between tissues and within tissues. Alkaloid structural types also showed different isotope labelling enrichments that matched their biosynthetic relationships.The work suggests that mevalonate derived 30-carbon alkaloids are formed in the phloem region prior to their conversion to 22-carbon alkaloids which accumulate in the epidermis, and sets the stage for further investigation into the biosynthetic pathway.\n","fileCount":"1485","fileSizeKB":"36780367","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Daphniphyllum macropodum (NCBITaxon:276776)","instrument":"Orbitrap Fusion","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Alkaloids;Daphniphyllum","pi":[{"name":"Benjamin Lichman","email":"benjamin.lichman@york.ac.uk","institution":"University of York","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"cbb352a6ddcf4e109b29d0d90473bb0a","id":"3013"}, {"dataset":"MSV000093905","datasetNum":"93905","title":"Quantitative Proteomics of axon regeneration promoted by Gangliosides and MTOR-Activating Small Molecules","user":"sbhattacharya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1706039979000","created":"Jan. 23, 2024, 11:59 AM","description":"The ability to regenerate damaged central nervous system (CNS) axons of existing neurons is a significant challenge in treating conditions of neurodegenerative disorders such as glaucoma. To achieve neuroregeneration, we evaluated small molecules to target the MTOR pathway for axonal growth. In this study, 3-month-old C57BL\/6J mice with equal gender distribution, a total of 2 lipid gangliosides and 4 small molecules were used. These are vehicle only, GM1, GM3, V0-Ophic, 3BDO, and Rapamycin.\nFor each mouse, optic nerve crush was performed in one eye. At 2 days post injury, the same eye had an intravitreal injection of one or a combination of the small molecules noted above. Two days before euthanasia (Day 12), fluorophore 488 coupled cholera toxin B (CTB-488) was injected intravitreally for axonal imaging at endpoints. After animals were euthanized, optic nerves were collected by dissection. Three identical biological replicates for each treatment group (that were not injected with CTB-488) were analyzed by mass spectrometry. \nProtein extraction was carried out by homogenization of the tissue in extraction buffer (Triethylammonium bicarbonate buffer, Sodium Chloride and Sodium dodecyl sulfate). Protein amounts were estimated and normalized across experimental samples via densitometry. Samples were reduced using Tris(2-carboxyethyl) phosphine hydrochloride, alkylated with iodoacetamide, and digested overnight with trypsin. TMT (Tandem Mass Tag) labelling was carried out using 3 sets of 13 tags from a 16plex TMT kit for quantification. Samples were combined, dried, and fractionated. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10.\nRaw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The mouse proteome was downloaded from UniProt and used as the target database for protein identification. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. The Normalization was set to total peptide amount and confidence to low.","fileCount":"98","fileSizeKB":"129251572","spectra":"0","psms":"50494","peptides":"34801","variants":"36396","proteins":"17664","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Axon Regeneration, Quantitative Proteomics, TMT labeled, Mouse, Optic Nerve","pi":[{"name":"Sanjoy Bhattacharya","email":"sbhattacharya@med.miami.edu","institution":"University of Miami","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048812","task":"fdbad334983d4a5f9107fad8d6484c4b","id":"3014"}, {"dataset":"MSV000093903","datasetNum":"93903","title":"Phosphoproteomic Analysis of PCB126 Impact on the Mouse Chronic-Binge Alcohol Feeding Model","user":"mmerchant","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705955293000","created":"Jan. 22, 2024, 12:28 PM","description":"Environmental pollutants, including polychlorinated biphenyls (PCBs) have been implicated in the pathogenesis of liver disease. To better understand how PCB126 promoted alcohol-associated liver disease (ALD) in our previous model, the current study utilized a phosphoproteomic approach for hypothesis generation regarding mechanisms of action. Briefly, male C57B\/6J mice were exposed to 0.2 mg\/kg polychlorinated biphenyl PCB126 or corn oil vehicle prior to ethanol (EtOH) or control diet feeding in the chronic-binge alcohol feeding model. Liver tissues were harvested during euthanasia and tissue collection, snap frozen in liquid nitrogen, and then were archived in a -80C freezer. For phosphoproteome analysis, six random liver tissues from four groups (N=24) were homogenized in 2% sodium dodecyl sulfate (SDS) radioimmunoprecipitation (RIPA) buffer with 1X HALT protease and phosphatase inhibitors. Lysates were trypsinized at a 1:20 (enzyme:sample) ratio and prepared following ProtiFi S-Trap mini spin column digestion protocol. Phospho-peptides were enriched with MagReSyn titanium ion - immobilized metal affinity chromatography (Ti-IMAC) microparticles following ReSyn Biosciences MagReSyn Ti-IMAC protocol. Samples were then purified using C18 PROTO 300 A Ultra MicroSpin columns, dried under a SpeedVac, and stored at -80C prior to peptide concentration assessment. Digests were fractionated by UPLC nanoflow liquid chromatography using PepMap RSLC C18 EASY-spray separating column at 40C with a 90-minute linear gradient. Eluates were introduced into an Exploris480 using an EASY-spray source (320C and 1.8kV). Full MS-ddMS2 method with a 3 second cycle time was generated in Xcalibur (v4.5.445.18) operating in positive polarity. RAW data files were separately searched in PeaksXpro (Bioinformatics Solutions Inc.; Waterloo, ON, Canada) using Denovo, PeaksDB, and PeaksPTM algorithms against the UniprotKB Mus musculus canonical protein sequences (proteomics ID: UP000000589) downloaded March 17, 2023. Label Free Quantification algorithm was then used with PeaksPTM results utilizing a mass error tolerance of 10 ppm and retention time shift tolerance of 6-minutes. Peptides were accepted at a 1% FDR threshold for consideration by the Label Free Quantification algorithm.","fileCount":"99","fileSizeKB":"34402150","spectra":"0","psms":"510593","peptides":"215571","variants":"262212","proteins":"27269","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"Orbitrap Exploris 480","modification":"MOD:00048 - \\\"A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine.\\\";MOD:00047 - \\\"A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine.\\\";MOD:00046 - \\\"A protein modification that effectively converts an L-serine residue to O-phospho-L-serine.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"liver;PCB;binge ethanol;chronic ethanol","pi":[{"name":"Timothy D. Cummins, PhD","email":"timothy.cummins@louisville.edu","institution":"University of Louisville","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048773","task":"cd69bec636234fa5b16c88146a941cbd","id":"3015"}, {"dataset":"MSV000093902","datasetNum":"93902","title":"leA nonenzymatic dependency on inositol-requiring enzyme 1 controls cancer cell cycle progression and tumor growth","user":"mnchoi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705953417000","created":"Jan. 22, 2024, 11:56 AM","description":"Endoplasmic-reticulum resident inositol-requiring enzyme 1alpha(IRE1) supports protein homeostasis via a cytoplasmic kinase-RNase module. Known cancer dependency on IRE1 entails its enzymatic activation of the transcription factor XBP1s and of RNA decay. We discovered that some cancer cells require IRE1 but not its enzymatic activity. IRE1 knockdown, but not enzymatic inhibition or XBP1 disruption, increased DNA damage and chromosome instability while engaging the TP53 pathway and cyclin-dependent kinase inhibitors, and attenuated cell cycle progression. IRE1 depletion downregulated factors involved in chromosome replication and segregation and in chromatin remodeling. Immunoelectron microscopy indicated that endogenous IRE1 can localize to the nuclear envelope. Thus, cancer cells can require IRE1 either enzymatically or nonenzymatically, with significant implications for IRE1's biological role and therapeutic targeting.","fileCount":"36","fileSizeKB":"39671888","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"DIA;IRE1;XBP1","pi":[{"name":"Avi Ashkenazi","email":"aa@gene.com","institution":"Genentech, Inc.","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"4c3580f6d32644e582bb3afa2a70a83d","id":"3016"}, {"dataset":"MSV000093899","datasetNum":"93899","title":"The development of a high-throughput kinase activity platform using nanoLC-MS\/MS with DIA approach for studying the anticancer mechanism of Taxol in ovarian cancer","user":"cjchen_01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705910235000","created":"Jan. 21, 2024, 11:57 PM","description":"Protein phosphorylation, a process mediated by protein kinases, plays a pivotal role in increasing protein diversity, thereby influencing various cellular functions. Peptide substrates have been employed for in vitro phosphorylation experiments using purified kinases or cell lysates. In this study, we have developed a quantitative, high-throughput platform for assessing multikinase activity, based on nanoLC-MS\/MS with data-independent acquisition (DIA) approach. This platform was evaluated by studying the kinase activity of Taxol- treated SKOV3 cells. A library containing 38 peptide substrates was designed and analyzed to indicate the activity of major kinases in cancer development. ","fileCount":"1143","fileSizeKB":"24429760","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"maXis II","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Kinase assay; Mass spectrometry; Data independent acquisition; Taxol","pi":[{"name":"Chao-Jung Chen","email":"cjchen@mail.cmu.edu.tw","institution":"Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 40402, Taiwan","country":"Taiwan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7eeaf9c2981c48e0afc111e3ea39d99e","id":"3017"}, {"dataset":"MSV000093898","datasetNum":"93898","title":"GNPS - Quinones identification standards analysis","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705834039000","created":"Jan. 21, 2024, 2:47 AM","description":"Non-targeted metabolomics of environmental samples ","fileCount":"121","fileSizeKB":"13889052","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:40903)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Quinones;Ferrihydrite-organic carbon","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fca31fca9a784302812b4bdc1caa8192","id":"3018"}, {"dataset":"MSV000093897","datasetNum":"93897","title":"PISA experiment 20 compounds test MIC concentrations 2","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705743418000","created":"Jan. 20, 2024, 1:36 AM","description":"Bacterial protein extracts inoculated with small molecules followed by thermal treatment ","fileCount":"159","fileSizeKB":"41986691","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"protein targets;antibiotics ","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9a6fa5f15a4d461ab349e9d121dfe3ec","id":"3019"}, {"dataset":"MSV000093895","datasetNum":"93895","title":"Comparative seed proteome profile reveals no alternation of major allergens of high yielding mung bean cultivars","user":"naproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705707742000","created":"Jan. 19, 2024, 3:42 PM","description":"Mung bean contains up to 25% of the protein, is one of the great sources of plant-based protein. Since many allergens also function as defense-related proteins, it is important to determine their abundance level in the high-yielding disease-resistant cultivars. In this study, for the first time, we compared the seed proteome of disease-resistant high-yielding mung bean cultivars developed by conventional breeding approach. Using label-free quantitative proteomic platform, we successfully identified and quantified a total of 1373 proteins. Comparative analysis between the high-yielding disease-resistant cultivar (MC5) and other three cultivars showed a total of 69 proteins were significantly altered in abundance and overlapped across the cultivars. Subsequent bioinformatic analysis of these altered proteins demonstrated that PDF1 (a defensin-like protein) exhibited high sequence similarity and epitope matching with the established peanut allergens (Ara h 12 and 13), indicating a potential mung bean allergen. Conversely, known mung bean allergen proteins such as Vig r 2, Vig r 4, LTP1, PR2, beta-Conglycinin, and Glycinin G4 showed no alternation in the MC5 compared to other cultivars. Taken together, our findings suggest that the known allergen profiles may not be impacted by the conventional plant breeding method to develop improved mung bean cultivars.","fileCount":"16","fileSizeKB":"3662971","spectra":"0","psms":"83028","peptides":"6755","variants":"8670","proteins":"1373","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vigna radiata (NCBITaxon:157791)","instrument":"Q Exactive HF-X","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Allergens, Cultivar, Seed, quantitative proteomics, diseases resistance ","pi":[{"name":"Nagib Ahsan","email":"nahsan@ou.edu","institution":"University of Oklahoma","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"17bbe7a67d5a4738baf3f319c47327cc","id":"3020"}, {"dataset":"MSV000093894","datasetNum":"93894","title":"Veneer is a webtool for rapid, standardized, and transparent interpretation, annotation, and reporting of mammalian cell surface glycoprotein capture data","user":"rebekahgundry","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705697308000","created":"Jan. 19, 2024, 12:48 PM","description":"uCSC data of B cells with and without PNGaseF; 4 PNGaseF vendor injections","fileCount":"23","fileSizeKB":"20112259","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00565 - \\\"modification from UniMod N-linked glycosylation\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"PNGaseF, cell surface, Veneer","pi":[{"name":"Rebekah Gundry","email":"rebekah.gundry@unmc.edu","institution":"University of Nebraska Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b1d45c20ee2b4bcbad888d005b315cac","id":"3021"}, {"dataset":"MSV000093893","datasetNum":"93893","title":"Nontargeted plasma proteomics analysis uncovers candidate biomarkers for renal disease and pulmonary hypertension in patients with sickle cell disease","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705686849000","created":"Jan. 19, 2024, 9:54 AM","description":"Fifteen microliters of plasma from sickle cell disease patients, and pooled samples, were diluted with 5% deoxycholate and 10 mM DTT, followed by heating at 80 degC for 30 min, alkylation with 25 mM iodoacteamide and digestion with modified trypsin for 4 h at 37 degC. After acidification, samples were filtered. ~35 micrograms of each sample was separated by direction injection and microflow LC (1 mm x 100 mm Waters ACQUITY Premier; 100 uL\/min) using a gradient of 3-28% acetonrile, and MS\/MS was acquired on a Thermo Exploris 480 using a 120K MS1 scan and 30K MS2 with a staggered\/overlapping method. Data analysis used Spectronaut 17. Study pool QC data, and individual files used for statistical analysis, are described in the accompanying metadata. ","fileCount":"234","fileSizeKB":"347716144","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"data-independent acquisition;microflow","pi":[{"name":"Allison E. Ashley-Koch","email":"Allison.ashleykoch@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD048716","task":"0b67296390a74e73aa32c0624c15edd1","id":"3022"}, {"dataset":"MSV000093891","datasetNum":"93891","title":"Oxidative Cyclization Reagents Reveal Tryptophan Cation-pi interactions","user":"xiaoxie","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705647821000","created":"Jan. 18, 2024, 11:03 PM","description":"Raw data of the project \"Oxidative Cyclization Reagents Reveal Tryptophan Cation-pi interactions\"","fileCount":"33","fileSizeKB":"22188422","spectra":"451321","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"Trp labeling;MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\";MOD:00412 - \\\"modification from UniMod artifact. OBSOLETE because UniMod entry 19 is now merged with UniMod 35 remap to MOD:00425 'monohydroxylated residue'.\\\"","keywords":"Chemoproteomics;Tryptophan","pi":[{"name":"Christopher J. Chang","email":"chrischang@berkeley.edu","institution":"UC Berkeley","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ccd7e749ea6e41848c074f713443a8e6","id":"3023"}, {"dataset":"MSV000093890","datasetNum":"93890","title":"Mitochondrial respiration is a targetable vulnerability of endocrine persistence in ER+ breast cancer","user":"madamo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705615678000","created":"Jan. 18, 2024, 2:07 PM","description":"Despite adjuvant treatment with endocrine therapies, estrogen receptor-positive (ER+) breast cancers recur in a significant proportion of patients. Recurrences are attributable to clinically undetectable endocrine-tolerant persister cancer cells that retain tumor-forming potential. We observed that persistence occurred stochastically without genetic predisposition. Genome-wide screening in persisters revealed a survival mechanism involving metabolic reprogramming with reliance upon mitochondrial respiration. Proteomic profiling showed reduced levels of glycolytic proteins in persisters. Metabolic tracing of glucose revealed an energy-depleted state in persisters where oxidative phosphorylation was required to generate ATP. Persisters exhibiting residual proliferation in human breast tumors following neoadjuvant endocrine therapy showed increased mitochondrial content. Pharmacological inhibition of oxidative phosphorylation suppressed the tumor-forming potential of persisters and synergized with the anti-estrogen fulvestrant to induce regression of patient-derived xenografts, supporting therapeutic targeting of mitochondrial metabolism to help eradicate residual disease.","fileCount":"66","fileSizeKB":"11587864","spectra":"0","psms":"570790","peptides":"412338","variants":"465868","proteins":"19940","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"ER+;breast cancer;mitochondrial respiration;glycolysis;oxidative phosphorylation;fulvestrant;endocrine therapy","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"The Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048700","task":"5db808c4e1b44d09a4889c4df913dc83","id":"3024"}, {"dataset":"MSV000093887","datasetNum":"93887","title":"Inflammation primes the kidney for recovery by activating AZIN1 A-to-I editing ","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705593546000","created":"Jan. 18, 2024, 7:59 AM","description":"The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and Adenosine Deaminase isoform switching. We found that A-to-I editing of Antizyme Inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery. ","fileCount":"61","fileSizeKB":"17771446","spectra":"0","psms":"328454","peptides":"113219","variants":"158323","proteins":"21540","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"HEK293T;LC-MS\/MS","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD048688","task":"cdd8b8e9eee948cca470389bf7ec5aab","id":"3025"}, {"dataset":"MSV000093886","datasetNum":"93886","title":"GNPS - Charting the Cannabis plant chemical space with computational metabolomics","user":"kami_KAZE007","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705588802000","created":"Jan. 18, 2024, 6:40 AM","description":"Leaf and flower extracts of Cannabis strains Amnesia haze (80% C.sativa and 20% C.indica) and Royal dutch cheese (70% C.indica and 30% C.sativa).","fileCount":"64","fileSizeKB":"3906127","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cannabis (NCBITaxon:3482)","instrument":"LC-qToF-MS;LCMS-9030, Shimadzu ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cannabis, Medicinal, LC-MS\/MS, Metabolic map","pi":[{"name":"Fidele Tugizimana","email":"ftugizimana@uj.ac.za","institution":"University of Johannesburg","country":"South Africa"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"22b747e8cb0b4524be77680d51a8883c","id":"3026"}, {"dataset":"MSV000093885","datasetNum":"93885","title":"GNPS - Test SynCom strains interaction 211223","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705583691000","created":"Jan. 18, 2024, 5:14 AM","description":"Microbial Synthetic Community resembling the Nasal human microbiome","fileCount":"57","fileSizeKB":"9044479","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbial community;microbiota;microbial interactions","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2e210c381c65403cb2bacefb42901426","id":"3027"}, {"dataset":"MSV000093884","datasetNum":"93884","title":"GNPS - Metabolic engineering of Streptomyces peucetius for biosynthesis of N,N-dimethylated anthracyclines","user":"mbhulst","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705565394000","created":"Jan. 18, 2024, 12:09 AM","description":"Daunorubicin and doxorubicin, two anthracycline polyketides produced by Streptomyces peucetius, are potent anticancer agents that are widely used in chemotherapy, despite severe side effects. Recent advances have highlighted the potential of producing improved derivatives with reduced side effects by incorporating L-rhodosamine, the N,N-dimethyl analogue of the native amino sugar moiety. In this study, we aimed to produce N,N-dimethylated anthracyclines by engineering the doxorubicin biosynthetic pathway in the industrial S. peucetius strain GOO1. To achieve this, we introduced genes from the aclarubicin biosynthetic pathway encoding the sugar N-methyltransferases AclP and AknX2. Furthermore, the native gene for glycosyltransferase DnrS was replaced with genes encoding the aclarubicin glycosyltransferases AknS and AknT. Additionally, the gene for methylesterase RdmC from the rhodomycin biosynthetic pathway was introduced. A new host was engineered successfully, whereby genes from the aclarubicin pathway were introduced and expressed. LC-MS\/MS analysis of the engineered strains showed that dimethylated sugars were efficiently produced, and that these were incorporated ino the anthracycline biosynthetic pathway to produce the novel dimethylated anthracycline N,N-dimethyldaunorubicin. Further downstream tailoring steps catalysed by the cytochrome P450 monooxygenase DoxA exhibited limited efficacy with N,N-dimethylated substrates. This resulted in only low production levels of N,N-dimethyldaunorubicin and no N,N-dimethyldoxorubicin, most likely due to the low affinity of DoxA for dimethylated substrates. S. peucetius GOO1 was engineered such as to produce N,N-dimethylated sugars, which were incorporated into the biosynthetic pathway. This allowed the successful production of N,N-dimethyldaunorubicin, an anticancer drug with reduced cytotoxicity. DoxA is the key enzyme that determines the efficiency of the biosynthesis of N,N-dimethylated anthracyclines, and engineering of this enzyme will be a major step forwards towards the efficient production of more N,N-dimethylated anthracyclines, including N,N-dimethyldoxorubicin. This study provides valuable insights into the biosynthesis of clinically relevant daunorubicin derivatives, highlighting the importance of combinatorial biosynthesis.\r\n","fileCount":"26","fileSizeKB":"918092","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces peucetius (NCBITaxon:1950)","instrument":"LCMS-9030;ACQUITY RDa Detector","modification":"-","keywords":"doxorubicin;anthracyclines;anticancer;metabolic engineering;Streptomyces;biosynthesis","pi":[{"name":"Prof. Gilles van Wezel","email":"g.wezel@biology.leidenuniv.nl","institution":"Leiden University","country":"the Netherlands"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"19ea6d98d9964f9b831af1012401d762","id":"3028"}, {"dataset":"MSV000093878","datasetNum":"93878","title":"ESI-MS\/MS of ADP-ribosylated RNA to Identify Site of Modification","user":"cdoering","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705449775000","created":"Jan. 16, 2024, 4:02 PM","description":"Spectra from an ESI-MS\/MS experiment performed on in vitro model RNA substrates treated with CmdT, an RNA ADP-ribosyltransferase. Spectra were used to determine the site of RNA modification by CmdT.","fileCount":"5","fileSizeKB":"2","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive","modification":"UNIMOD:213 - \\\"ADP Ribose addition.\\\"","keywords":"phage defense;toxin-antitoxin systems;ADP-ribosyltransferase","pi":[{"name":"Michael Laub","email":"laub@mit.edu","institution":"Massachusetts Institute of Technology","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ea303fa117f843d7a1fc9ab913b02fe0","id":"3029"}, {"dataset":"MSV000093876","datasetNum":"93876","title":"Ho_BLM_TOP3A_RMI_BioID_P130_Velos_Elite","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705429444000","created":"Jan. 16, 2024, 10:24 AM","description":"This dataset consists of 25 raw MS files and associated peak lists and results files, acquired on a Thermo LTQ Velos Pro or Thermo Orbitrap Elite mass spectrometer operated in Data Dependent Acquisition mode. \nSamples were generated by Edith Cheng. Affinity purifications and mass spectrometry acquisition was performed by Wade Dunham. Analysis was performed by Jennifer Ho, Wade Dunham, Edith Cheng, Cassandra Wong, Anne-Claude Gingras, and Grant Brown. \nThe files are associated with a manuscript submitted for publication by Jung Jennifer Ho et al. The main goal of this paper was to profile the proximity interactome of BLM-TOP3A-RMI1-RMI2 (BTRR) complex to identify proteins that suppress recombination in DNA repair. This dataset identifies the importance of RAD54L2 for the recruitment of Bloom (BLM) helicase to promote non-crossover recombination. \nGrant W. Brown is the corresponding author of the manuscript (grant.brown@utoronto.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n","fileCount":"157","fileSizeKB":"52811730","spectra":"0","psms":"1093949","peptides":"126022","variants":"171894","proteins":"73264","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos;LTQ Orbitrap Elite","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BLM;TOP3A;RMI1;RMI2;BioID;Bloom helicase","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048612","task":"81a3b3a08fc04649910918ca417da2ee","id":"3030"}, {"dataset":"MSV000093875","datasetNum":"93875","title":"An XIC-centric approach for improved identification and quantification in proteomic data analyses","user":"zhengzhang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705427438000","created":"Jan. 16, 2024, 9:50 AM","description":"An XIC-centric approach for improved identification and quantification in proteomic data analyses","fileCount":"3","fileSizeKB":"3919080","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"XIC","pi":[{"name":"Guanghui Wang","email":"guanghui.wang@nist.gov","institution":"NIST","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"586329aeff2745deb52750093c296b35","id":"3031"}, {"dataset":"MSV000093873","datasetNum":"93873","title":"Toggling of BRD4 functions is triggered through its phosphorylation by JNK","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705423079000","created":"Jan. 16, 2024, 8:37 AM","description":"BRD4 is a key regulatory factor in multiple cancers and cellular stress responses with pleotropic functions. BRD4 regulates chromatin remodeling and transcription through its histone acetyltransferase (HAT) and kinase activities, respectively. The mechanism responsible for switching BRD4 from a chromatin to transcriptional regulator is currently unknown. Here, we report that in response to a broad range of stimuli, this switch is mediated by the JNK kinase which directly interacts with BRD4. JNK specifically phosphorylates human BRD4 at Ser1117, Thr1186 and Thr1212, triggering transient BRD4 release from chromatin. JNK phosphorylation of BRD4 halts its HAT-mediated chromatin regulation and activates its transcription-enhancing kinase function. BRD4 release from chromatin is necessary to toggle between its enzymatic activities: chromatin-bound BRD4 is kinase inactive and RNA Pol II-bound BRD4 does not acetylate chromatin. BRD4 release from chromatin augments its interaction with and phosphorylation of key transcriptional regulators RNA Pol II, PTEFb and c-MYC. The PP4 phosphatase dephosphorylates JNK phosphorylated BRD4 in the nucleoplasm, which promotes its interaction with RNA Pol II at transcriptionally active sites. Accordingly, JNK-mediated release of BRD4 from chromatin leads to significantly elevated transcription of BRD4-regulated immune and inflammatory response genes through enhanced BRD4-Pol II interaction at the promoters of these genes. JNK phosphorylation of BRD4 occurs during T-cell activation and is required for epithelial to mesenchymal transition (EMT) in prostate cancer cells. These findings thus characterize a novel mechanism that triggers the transition of BRD4 from a chromatin regulator to transcriptional activator during stress\/immune\/inflammatory responses and EMT. ","fileCount":"29","fileSizeKB":"18692623","spectra":"727728","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse;Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"BRD4, JNK, phospho-BRD4, Histone acetyltransferase, Kinase, Chromatin de-compaction, Transcription activation","pi":[{"name":"Dinah Singer","email":"dinah.singer@nih.gov","institution":"NCI\/NIH","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f20062510a60475b8ae27eae18e32d8f","id":"3032"}, {"dataset":"MSV000093872","datasetNum":"93872","title":"GNPS - HoloFish - Untargeted Metabolomics","user":"JacobAgerbo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705405816000","created":"Jan. 16, 2024, 3:50 AM","description":"Sample Collection\r\nSamples used for this study were obtained as part of the HoloFish project (Norwegian Seafood Research Fund, project no. 901436). This cohort has been described previously 19. Briefly, we sampled 460 ready-to-harvest Atlantic salmon from a commercial production site close to Bergen, Norway, owned by Leroy Seafood Group in April 2018. Samples were obtained from two groups reared in separate sea pens and fed two different standard commercial diets. These diets have been anonymised but were manufactured respectively by BioMar and EWOS in 2018.\r\n\r\n\r\n\r\nSix biological samples were taken from each fish, including muscle tissue for fatty acid profiling, gill tissue for host genomics, gut epithelia for host transcriptomics, gut epithelial cell scrapes for 16S metabarcoding and two gut content samples for metagenomics and metabolomics.\r\nApproximate 100 mg distal gut content for each individual was sampled for metabolomics. Gut content for metabolomics was preserved at -80 degrees Celsius. All the sampling tools and equipment used for each sample were sterile.\r\n\r\nExtraction\r\nGut content samples were cryo-homogenised in 25% water, 25% methanol and 50% dichloromethane in a 1:15 sample: solvent ratio (w:v). Homogenisation was carried out using an OMNI Bead Ruptor 24, using liquid nitrogen to keep homogenised samples below 0 degrees Celsius to minimise degradation of metabolites during extraction. Homogenates were centrifuged at 20,000 g (0 degrees Celsius) and the polar phase from all samples was concentrated using SpeedVac (ThermoFisher Scientific) and resuspended in 200 microL 5% methanol. Four procedural blanks were included in homogenisation. A volume of 100 microL of all samples was collected into a Quality Control sample used for normalisation to enhance the detection of metabolites.\r\n\r\nChromatography\r\nSamples were measured on a nano-flow ultra-high pressure liquid chromatography tandem high-resolution mass spectrometry analysis.\r\n\r\nMass spectrometry\r\nMetabolites were detected using a Q Exactive HF Hybrid Quadrupole-Orbitrap Mass Spectrometer (ThermoFisher Scientific) operated in positive ion data-dependent acquisition mode.\r\n\r\nData Transformation\r\nThermoFisher Scientific UHPLC-Orbitrap-MS\/MS RAW files were converted into mzML files using Proteo Wizard. For an increased deciphering of molecular spectres, MZmine2 was applied for mass detection of MS1 and MS2 spectres, followed by chromatogram detection and deconvolution. Subsequently, detected isotopes and features were grouped according to a tolerance of mass-charges (5 ppm for m\/z) and retention time (6 sec.) and the features were further aligned according to retention time and m\/z. Lastly, only features with an MS2 spectrum were kept for further substructural analysis and in silico analysis.\r\n","fileCount":"363","fileSizeKB":"14045699","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Salmo salar (NCBITaxon:8030)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomics;Gut microbiome;Atlantic salmon;Aquaculture","pi":[{"name":"Jacob Rasmussen","email":"jacob.rasmussen@bio.ku.dk","institution":"University of Copenhagen","country":"Denmark"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"6c85395e512540a1b0bf2822c6c6478d","id":"3033"}, {"dataset":"MSV000093870","datasetNum":"93870","title":"Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes","user":"apetelski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705358333000","created":"Jan. 15, 2024, 2:38 PM","description":"Single-cell proteomics analysis of human oocytes from both young and old women","fileCount":"77","fileSizeKB":"75267893","spectra":"1218934","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"NA","keywords":"single-cell;proteostasis;maternal age oocytes;aging","pi":[{"name":"Montserrat Barragan Monasterio","email":"mbarragan@eugin.es","institution":"Eugin Clinic","country":"Spain"},{"name":"Nikolai Slavov","email":"n.slavov@northeastern.edu","institution":"Northeastern University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1fef5b5d50874184aac8cf254a3654c0","id":"3034"}, {"dataset":"MSV000093869","datasetNum":"93869","title":"GNPS - KNU_NPClab-LCMS_2023_47peppers","user":"sych426","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705302410000","created":"Jan. 14, 2024, 11:06 PM","description":"KNU_NPClab-LCMS_2023_47peppers (white peppers, black peppers and a red pepper)","fileCount":"95","fileSizeKB":"8833127","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Piper nigrum (NCBITaxon:13216)","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Piper nigrum;peppers","pi":[{"name":"Heejung Yang","email":"heejyang@kangwon.ac.kr","institution":"Kangwon National University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5aa8237992b440d5a31ddebad70b4585","id":"3035"}, {"dataset":"MSV000093868","datasetNum":"93868","title":"GNPS-compositae_MN library_240115","user":"cho_chae_yeon","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705296986000","created":"Jan. 14, 2024, 9:36 PM","description":"These datasets are raw, mzML files to compare selective compounds from Compositae.","fileCount":"253","fileSizeKB":"24480129","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Asteraceae (NCBITaxon:4210)","instrument":"Orbitrap Exploris 120","modification":"-","keywords":"compositae","pi":[{"name":"Heejung Yang","email":"heejyang@kangwon.ac.kr","institution":"Kangwon National University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"df8b5a17f89b4809aa388d474760eb85","id":"3036"}, {"dataset":"MSV000093867","datasetNum":"93867","title":"Automated single-cell proteomics covering over four orders of magnitude at high throughput","user":"cctortec","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705265862000","created":"Jan. 14, 2024, 12:57 PM","description":"Single-cell proteomics analysis of HEK293 and THP-1 cells on the timsTOF Ultra.","fileCount":"8128","fileSizeKB":"806273222","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF SCP","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"single-cell proteomics;timsTOF Ultra;proteoCHIP","pi":[{"name":"Steven A. Carr","email":"scarr@broadinstitute.org","institution":"Broad Institute of MIT and Harvard","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c2180ca9eff4640b60576aa500d8721","id":"3037"}, {"dataset":"MSV000093865","datasetNum":"93865","title":"Identification by Shotgun Proteomics with Q-Exactive Hybrid Quadripole-Orbitrap High Resolution Tandem Mass-Spectrometry, Histone isoforms\u2019 Hypermethylation Phenotype as A Hallmark Characteristic of Human-IDH-Mutant High-Grade Gliomas ","user":"KAOUTHARLOUATI7","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705252195000","created":"Jan. 14, 2024, 9:09 AM","description":"Histone variant-post-translational modifications (PTMs) have been allied to various pathological processes, especially in cancer-onset, envisaged as obvious epigenetic biomarkers-based genotoxicity and as predictors for pathological diagnosis and prognosis. Consequently, their mapping and characterization constitute a critical field of study facilitated by the recent advances in the Mass spectrometry (MS) high-throughput technique, which has emerged as the most powerful tool to achieve insights into chromatin biology and epigenetics.\r\nThe current study endeavored to the analysis of histone-isoforms\u2019 methylation in neural cells induced by environmental stressors such as pesticides. Our protocol consisted first of a 3D in-vitro developing neurospheroid model derived from human IDH-mutant high-grade gliomas, then treatment by pesticide mixture at the inhibitory concentration IC50. Afterwards, histones were extracted, precipitated, and derivatized by propionylation prior trypsin digestion for analysis by the most popular bottom-up proteomics-based approach using a nano flow-UHPLC coupeled to Q Exactive HF hybrid quadrupole-Orbitrap high resolution tandem mass spectrometry.\r\nRaw MS files were searched against human protein database based on the species of the samples using the MAXQUANT software. The ionization was performed in a positive-ion mode and the mass spectrometer was operated in the data-dependent acquisition (DDA) mode. Histone isoforms\u2019 methylation were validated manually by De novo peptide sequencing using the \u201CPEAKS STUDIO\u201D software package, which consisted in comparing the MS\/MS spectra of peptide sequences between treated and non-treated spheroids. \r\nThe results revealed a hypermethylation phenotype in histone isoforms, which is a hallmark characteristic of Isocitrate-Dehydrogenase (IDH)-mutated high-grade gliomas, envisaged as an adaptive strategy adapted by cancer cells to overcome stress and promote invasiveness. ","fileCount":"210","fileSizeKB":"782476","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Ultimate 3000 nano UHPLC system (ThermoFisher Scientific, USA) with a Q Exactive HF hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific, USA), an ESI nanospray source, a higher energy collisional dissociation (HCD) fragmentation mode and data-dependent acquisition (DDA) mode for peptide sequencing.","modification":"UNIMOD:34 - \\\"Methylation.\\\"","keywords":"Histone Post-Translational Modifications;Epigenetics;Neurospheroids;Tandem Mass Spectrometry;Genotoxicity;Biomarkers;De novo peptide sequencing.;Histone-isoforms;High-grade gliomas;Grade-IV astrocytomas;Hypermethylation;Bottom-up proteomic-based approach","pi":[{"name":"Kaouthar Louati","email":"kaouthar.louati@fphm.u-monastir.tn","institution":"University of Monastir, Faculty of Pharmacy, Laboratory of Chemical, Pharmacological and Galenic Drug Development- LR12ES09, Road Avicenne 5000, Monastir, Tunisia","country":"Tunisie"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD048530","task":"7daf2c5cb6b147b780236ef23653fa04","id":"3038"}, {"dataset":"MSV000093861","datasetNum":"93861","title":"Cauldrons of Bronze Age nomads","user":"Wilkin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705185593000","created":"Jan. 13, 2024, 2:39 PM","description":"Protein analysis of Bronze Age Cauldron residues. Found blood from ruminant caprines, and milk proteins from bovids, including yak (Bos mutus).","fileCount":"22","fileSizeKB":"2424702","spectra":"0","psms":"2440","peptides":"992","variants":"1028","proteins":"3576","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ovis aries (NCBITaxon:9940);Capra sp. (NCBITaxon:61294)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:366 - \\\"Deamidation in presence of O18.\\\";MOD:00768 - \\\"Oxidation of methionine to methionine sulfone with neutral loss of CH3SO2H.\\\"","keywords":"archaeology;milk;blood;ancient proteins","pi":[{"name":"Shevan Wilkin","email":"shevan.wilkin@uzh.ch","institution":"University of Zurich (UZH)","country":"Switzerland"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048524","task":"e4d7fde7bfb34c5c99cadcdebe05245c","id":"3039"}, {"dataset":"MSV000093857","datasetNum":"93857","title":"Pla2g12b binding proteins in Zebrafish","user":"syjung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705115152000","created":"Jan. 12, 2024, 7:05 PM","description":"We injected larvae with the wild-type rescue plasmid described above, and performed co-immunoprecipitation and mass spectrometry (co-IP\/MS) against the highly specific 3x-FLAG epitope linked to Pla2g12b. The top five most abundant proteins included the core components of the TRL assembly pathway (ApoB and the two Subunits of Mtp (Mttp and Pdi\/P4hb)), as well as various chaperone proteins . These interactions suggest that Pla2g12b participates directly in TRL biogenesis, and may promote efficient channeling of lipids to ApoB by linking it more tightly to the transfer protein Mtp. ","fileCount":"61","fileSizeKB":"42393883","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Q Exactive","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Pla2g12b","pi":[{"name":"Steve Farber","email":"sfarber3@jhu.edu","institution":"Johns Hopkins University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048516","task":"27dc3059e31f41fcbaa3c205517c5148","id":"3040"}, {"dataset":"MSV000093854","datasetNum":"93854","title":"Diagnosing and staging epithelial ovarian cancer by serum glycoproteomic profiling","user":"GX_InterVenn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705091798000","created":"Jan. 12, 2024, 12:36 PM","description":"Background \nThere is a pending need to identify biomarkers for early screening, triaging and staging in epithelial ovarian cancer (EOC). Glycoproteomics has shown promise for biomarker discovery.\n\nMethods\nWe applied glycoproteomics to serum of EOC patients (n=145), patients with benign lesions (n=151) and healthy controls (n=55). A total of 653 peptides and glycopeptides were quantified and assessed in multivariable models. Additionally, we investigated glycosylation patterns in serum and in tissues.\n\nResults\nA signature panel of 27 biomarkers distinguished benign lesions from EOC with sensitivity and specificity of 83.5% and 90.1% (training set), and of 86.7 and 86.7% (test set), respectively. ROC analysis demonstrated strong performance across a range of cutoffs (training set AUC of 0.953; test set AUC of 0.873). Fucosylated markers were higher in late-stage EOC and distinguished early-stage from late-stage EOC. A similar upregulation of fucosylated multi-antennary glycans was found in late-stage EOC tissues. \n\nConclusions\nBlood glycopeptide biomarkers distinguish benign from malignant pelvic masses, and early- from late-stage EOC. Glycosylation profiles of circulating glycoproteins and tumor tissues may be driven by shared mechanisms. Our findings demonstrate the power of blood glycoproteomics for EOC diagnosis and staging that warrants further clinical evaluation.\n","fileCount":"2","fileSizeKB":"19","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6495C Triple Quadrupole LC\\\/MS","modification":"glycosylation","keywords":"ovarian cancer;glycoproteomics;biomarkers","pi":[{"name":"Flavio Schwarz","email":"flavio.schwarz@venn.bio","institution":"InterVenn Biosciences","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a5ce434f30d24245969e0e45c3b0078d","id":"3041"}, {"dataset":"MSV000093851","datasetNum":"93851","title":"SIAH3 is frequently epigenetically silenced in cancer and regulates mitochondrial metabolism - Expression Proteomics Dataset","user":"graumann","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705069781000","created":"Jan. 12, 2024, 6:29 AM","description":"Of the seven in absentia homologue (SIAH) family, three members have been identified in the human genome. In contrast to the E3 ubiquitin ligase encoding SIAH1 and SIAH2, little is known on the regulation and function of SIAH3 in tumorigenesis. In this study, we reveal that SIAH3 is frequently epigenetically silenced in different cancer entities, including cutaneous melanoma, lung adenocarcinoma and head and neck cancer. Low SIAH3 levels correlate with an impaired survival of cancer patients. Additionally, induced expression of SIAH3 reduces cell proliferation. Functionally, SIAH3 negatively affects cellular metabolism by shifting cells form aerobic oxidative phosphorylation to glycolysis. SIAH3 is localized in the mitochondrion and interacts with proteins involved in mitochondrial ribosome biogenesis and translation. We also report that SIAH3 interacts with ubiquitin ligases, including SIAH1 or SIAH2, and is degraded by them. These results suggest that SIAH3 acts as an epigenetically controlled tumor suppressor by regulating cellular metabolism through the inhibition of oxidative phosphorylation.","fileCount":"29","fileSizeKB":"63189336","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"SIAH;metabolism;hypermethylation;cancer;epigenetics","pi":[{"name":"Reinhard H. Dammann","email":"reinhard.dammann@gen.bio.uni-giessen.de","institution":"Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048509","task":"67c35a5cdbe647cda9df5eebf5e0a6c3","id":"3042"}, {"dataset":"MSV000093850","datasetNum":"93850","title":"SIAH3 is frequently epigenetically silenced in cancer and regulates mitochondrial metabolism - SIAH3 Interactomics","user":"graumann","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705069352000","created":"Jan. 12, 2024, 6:22 AM","description":"Of the seven in absentia homologue (SIAH) family, three members have been identified in the human genome. In contrast to the E3 ubiquitin ligase encoding SIAH1 and SIAH2, little is known on the regulation and function of SIAH3 in tumorigenesis. In this study, we reveal that SIAH3 is frequently epigenetically silenced in different cancer entities, including cutaneous melanoma, lung adenocarcinoma and head and neck cancer. Low SIAH3 levels correlate with an impaired survival of cancer patients. Additionally, induced expression of SIAH3 reduces cell proliferation. Functionally, SIAH3 negatively affects cellular metabolism by shifting cells form aerobic oxidative phosphorylation to glycolysis. SIAH3 is localized in the mitochondrion and interacts with proteins involved in mitochondrial ribosome biogenesis and translation. We also report that SIAH3 interacts with ubiquitin ligases, including SIAH1 or SIAH2, and is degraded by them. These results suggest that SIAH3 acts as an epigenetically controlled tumor suppressor by regulating cellular metabolism through the inhibition of oxidative phosphorylation. ","fileCount":"12","fileSizeKB":"33723433","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"SIAH;metabolism;hypermethylation;cancer;epigenetics","pi":[{"name":"Reinhard H. Dammann","email":"reinhard.dammann@gen.bio.uni-giessen.de","institution":"Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048508","task":"f4540df893f4495b8204990f87ff2477","id":"3043"}, {"dataset":"MSV000093849","datasetNum":"93849","title":" Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids","user":"aad100","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705067212000","created":"Jan. 12, 2024, 5:46 AM","description":"Patterning and growth are fundamental features of embryonic development that must be tightly coordinated during morphogenesis. While metabolism is known to control cell growth, how it impacts patterning and links to morphogenesis is poorly understood. To understand how metabolism impacts early mesoderm specification during gastrulation, we used in vitro mouse embryonic stem (ES) cell-derived gastruloids, due to ease of metabolic manipulations and high-throughput nature. Gastruloids showed mosaic expression of glucose transporters co-expressing with the mesodermal marker T\/Bra. To understand the significance of cellular glucose uptake in development, we used the glucose metabolism inhibitor 2-deoxy-D-glucose (2-DG). 2-DG blocked the expression of T\/Bra and abolishes axial elongation in gastruloids. Surprisingly, removing glucose completely from the medium did not phenocopy 2-DG treatment despite a significant decline in glycolytic intermediates occurring under both conditions. As 2-DG can also act as a competitive inhibitor of mannose in protein glycosylation, we added mannose together with 2-DG and found that it could rescue the mesoderm specification. We corroborated these results in vivomouse embryos where supplementing mannose rescued the 2-DG mediated phenotype of mesoderm specification and proximo-distal elongation of the primitive streak. We further showed that blocking production and intracellular recycling of mannose abrogated mesoderm specification. At molecular level, proteomics analysis revealed that mannose reversed glycosylation of the Wnt pathway regulator, Secreted Frizzled Receptor, Frzb, expressed in the primitive streak of the mouse embryo. Our study showed how mannose linked metabolism to glycosylation of a developmental pathway component, crucial in patterning of mesoderm and morphogenesis of gastruloids. ","fileCount":"30","fileSizeKB":"9169476","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Gastruloids;Mesoderm;Mannose;N-glycosylation;Glycoprotein;Wnt","pi":[{"name":"Benjamin Steventon","email":"bjs57@cam.ac.uk","institution":"University of Cambridge","country":"United Kingdom"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD048505","task":"866b83d86ba743fbac9402bea84c4b55","id":"3044"}, {"dataset":"MSV000093844","datasetNum":"93844","title":"GNPS Fecal Microbiota Transplant Bile Acid","user":"Gzhang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705012504000","created":"Jan. 11, 2024, 2:35 PM","description":"Bile acid and conjugates that extracted from the human fecal sample ","fileCount":"1599","fileSizeKB":"17069713","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6560 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bile acid","pi":[{"name":"Erin Baker","email":"erinmsb@unc.edu","institution":"UNC Chapel Hill","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d3f0e2f91dce4dffa6f30d75418865c7","id":"3045"}, {"dataset":"MSV000093843","datasetNum":"93843","title":"The Antigen Presentation Landscape of Cytokine-Stressed Human Pancreatic Islets","user":"padmananaware","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705011879000","created":"Jan. 11, 2024, 2:24 PM","description":"MHC-I and MHC-II (HLA-DR, HLA-DQ, HLA-DP) bound peptide elution from cytokine treated human pancreatic islets and homologous spleen donors","fileCount":"157","fileSizeKB":"37688755","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive;Orbitrap Fusion Lumos","modification":"variable modifications of oxidized methionine and pyroglutamic acid for N-terminal glutamine","keywords":"Immunopeptidome, Human Islets, Human Spleen","pi":[{"name":"Lawrence J. Stern","email":"Lawrence.Stern@umassmed.edu","institution":"UMASS Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b0735941bba047119c03dec7596e8820","id":"3046"}, {"dataset":"MSV000093842","datasetNum":"93842","title":"IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705006730000","created":"Jan. 11, 2024, 12:58 PM","description":"Multiple myeloma (MM) is an incurable malignancy of plasma cells that exploits transcriptional networks driven by IRF4. To discover unique molecular vulnerabilities in MM centered on IRF4, we employ a multi-omics approach integrating functional genomics screening, spatial proteomics, and global chromatin mapping. We find that ARID1A, a member of the SWI\/SNF chromatin remodeling complex, is both required for IRF4 expression and functionally associated with IRF4 protein on chromatin. Deletion of Arid1a in activated murine B cells thwarts subsequent plasma cell differentiation by disrupting IRF4-dependent transcriptional networks, therefore defining ARID1A as a novel plasma cell vulnerability. Targeting ARID1A-dependent SWI\/SNF activity via SMARCA2\/4 inhibition induces a rapid loss of IRF4-target gene expression and quenches global amplification of oncogenic gene expression driven by MYC, resulting in profound toxicity to MM cells. Notably, MM patients with aggressive disease have markers of SWI\/SNF activity, and SMARCA2\/4 inhibitors retain their activity in immunomodulatory drug (IMiD)-resistant MM cells. To fully harness the potential of these drugs, we use combinatorial drug screens to uncover profound synergistic toxicity between SMARCA2\/4 and MEK inhibitors. Thus, targeting SWI\/SNF activity potently represses an IRF4-MYC feed forward loop and provides a feasible path to effectively treat this incurable disease.","fileCount":"13","fileSizeKB":"16596405","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"multiple myeloma, SWI\/SNF, IRF4, plasma cells","pi":[{"name":"Ryan Young","email":"youngrm@nih.gov","institution":"NCI\/NIH","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9aeaaf58906b4d278c9ebdad88b7ac4a","id":"3047"}, {"dataset":"MSV000093840","datasetNum":"93840","title":"Osteomacs promote maintenance of murine hematopoiesis through megakaryocyte-induced upregulation of Embigin and CD166","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705004840000","created":"Jan. 11, 2024, 12:27 PM","description":"Maintenance of hematopoietic stem cell (HSC) function in the niche is an orchestrated event. Osteomacs (OM), are key cellular components of the niche. Previously, we documented that osteoblasts, OM, and megakaryocytes interact to promote hematopoiesis. Here, we further characterize OM and identify megakaryocyte-induced mediators that augment the role of OM in the niche. Single cell mRNAseq, mass spectrometry, and CyTOF examination of megakaryocyte-stimulated OM suggested that upregulation of CD166 and Embigin on OM augment their hematopoiesis maintenance function. CD166 knockout OM or shRNA-Embigin knockdown OM, confirmed that loss of these molecules significantly reduced OM ability to augment the osteoblast-mediated hematopoietic enhancing activity. Recombinant CD166 and Embigin partially substituted for OM function, characterizing both proteins as critical mediators of OM hematopoietic function. Our data identify Embigin and CD166 as OM-regulated critical components of HSC function in the niche and potential participants in various in vitro manipulations of stem cells.","fileCount":"5","fileSizeKB":"4471224","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Osteomacs;hematopoiesis;osteoblasts;megakaryocytes;CD166;Embigin","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"},{"name":"Edward Srour","email":"esrour@iu.edu","institution":"Indiana University School of Medicine","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d3a468ac8c9544ccb9f7543df435a55b","id":"3048"}, {"dataset":"MSV000093838","datasetNum":"93838","title":"Uncovering missing glycans and unexpected fragments with pGlycoNovo: a full-range Y-ion dynamic searching strategy for site-specific glycosylation analysis across species","user":"Mingqiliu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1705000846000","created":"Jan. 11, 2024, 11:20 AM","description":"Precision mapping of glycans at the site-specific level using mass spectrometry data has emerged as a crucial approach for glycan discovery in modern glycoproteomics and glycobiology. However, the extensive diversity of glycan compositions within and across species far surpasses the capacity of existing software databases. Consequently, the identification of glycans not included in the database or lacking prior compositional knowledge during large-scale glycoproteomic analyses poses a significant challenge. Here, we present pGlycoNovo, a software platform for analyzing intact glycopeptides featuring rare glycan attachments within the pGlyco3 software environment. ","fileCount":"897","fileSizeKB":"706594527","spectra":"8125098","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Arabidopsis thaliana (NCBITaxon:3702);Caenorhabditis elegans (NCBITaxon:6239);Drosophila (NCBITaxon:7215);Danio rerio (NCBITaxon:7955)","instrument":"Orbitrap Fusion","modification":"MOD:00733 - \\\"A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with an N-acetylglucosamine group through a glycosidic bond.\\\"","keywords":"pGlyco;Glycosylation;De novo","pi":[{"name":"Weiqian Cao","email":"wqcao@fudan.edu.cn","institution":"Institutes of Biomedical Sciences,Fudan University","country":"China"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD048469","task":"b8d4076915d641fc8a782314c4510af2","id":"3049"}, {"dataset":"MSV000093832","datasetNum":"93832","title":"GNPS - CCA_Exometabolites_KaneoheBay2023","user":"zquinlan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704935515000","created":"Jan. 10, 2024, 5:11 PM","description":"DOM extracted from the CCA Hydrolithon reinboldii in during a 8-hour incubation experiment in Kaneohe Bay, O'ahu, HI, USA","fileCount":"57","fileSizeKB":"3226105","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hydrolithon reinboldii (NCBITaxon:389195)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Crustose Coralline Algae;Coral Reefs;Dissolved organic matter;DOM;Exometabolites","pi":[{"name":"Daniel Wangpraseurt","email":"dwangpraseurt@ucsd.edu","institution":"Scripps Institution of Oceanography","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1ee11f0ed019418d856eeb2dbccd496f","id":"3050"}, {"dataset":"MSV000093831","datasetNum":"93831","title":"GNPS - Evolution of the earliest stages of ovarian cancer from mutant fallopian tube epithelial cells","user":"MFJ003","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704934306000","created":"Jan. 10, 2024, 4:51 PM","description":"Ovarian cancer is also known as a silent killer as women are usually diagnosed in advanced stages when the disease has already spread to vital peritoneal organs leading to poor survival. Therefore, improving outcomes for this disease would require a greater understanding of the earliest stages, where the disease can be cured with current treatments. Fallopian tubes (FTs) are a site of origin of ovarian cancer. Here, by combining gene sequencing, proteomics, organoids, mouse genetics, lineage tracing, and quantitative modeling, we showed that mutant Pax8+ FT progenitor cells gain clonal growth advantage over their wild-type neighbors and expand over time, colonizing large areas of FT epithelium, resulting in the formation of pre-cancerous lesions. The growth of these precursor lesions is modulated by ovarian hormones, where estrogen promotes and progesterone suppresses their growth. Collectively, this study provides insight into how a single mutant FT epithelial cell leads to early ovarian cancer evolution. ","fileCount":"31","fileSizeKB":"19579904","spectra":"0","psms":"314616","peptides":"184133","variants":"229877","proteins":"22943","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ovary;cancer;fallopian tube;oviduct;gynecological cancer","pi":[{"name":"Dr Pradeep Tanwar ","email":"pradeep.tanwar@newcastle.edu.au","institution":"The University of Newcastle","country":"Australia"},{"name":"Muhammad Fairuz Jamaluddin","email":"muhammad.jamaluddin@newcastle.edu.au","institution":"University of Newcastle","country":"Australia"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048419","task":"5a86e1bcc42b44c0be5feed494c91585","id":"3051"}, {"dataset":"MSV000093813","datasetNum":"93813","title":"GNPS - Microbial and host compensation in a model of leucine breakdown deficiency","user":"bwf7","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704919606000","created":"Jan. 10, 2024, 12:46 PM","description":"Representative MS\/MS data for WT and mccc-1 mutant C. elegans reared on Comamonas aquatica. Data in both positive and negative ionization mode, as indicated in the files names. The worm bodies (endo-metabolome) and conditioned media (exo-metabolome) were harvested, extracted, and analyzed separately.","fileCount":"17","fileSizeKB":"3512335","spectra":"94864","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Q Exactive;Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolism;Metabolomics;Leucine;C. elegans;Caenorhabditis elegans;Host-Microbe;Microbiome","pi":[{"name":"A.J. Marian Walhout","email":"marian.walhout@umass.edu","institution":"University of Massachusetts Chan Medical School","country":"United States"},{"name":"Frank Schroeder","email":"schroeder@cornell.edu","institution":"Cornell University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"223bcbebee014279b7ecdeb7296b1e12","id":"3052"}, {"dataset":"MSV000093812","datasetNum":"93812","title":"The Longevity Factor Spermidine is Part of a Highly Heritable Complex Erythrocyte Phenotype Associated With Longevity ","user":"jericha66","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704918916000","created":"Jan. 10, 2024, 12:35 PM","description":"Proteomics of red blood cells collected from twin study (n = 36; 18 twin pairs)","fileCount":"31","fileSizeKB":"5011066","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Red blood cells","pi":[{"name":"Thomas Raife","email":"TRaife@uwhealth.org","institution":"University of Wisconsin-Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"83fdbe138b104579bbf2975b183c5cac","id":"3053"}, {"dataset":"MSV000093805","datasetNum":"93805","title":"2022 Mated-unmated honey bee queen comparison","user":"abbichapman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704910928000","created":"Jan. 10, 2024, 10:22 AM","description":"Hemolymph from mated and unmated honey bee queens collected in summer 2022. ","fileCount":"4","fileSizeKB":"25738311","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis mellifera (NCBITaxon:7460)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"honey bee;honey bee queen;honey bee hemolymph","pi":[{"name":"Leonard Foster","email":"foster@msl.ubc.ca","institution":"University of British Columbia","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b6d82fcc5a0d4dab97ac2fa0037deae8","id":"3054"}, {"dataset":"MSV000093803","datasetNum":"93803","title":"Bone proteomics methods optimisation for forensic investigations","user":"NUPPA","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704889831000","created":"Jan. 10, 2024, 4:30 AM","description":"The application of human bone in forensic proteomics is an expanding novel purpose in the aim of successfully quantifying biological estimations used in medico-legal investigations with greater accuracy. In this project, different extraction protocols were tested on n=30 human bone samples, including S-Trap technology with two different lysis buffer, and ZipTips. Additionally, a comparison was made between data-dependent acquisition (DDA) and data-independent acquisition (DIA) mode. \nResults showed less missing data using S-Traps instead of the more routine reverse-phase media tips (ZipTip). The type of lysis buffer when using S-Traps does not impact largely the analysis conducted in forensic proteomic workflows. Lastly, it was found that when open-source software is used for data processing for both DDA and DIA modes, DIA has the upper advantage in terms of acquiring a larger number of proteins due to its greater sensitivity to those with a lower abundance.\n","fileCount":"217","fileSizeKB":"128415906","spectra":"7752435","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"Bone proteomics;protein extraction;mass spectrometry;forensic science;acquisition mode ","pi":[{"name":"Noemi Procopio","email":"nprocopio@uclan.ac.uk","institution":"University of Central Lancashire","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048383","task":"4ba79f158be744e0b10dc8389963e08e","id":"3055"}, {"dataset":"MSV000093802","datasetNum":"93802","title":"GNPS - Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life: a randomized controlled interventional trial with infant formula","user":"kkleigrewe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704884706000","created":"Jan. 10, 2024, 3:05 AM","description":"Microbiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, infant formula and solid foods. In this randomized controlled intervention study, longitudinal sampling of infant stools (n=998) showed similar development of fecal bacterial communities between formula- and breast-fed infants during the first year of life (N=210). Infant formula supplemented with galacto-oligosaccharides (GOS) was most efficient to sustain high levels of bifidobacteria compared to formula containing B. longum and B. breve or placebo. Metabolite (untargeted) and bacterial profiling (16S rRNA\/shallow metagenomics sequencing) revealed 24-hour oscillations and integrated data analysis identified circadian networks. Rhythmicity in bacterial diversity, specific taxa and functional pathways increased with age and was most pronounced following breast-feeding and GOS-supplementation. Circadian rhythms in dominant taxa were discovered ex-vivo in a chemostat model. Hence microbiota rhythmicity develops early in life, likely due to bacterial intrinsic clock mechanism and is affected by diet.","fileCount":"530","fileSizeKB":"11632014","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"metabolomics","keywords":"Circadian rhythmicity;infant microbiome;bifidobacteria;Galtacto-oligosaccarides;intervention trial;infant formula;breast milk;gut chemostat","pi":[{"name":"Dirk Haller","email":"dirk.haller@tum.de","institution":"Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"af1d1dc0d1f74c3995931f9c551e1baf","id":"3056"}, {"dataset":"MSV000093801","datasetNum":"93801","title":"The primate-specific Nedd4-1-NE localizes to late endosomes in response to amino acids to suppress autophagy","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704843787000","created":"Jan. 9, 2024, 3:43 PM","description":"Data deposited contain results from proximity-dependent biotinylation LC-MS (BioID) experiments in which T-REx Flp-In HEK293 cells express NEDD4 protein versions in-frame with biotin carboxylase miniTurbo.","fileCount":"111","fileSizeKB":"33387477","spectra":"0","psms":"1142389","peptides":"93687","variants":"146349","proteins":"30365","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"BioID, miniTurbo, biotin, streptavidin, T-REx Flp-In HEK293, NEDD4 ","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048366","task":"05aa34c387ff4c269cbff13fba347d20","id":"3057"}, {"dataset":"MSV000093798","datasetNum":"93798","title":"Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles","user":"trendsetter","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704822044000","created":"Jan. 9, 2024, 9:40 AM","description":"The recognition of aging as a risk factor for chronic, inflammatory and malignant diseases 1 led to increased efforts to identify its underlying molecular mechanisms. The hallmarks of aging, initially defined ten years ago, have been recently expanded to comprise genome instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation and dysbiosis 2. Signaling pathways 3 converging on key transcription factors remodel gene expression and ultimately cellular function in an agedependent manner. Signal transduction relies heavily on protein phosphorylation, the most common posttranslational modification. PhosphoSitePlus, the main repository used in the field, currently contains 320000 nonredundant phosphosites, of which are annotated to a corresponding kinase 12. The catalog continues to grow, due to increasingly sensitive measurement technologies and diverse analysis approaches 13,14. \n\nAging-related changes in protein phosphorylation has so far been studied in the mouse liver 15. Other studies focused on interfering with specific aging hallmarks, for example determining phosphorylation changes induced in the muscle of aged mice by the short term treatment with elamipretide, a drug that reduces the formation of free radicals in mitochondria 16,17. In parallel, numerous studies have started to explore approaches to slow down the aging process and improve lifespan. Ongoing clinical trials involve exercise, intermittent fasting and calorie restriction 18, as well as compounds that target key molecular pathways such as nutrient sensing. The molecular signature of such interventions has been determined at the mRNA and protein level in various tissues 19, including mouse muscles 20,21. However, the remodeling of signaling pathways upon these interventions remains relatively uncharted. \n\nIn previous work we have demonstrated that individual mouse muscles have distinct functional responses to the longterm treatment with calorie restriction (CR) and rapamycin (RM) and we have determined the underlying mRNA level expression signatures 22. In this study we expand on this work, determining the protein phosphorylation dynamics of four muscles, soleus, tibialis anterior, triceps brachii and gastrocnemius, from adult (10 months 10M), geriatric (30M), and 30 months-old mice that were either calorie restricted (30MCR) or treated with rapamycin (30MRM) from 15 months of age. We robustly detected 6960 phospho sites across samples, 1415 of which are not represented in the PhosphoSitePlus database. We demonstrate that CR and RM have largely consistent, but quantitatively distinct, long-term effects on the phosphoproteome, reverting agerelated changes to different degrees and in muscledependent manners. Our data expands the catalog of protein phosphorylation sites in the mouse, providing important information regarding their tissuespecificity. \n","fileCount":"386","fileSizeKB":"493174427","spectra":"11833402","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos;Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"rapamycin;aging;phosphoproteomics","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"},{"name":"Mihaela Zavolan","email":"mihaela.zavolan@unibas.ch","institution":"Biozentrum, University of Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048356","task":"aacf0e9138b246b9a85cc91076d32562","id":"3058"}, {"dataset":"MSV000093797","datasetNum":"93797","title":"GNPS - Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry","user":"EvoleneD","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704798930000","created":"Jan. 9, 2024, 3:15 AM","description":"Raw data for ultralong transients (> 25 s) measurements corresponding to single particle Orbitrap-based CDMS analysis or ensemble native MS.","fileCount":"7","fileSizeKB":"20495977","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"GroEL (E. coli);Apoferritin (recombinant, human);Bovine Serum Albumin;Cytochrome c (from equine heart);Alcohol dehydrogenase (from Saccharomyces cerevisiae)","instrument":"Q Exactive UHMR","modification":"NA","keywords":"CDMS;native MS;proteins","pi":[{"name":"Albert J.R. Heck ","email":"a.j.r.heck@uu.nl","institution":"Utrecht University","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f879625786c24284ac634f159e3f866a","id":"3059"}, {"dataset":"MSV000093796","datasetNum":"93796","title":"Quantitative analysis of ribosomal protein expression in bacteria","user":"rusconi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704795554000","created":"Jan. 9, 2024, 2:19 AM","description":"Analysis of ribosomal proteins purified as ribosome particles. Two set of samples were analyzed: 1) ribosomes purified from bacteria expressing sgRNA that does not target any ribosomal RNA gene (control); 2) ribosomes purified from bacteria expressing sgRNA targeting three ribosomal RNA genes. The aim of the project is to quantify the peptides and compare both sets of samples. The ribosomal peptides prepared from the bacteria expressing the sgRNA targeting the rRNA genes are expected to be less abundant than in the control samples. The two sample sets are the following: A-D (four biological replicates) are the samples from the bacteria expressing functional sgRNA downregulating three rRNA genes. E-H (four biologicial replicates) are the control samples from the bacteria expressing sgRNA that do not target any rRNA gene. All the sampes were spiked with an almost equivalent amount of ribosomes from a WT strain grown in almost 100% 13C and 15N labelled minimum medium. Ribosomes were purified according to published protocols. Basically, the ribosome particles are sedimented by ultra-centrifugation in a saccharose-rich medium. The recovered pellets were resuspended for electrophoretic migration (stacking gel only) for later in-gel trypsinolysis. The obtained peptides were extracted from the gel according to standard procedures and analyzed by LC-MS\/MS on a QExactivePlus Orbitrap mass spectrometer (Thermo scientific). The raw data were converted to mzXML (raw data files) and processed using our proteomics software suite (i2MassChroQ, see http:\/\/pappso.inrae.fr\/en\/bioinfo\/). The database search engine was X!Tandem, that produces, for each MS run file analyzed, a corresponding XML file, that we submit here as the database search identification data files). The X!Tandem program was first configured to run without accounting for labelled peptides (one set of \"light-only\" XML files were thus generated by X!Tandem). Then, X!Tandem was configured to account for all the residues labelled 100% with 13C and 15N (one set of \"heavy-only\" XML files were thus generated by X!Tandem). We loaded first the \"light-only\" X!Tandem-generated XML files in i2MassChroq, checked the quality of the data and wrote to disk an XPIP (i2MassChroq project file) file for the four replicates of both sample sets all taken together. Then we did this likewise for the \"heavy-only\" X!Tandem-generated XML files (at this time we configured i2MassChroQ to look for heavy-isotope-labelled peptides). We finally open the two XPIP files (light-only and heavy-only) and save the combination of the data to a new XPIP file (light-and-heavy). The quantitative analysis was performed inside the i2MassChroq's MassChroQ module which is then directed to write a spreadsheet file with all the identification\/quantification data of the peptides. That spreadsheet file was then used within GNU-R to perform data reformatting and peptide quantification work (comparison of the amount of selected peptides belonging to known ribosome subunits between the two data sets).","fileCount":"43","fileSizeKB":"10891379","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap QExactive Plus","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";MOD:00721 - \\\"A protein modification that effectively oxygenates an L-methionine residue to L-methionine sulfoxide S-diastereomer.\\\"","keywords":"bacteria;ribosome;quantification","pi":[{"name":"Michel Arthur","email":"michel.arthur@crc.jussieu.fr","institution":"Centre de Recherche des Cordeliers, INSERM","country":"France"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD048334","task":"98671ce559c241ee82f45803039afcae","id":"3060"}, {"dataset":"MSV000093794","datasetNum":"93794","title":"Trichomonas vaginalis 20S proteasome subunit specific MSP-MS","user":"bhurysz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704754003000","created":"Jan. 8, 2024, 2:46 PM","description":"MSP-MS data for Tv20S. Data files are named PF_Treatment_concentration_time_replicate. Possibilities include\nTreatment: \n1-45 = CP-17\nCFZ = carfilzomib AND CP-17 both at 10uM.\n616 = KZR-616\nDMSO = DMSO\nConcentration: 10uM or 1uM\nTime:\nNTC = 0h\n3 = 3h\n20 = 20h\n38 = 38h\nReplicate: 1-4 ","fileCount":"164","fileSizeKB":"80503636","spectra":"0","psms":"76563","peptides":"1511","variants":"2029","proteins":"236","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic construct (NCBITaxon:32630)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Tv20S;MSP-MS;trichomonas vaginalis;substrate profiling","pi":[{"name":"Anthony O'Donoghue","email":"ajodonoghue@ucsd.edu","institution":"UCSD","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048324","task":"93f8409b7fac4707b73a70942983c902","id":"3061"}, {"dataset":"MSV000093793","datasetNum":"93793","title":"Identification of a Resistance Exercise-Specific Signaling Pathway that Drives Skeletal Muscle Growth","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704750686000","created":"Jan. 8, 2024, 1:51 PM","description":"This data set contains phosphoproteomic data and proteomic data across four 16-plex TMT channels. The goal of the project was to identify the proteomic and phosphoproteomic signature of resistance and endurance exercise. ","fileCount":"257","fileSizeKB":"135316039","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phosphoproteomics;muscle;human skeletal muscle","pi":[{"name":"Josh J. Coon","email":"jcoon@chem.wisc.edu","institution":"University of Wisconsin - Madison","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3aa81506833f4c8aad03f86f11e6eef0","id":"3062"}, {"dataset":"MSV000093787","datasetNum":"93787","title":"GNPS - LC profile of streptomyces tagetis","user":"kimkami2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704712315000","created":"Jan. 8, 2024, 3:11 AM","description":"Metabolic profiling of Streptomyces tagetis sp. nov.","fileCount":"3","fileSizeKB":"191405","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"streptomyces tagetis","instrument":"Xevo G2-S QTof","modification":"Nothing","keywords":"Streptomyces","pi":[{"name":"Hyunwoo Kim","email":"hwkim8906@dongguk.edu","institution":"Dongguk University - Seoul","country":"South Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bdedddb3acde467681408444e4662c0a","id":"3063"}, {"dataset":"MSV000093786","datasetNum":"93786","title":"GNPS - Feature-based molecular networking of pyrones in actinobacteria","user":"zhuboyu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704710150000","created":"Jan. 8, 2024, 2:35 AM","description":"We analyzed crude extracts from different actinobacteria by LC-MS\/MS and analyzed the data by feature-based molecular networking to explore the structural diversity of pyrone compounds.","fileCount":"14","fileSizeKB":"1501377","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces (NCBITaxon:1883);Nocardiopsis (NCBITaxon:2013)","instrument":"Orbitrap Exploris 240","modification":"NA","keywords":"actinobacteria, metabolomics, pyrone, molecular networking","pi":[{"name":"Boyu Zhu","email":"zhuby@idsse.sc.cn","institution":"Institute of Deep-sea Science and Engineering, Chinese Acadenmy of Science","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f4996b7d4e944e5c9d4a577e593fbc86","id":"3064"}, {"dataset":"MSV000093785","datasetNum":"93785","title":"GNPS - RORDEPs in supernatants of Rumincoccus torques strains cultures","user":"yongfan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704704919000","created":"Jan. 8, 2024, 1:08 AM","description":"This dataset contains the raw proteomics data acquired using a Orbitrap Exploris 480 from bacterial supernatants in R. torques ATCC 27756 culture, and collected from human plasma for the detection of two bacterial polypeptides called RORDEP1 and 2.","fileCount":"9","fileSizeKB":"3565162","spectra":"62844","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ruminococcus torques ATCC 27756 (NCBITaxon:411460);Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"NA","keywords":"RORDEPs, bacterial supernatant, human plasma","pi":[{"name":"Yong Fan","email":"yong.fan@sund.ku.dk","institution":"Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"65c5e61e608945699b79ae99697bdb75","id":"3065"}, {"dataset":"MSV000093784","datasetNum":"93784","title":"The TRIP12 E3 Ligase Induces Interaction Between the SWI\/SNF Component BRG1 and Beta-catenin to Promote Wnt Signaling","user":"madamo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704577485000","created":"Jan. 6, 2024, 1:44 PM","description":"SWItch\/Sucrose Non-Fermentable (SWI\/SNF) chromatin remodeling complexes displace nucleosomes to promote the access of transcription factors to enhancers and promoters. Despite the critical roles of SWI\/SNF in animal development and tumorigenesis, how signaling pathways recruit SWI\/SNF complexes to their target genes is unclear. Here, we demonstrate that target gene activation mediated by Beta-catenin, the essential transcriptional coactivator in the Wnt signal transduction pathway, requires ubiquitylation of the SWI\/SNF component Brahma-related gene-1 (BRG1) by the E3 ubiquitin ligase Thyroid Hormone Receptor Interactor 12 (TRIP12). TRIP12 depletion in Drosophila, zebrafish, mouse organoids, and human cells attenuates Wnt signaling. Genetic epistasis experiments place TRIP12 activity downstream of the Beta-catenin destruction complex. TRIP12 interacts with and ubiquitylates BRG1, and BRG1 depletion blocks TRIP12-mediated Wnt pathway activation. TRIP12 promotes BRG1 binding to Beta-catenin in the presence of Wnt. Our findings support a model in which TRIP12 ubiquitylates BRG1 in the presence of Wnt and promotes its interaction with Beta-catenin, thereby bringing SWI\/SNF to Wnt target genes. Our studies suggest a general mechanism by which cell signaling induces the interaction between BRG1 and pathway-specific transcription factors to recruit SWI\/SNF complexes to their appropriate target genes.","fileCount":"100","fileSizeKB":"10829010","spectra":"0","psms":"688749","peptides":"198756","variants":"216006","proteins":"17634","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus;Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"TRIP12;E3 ligase;SWI\/SNF;BRG1;Beta-catenin;Wnt;nucleosome;ubiquitylation","pi":[{"name":"Arminja Kettenbach","email":"arminja.n.kettenbach@dartmouth.edu","institution":"The Geisel School of Medicine at Dartmouth","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048292","task":"d77d899c41c444c28f69ec988d24da68","id":"3066"}, {"dataset":"MSV000093783","datasetNum":"93783","title":"Effect of the 35 nm and 70 nm size exclusion chromatography (SEC) column and plasma storage time on separated extracellular vesicles","user":"balbisimirjam","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704576068000","created":"Jan. 6, 2024, 1:21 PM","description":"Extracellular vesicles from human blood plasma - optimization of size exclusion chromatography, comparison of fresh and frozen samples","fileCount":"73","fileSizeKB":"83837687","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"maXis II;Orbitrap Exploris 240","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";MOD:00256 - \\\"A protein modification that dioxygenates an L-methionine residue to L-methionine sulfone.\\\"","keywords":"extracellular vesicles;blood plasma;size exclusion chromatography;proteomics","pi":[{"name":"Zsolt Rad\uFFFDk","email":"cix21@yahoo.com","institution":"Hungarian University of Sport Science - Research Center for Molecular Exercise Science","country":"Hungary"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"252975ba053348459a35526e27150fee","id":"3067"}, {"dataset":"MSV000093782","datasetNum":"93782","title":"GNPS - 20240105 ISS standard validation negative ionization","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704503697000","created":"Jan. 5, 2024, 5:14 PM","description":"Standard validation of annotations from space station surfaces, negative ionization","fileCount":"76","fileSizeKB":"2254808","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Q Exactive","modification":"NA","keywords":"chemical standard;space station surface;negative ionization","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1d29b09b60f143f698ddc50db7876cb2","id":"3068"}, {"dataset":"MSV000093781","datasetNum":"93781","title":"GNPS - 20240105 ISS standard validation positive","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704503541000","created":"Jan. 5, 2024, 5:12 PM","description":"Standard validation for annotations from space station surface","fileCount":"81","fileSizeKB":"2589733","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Q Exactive","modification":"NA","keywords":"chemical standard;space station surfaces","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b1eb1a6db9134b6d887618fb0b58dbbf","id":"3069"}, {"dataset":"MSV000093780","datasetNum":"93780","title":"Analysis of ubiquitination sites in Neh2Dual-sGFP substrate","user":"DanKraut","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704500603000","created":"Jan. 5, 2024, 4:23 PM","description":"Determination of ubiquitination sites on an artificial substrate consisting of an Neh2 domain from Nrf2 that has been modified to be able to be ubiquitinated with three different E3 ligase systems, Ubr1 (which forms K48 linkages), Rsp5 (which forms K63 linkages) and Cul3\/Rbx1\/Keap1 (which forms branched linkages).","fileCount":"23","fileSizeKB":"3480815","spectra":"5472","psms":"3266","peptides":"788","variants":"2121","proteins":"13","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Saccharomyces cerevisiae (NCBITaxon:4932);Homo sapiens (NCBITaxon:9606);Escherichia coli (NCBITaxon:562)","instrument":"TripleTOF 5600","modification":"UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:535 - \\\"Ubiquitination.\\\"","keywords":"ubiquitin;degron;E3 ligase","pi":[{"name":"Daniel Kraut","email":"daniel.kraut@villanova.edu","institution":"Villanova University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"cbdd817c0c454e668f7288774e38d5f8","id":"3070"}, {"dataset":"MSV000093775","datasetNum":"93775","title":"Multivalent coiled-coil interactions enable full-scale centrosome assembly and strength","user":"alemoff","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704467972000","created":"Jan. 5, 2024, 7:19 AM","description":"Cross-linked samples consist of monomeric SPD-5 which were incubated with either kinase dead or constitutively active PLK-1 plus ATP-MgCl2 in a 150mM KCl, 25mM HEPES, pH7.4 buffer for 2 hours at room temperature. Samples were then cross-linked using 8mM DMTMM for 45min and quenched with 50 mM ammonium bicarbonate for 15 min at RT shaking at 300rpm. Samples ran on a 16-20% SDS-page gel revealing a monomer band and a dimer band in both conditions using a Commassie based stain. Monomer bands were excised, then digested overnight with trypsin (Pierce), reduced with DTT and alkylated with iodoacetamide (Sigma-Aldrich). Samples were cleaned using solid-phase extraction with an Oasis HLB plate, then injected into an Orbitrap Fusion Lumos mass spectrometer coupled to an Ultimate 3000 RSLC-Nano liquid chromatography system.\n\nSamples 1122415-1122420: de-phosphorylated\nSamples 1123298-1123300: phosphorylated","fileCount":"25","fileSizeKB":"43822793","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Centrosomes;Cell Division;Microtubules;Tensile Forces;C. elegans","pi":[{"name":"Jeffrey Woodruff","email":"jeffrey.woodruff@utsouthwestern.edu","institution":"UT Southwestern Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c0d0e962ae4f4b6e87302807b1158141","id":"3071"}, {"dataset":"MSV000093770","datasetNum":"93770","title":"Mechanisms of microbial magnetite oxidation by Sideroxydans lithotrophicus ES-1","user":"yayu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704419060000","created":"Jan. 4, 2024, 5:44 PM","description":"Iron-oxidizing bacteria are widely found in natural and man-made environments where they influence varied biogeochemical cycles. Despite their prevalence, the mechanisms and Fe(II) substrates used by these organisms remain understudied. To date, there has been limited exploration of the ability of iron-oxidizing bacteria to utilize solid minerals as electron donors. Sideroxydans lithotrophicus ES-1 is a robust, facultative iron oxidizer with multiple enzymatic pathways for iron oxidation, making it a prime candidate for evaluating extracellular electron uptake mechanisms. In this study, S. lithotrophicus ES-1 was grown on dissolved Fe(II)-citrate and three preparations of magnetite that provided different ratios of soluble and solid Fe(II). S. lithotrophicus ES-1 grew equally well on the different batches of magnetite, suggesting it can adapt to the type of iron present during growth. S. lithotrophicus ES-1 oxidized all available dissolved Fe2+ released from magnetite, and continued to build biomass when only solid Fe(II) remained. Quantitative proteomic analyses of S. lithotrophicus ES-1 grown on these substrates revealed proteome remodeling in response to electron donor and growth state, and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, the MtoAB complex was only expressed during growth on the solid magnetite, suggesting these proteins play a role in oxidation of solid minerals in S. lithotrophicus ES-1. A set of cupredoxin domain-containing proteins were also identified that were specifically expressed during solid iron oxidation. This work confirmed the iron oxidizer, S. lithotrophicus ES-1, utilized distinct extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II)-citrate. The presence of multiple pathways, and the ability to regulate their expression and use, could benefit iron-oxidizing bacteria that encounter various electron donors in their environments. ","fileCount":"73","fileSizeKB":"75587134","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sideroxydans lithotrophicus (NCBITaxon:63745)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Quantitative proteomics;E3technology;Sideroxydans lithotrophicus ES-1;Extracellular electron transport","pi":[{"name":"CLARA CHAN","email":"cschan@udel.edu","institution":"School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6185a143ba0b4573803ee09a251ef9e2","id":"3072"}, {"dataset":"MSV000093768","datasetNum":"93768","title":"A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival","user":"brettsp1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1704404462000","created":"Jan. 4, 2024, 1:41 PM","description":"Lysosomal damage is a major threat to cell survival. Our previous work has reported that lysosomal damage induces stress granule (SG) formation. However, the significance of SG formation on cell fate and the precise mechanisms by which lysosomal damage triggers SG formation remains unclear. Here, we show that SG formation is initiated through a novel calcium-dependent pathway and plays a significant role in promoting cell survival in response to lysosomal damage. Mechanistically, we demonstrate that during lysosomal damage, ALIX (ALG2-interacting protein X) together with its partner, the calcium-binding protein ALG2, transduces lysosomal damage signals by detecting calcium leakage to induce SG formation by controlling the phosphorylation of eIF2alpah. ALIX facilities SG formation by coordinating the upstream regulation of eIF2alpha phosphorylation via PKR and PACT. We also found this regulatory event of SG formation occur on damaged lysosomes. Collectively, these investigations reveal novel insight into the precise regulation of SG formation, and the interaction between damaged lysosomes and stress granules. 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This is data backup for the positive mode polar HILIC column dataset.","fileCount":"368","fileSizeKB":"4140351","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Trypanosoma cruzi (NCBITaxon:5693)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"chagas disease;human serum;disease progression;polar HILIC;metabolomics","pi":[{"name":"Dr. McCall","email":"lmccall@ou.edu","institution":"OU","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"25e165d510f64156a6c0b8e590ab74cb","id":"3091"}, {"dataset":"MSV000093739","datasetNum":"93739","title":"Constitutively active Gli2 co-IP\/MS in ciliated and unciliated cells","user":"pniewiadomski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703941156000","created":"Dec. 30, 2023, 4:59 AM","description":"Co-IP\/MS of HA-Gli2 (P1-6A), the constitutively active mutant of Gli2 in NIH\/3T3 Flp-in cells. The cells were either ciliated or depleted of cilia by expression of the dominant negative mutant of Kif3a (dnKif3a). Sample 8033:A is ciliated cells, sample 8033:B is unciliated cells.","fileCount":"8","fileSizeKB":"54063","spectra":"0","psms":"17594","peptides":"3111","variants":"3871","proteins":"610","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Gli proteins;Hedgehog signaling;Primary cilium;co-IP\/MS","pi":[{"name":"Pawel Niewiadomski","email":"p.niewiadomski@cent.uw.edu.pl","institution":"University of Warsaw","country":"Poland"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"1890e67d5ffd4ae6849b8d267bbca9cb","id":"3092"}, {"dataset":"MSV000093738","datasetNum":"93738","title":"Gli3 co-IP\/MS in SAG-treated NIH\/3T3 cells","user":"pniewiadomski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703936766000","created":"Dec. 30, 2023, 3:46 AM","description":"Co-IP\/MS of Gli3 from NIH\/3T3 cells treated with the smoothened agonist SAG fractionated into nuclear and cytoplasmic fractions. 10091, 10092, 10093, 10095, 10096 are nuclear fraction samples, 10094, 10097 are cytoplasmic fraction samples. ","fileCount":"24","fileSizeKB":"141866","spectra":"0","psms":"12089","peptides":"6988","variants":"8433","proteins":"2023","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"LTQ Orbitrap Velos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:7 - \\\"Deamidation.\\\";MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\"","keywords":"Hedgehog signaling;Gli proteins;Smoothened agonist (SAG);co-IP","pi":[{"name":"Pawel Niewiadomski","email":"p.niewiadomski@cent.uw.edu.pl","institution":"University of Warsaw","country":"Poland"},{"name":"Rajat Rohatgi","email":"rrohatgi@stanford.edu","institution":"Stanford University School of Medicine","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"b93cfe207f8247b388cce7049dc80db0","id":"3093"}, {"dataset":"MSV000093737","datasetNum":"93737","title":"Combinatorial Synthesis Test For this Tutorial","user":"kyvittali","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703921860000","created":"Dec. 29, 2023, 11:37 PM","description":"al;kdfjal;kdjfa;ldjsfla;kdjfl;akjdflkajddfl;kajdf;lkajds","fileCount":"4","fileSizeKB":"236798","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Not Applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"GNPS-CMMC-library","pi":[{"name":"Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1eb5eca6f1e4437480e396a49fd57e36","id":"3094"}, {"dataset":"MSV000093736","datasetNum":"93736","title":"Proteomics of periphery blood in Aortic Dissection","user":"yufeizhao","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703907949000","created":"Dec. 29, 2023, 7:45 PM","description":"Serum protein changes in aortic dissection patients and healthy subjects were identified. LC-MS\/MS biospectrometry was performed for 2 groups, combined with reductase hydrolysis of protein molecules in solution and high-resolution and sensitive LC-MS\/MS detection.","fileCount":"3","fileSizeKB":"1052","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Bruker Daltonics instrument model","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"aortic dissection","pi":[{"name":"Yufei Zhao","email":"yufeizhaoo@163.com","institution":"Zhongshan Hospital, Fudan University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0a6d8710fae54473a690f8f59f5e9d01","id":"3095"}, {"dataset":"MSV000093735","datasetNum":"93735","title":"GNPS-CMMC-library - Combinatorial Synthesis with Decarboxylated Amino Acids","user":"cal020","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703907949000","created":"Dec. 29, 2023, 7:45 PM","description":"Combinatorial synthesis of tryptamine, tyramine, serotonin, dopamine, putrescine, cadaverine, agmatine, histamine, and phenethylamine with acetic anhydride, butyric anhydride, acryloyl chloride, hexanoyl chloride, decanoyl chloride, palmitoyl chloride, and stearoyl chloride respectively. The files also contain the synthesis of tryptamine specifically with acetic anhydride and butyric anhydride respectively. ","fileCount":"19","fileSizeKB":"2093992","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"GNPS-CMMC-library","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9d2ddeaf7a274e8eaa4d99500210f160","id":"3096"}, {"dataset":"MSV000093733","datasetNum":"93733","title":"Integrating mutliple datasets to identify protein ligand interactions in Ecoli-set2","user":"venkatesh04","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703788635000","created":"Dec. 28, 2023, 10:37 AM","description":"Integrating two chromotography techniques data set2-DIA experiment","fileCount":"18","fileSizeKB":"37304671","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Exploris 480","modification":"oxidation [M]","keywords":"chromotography, metabolomics, proteomics, systems biochemistry","pi":[{"name":"Venkatesh Thirumalaikumar","email":"vpthirum@purdue.edu","institution":"Purdue University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"47a2653900494c3cb7888bbfec42ef8e","id":"3097"}, {"dataset":"MSV000093732","datasetNum":"93732","title":"UBQLN2 Governs Lipid Metabolism Linked to Neurodegeneration in ALS\/FTD","user":"haolab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703730063000","created":"Dec. 27, 2023, 6:21 PM","description":"Missense mutations in UBQLN2, a protein quality control factor, are associated with neurodegenerative diseases amyotrophic lateral sclerosis (ALS) overlapping with frontotemporal dementia (FTD). The mechanisms by which these mutations lead to neurodegeneration are not fully understood. Here we describe a critical role for UBQLN2 in regulating cellular lipid metabolism, which is crucial for cell survival under nutrient stress. The stress dependent regulation of lipid metabolism by UBQLN2 is mediated by ILVBL, a UBQLN2 substrate and a key enzyme in lipid turnover. The function of UBQLN2 in promoting ILVBL degradation and maintaining intracellular lipids was compromised by ALS\/FTD-linked mutations in UBQLN2. As a result of the lipid dysregulation, synaptic vesicles were deficient and neuronal death was exacerbated in mutant UBQLN2 transgenic mice or human iPSCs derived motor neurons and cortical organoids. Replenishing lipids or restoring UBQLN2 function could reverse the deficits in the UBQLN2 mutant neurons under nutrient stress. Our study reveals UBQLN2 essential role in lipid metabolism and suggests metabolic imbalance underlying ALS\/FTD and related neurodegenerative conditions.","fileCount":"16","fileSizeKB":"32780232","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"UBQLN2;ALS;FTD;frontotemporal dementia ;amyotrophic lateral sclerosis ;motor neuron;dynamic SILAC;dSILAC;SILAC;pSILAC","pi":[{"name":"Ling Hao","email":"linghao@gwu.edu","institution":"The George Washington University","country":"United States of America "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD048152","task":"35a3cf96ea5d43a19b42af847f9f9aba","id":"3098"}, {"dataset":"MSV000093730","datasetNum":"93730","title":"Proteins associated with Impaired Acrosomal Exocytosis (IAE) can be identified in sperm from subfertile Thoroughbred stallions by using data-independent acquisition mass spectrometry (DIA-MS)","user":"stweintraub","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703706869000","created":"Dec. 27, 2023, 11:54 AM","description":"Thoroughbred stallions that carry a double-homozygous genotype A\/A-A\/A for SNPs rs397316122 and rs69101140 in exon 5 of the FKBP6 gene (chr13; EquCab3.0) are uniquely subfertile due to impaired acrosomal exocytosis (IAE). However, clear causation of this condition has not been determined. In the current study, the sperm proteome in frozen\/thawed semen from three fertile TB stallions and three subfertile TB stallions (FKBP6 genotype A\/A-A\/A) was studied using mass spectrometry-based global proteomics. Sperm from both stallion groups were incubated in Lactate-Modified Whitten's (Lac-MW) medium to induce spontaneous acrosomal exocytosis in viable sperm (AE\/Viable). At 0h, 2h, 4h, and 6h, sperm aliquots were removed for analysis for AE\/Viable using flow cytometry (Fixable Live\/Dead Red + FITC-PSA) global proteomics via data-independent acquisition mass spectrometry (DIA-MS). Student's t-tests and two-way ANOVA with Benjamini-Hochberg multiple testing correction (FDR q-value 0.05) were used to determine differences in AE\/Viable and protein relative abundance between experimental groups and incubation periods. At 4h and 6h of incubation, the mean AE\/Viable was higher in the fertile than in the subfertile stallions (41 and 44% vs. 14 and 16%, respectively; p < 0.05). A total of 2220 proteins was identified by DIA-MS. Using strict selection criteria (FDR 1.0%, q-value < 0.05, and fold-change < 1.5 or > 1.5), 140 proteins were found to be differentially abundant in sperm from the subfertile stallions when compared to that of the fertile stallions (83 less and 57 more abundant) at 0h incubation. Using bioinformatic analyses, most of the proteins of lower abundance in sperm from subfertile stallions were found to be overrepresented in the \"metabolism\" (32 proteins) and \"metabolism of lipids\" (18 proteins) pathways (Homo sapiens orthologs; Reactome database). Two of these proteins, arylsulfatase F (ARSF; log2 fold change = -2.0; p < 0.05) and zona pellucida-binding protein 2 (ZPBP2; log2 fold change = -1.7; p < 0.05), are acrosomal proteins known to play a fundamental role in sperm-oocyte binding. By using immunofluorescence, at 0h of incubation in MW-Lac, ARSF was identified at the acrosome, mid-, and principal piece in sperm from fertile TB stallions, while only at the mid-and principal piece in sperm from subfertile TB stallions. No evidence of ZPBP2 was observed in sperm from both stallion groups at 0h incubation in Lac-MW. Sperm from subfertile Thoroughbred stallions were bound to porcine zonae pellucidae at a lower frequency than sperm from fertile Thoroughbred stallions. In conclusion, DIA-MS is a powerful tool to identify candidate proteins that contribute to the etiology of IAE in Thoroughbred stallions, including proteins of acrosome origin that have a role in the sperm-oocyte binding process.","fileCount":"32","fileSizeKB":"57023375","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Equus caballus (NCBITaxon:9796)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"stallion sperm;Thoroughbred;impaired acrosomal exocytosis;proteomics;mass spectrometry;acrosome enzymes;arylsulfatase F;zona pellucida-binding protein 2","pi":[{"name":"Charles C. Love, D.V.M., Ph.D.","email":"clove@cvm.tamu.edu","institution":"Texas A&M University, School of Veterinary Medicine and Biomedical Sciences","country":"U.S.A."}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048150","task":"f0c93cb3bec4460dbfb9c439c0ada22d","id":"3099"}, {"dataset":"MSV000093729","datasetNum":"93729","title":"cyanolichen collection North West United State ","user":"yux_OSU1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703631889000","created":"Dec. 26, 2023, 3:04 PM","description":"Cyanolichen collections from NW US (Oregon, Washington, North California), collected from 2019~2023. Including several Lobaria sp, Nephroma sp, Collema sp and Peltigera sp. ","fileCount":"87","fileSizeKB":"4408918","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Nostoc sp. 'Lobaria scrobiculata cyanobiont' (NCBITaxon:150843);Lobaria oregana (NCBITaxon:63753);Lobaria pulmonaria (NCBITaxon:86794);Lobariaceae (NCBITaxon:129109);Lobaria anomala (NCBITaxon:169139);Lobaria scrobiculata (NCBITaxon:176461);Nephroma (NCBITaxon:48858);Nephroma laevigatum (NCBITaxon:203386);Nephroma parile (NCBITaxon:203387);Peltigera leucophlebia (NCBITaxon:52883);Peltigera collina (NCBITaxon:78473);Collema (NCBITaxon:203431)","instrument":"6545 Q-TOF LC\\\/MS","modification":"raw data file ","keywords":"Lichen cyanobacterial algae fungi symbios","pi":[{"name":"Kerry McPhail","email":"kerry.mcphail@gmail.com","institution":"Oregon State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fbeb6b30f7a1409d82bee27fbe6ea0af","id":"3100"}, {"dataset":"MSV000093728","datasetNum":"93728","title":"Large scale, quantitative top-down proteomic analysis of human frontal gyrus brain tissue samples in the context of Alzheimer's disease","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703610514000","created":"Dec. 26, 2023, 9:08 AM","description":"15-35 mg brain tissue plugs derived from dorsal lateral prefrontal cortex (DLPFC) were homogenized on ice with a pellet pestle homogenizer in a 1.5 mL LoBind Eppendorf tube after addition of 8 uL hexafluoroisopropanol (HFIP) \/ mg tissue. Once tissue was fully disrupted, an equivolume amount of homogenization buffer (HB, consisting of 8 M urea, 10 mM ammonium bicarbonate (ABC), 10 mM tris(2-carboxyethyl)phosphine (TCEP), 2 mM EDTA) was added and then vortexed for 1 min, before separation into soluble (referred to as \"AB\" in the datasets) and insoluble (referred to as \"WO\" in the datasets) fractions. Samples were analyzed using a Waters NanoACQUITY UPLC system with mobile phases consisting of 0.2% FA in H2O (Mobile Phase A) and 0.2% FA in ACN (Mobile Phase B). Both trapping-precolumn (200 um i.d., 5-cm length) and analytical column (100 um i.d., 50-cm length) were slurry-packed with C2 packing material (5 um and 3 um for trap\/analytical respectively, 300 A, Separation Methods Technology). Samples were loaded into a 10 uL loop, corresponding to 2.5 or 5 ug of loaded material and injected onto the trapping column with an isocratic flow of 1% B at 5 uL\/min over 15 min for desalting. Separation was performed with a 1% to 50% B gradient over 160 min at 300 nL\/min. For MS\/MS analysis of proteins, the NanoACQUITY system was coupled to a Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer equipped with the FAIMS Pro interface. Source parameters included electrospray voltage of 2.2 kV, transfer capillary temperature of 275 C, and ion funnel RF amplitude of 30%. FAIMS was set to standard resolution without supplementary user-controlled carrier gas flow and a dispersion voltage (DV) of -5 kV (equivalent to a dispersion field of -33.3 kV\/cm), while the compensation voltage (CV) switched between three voltages (-50,-40, and -30) throughout data collection (referred to as \"internal CV stepping\"). The Fusion Lumos was set to \"Intact Protein\" application mode, and data was collected as full profile. Proteoform identification was performed with TopPIC version 1.5.4. Settings for TopPIC included a precursor window of 3 m\/z, mass error tolerance of 15 ppm, a proteoform cluster error tolerance of 0.8 Da, a mass shift upper bound of 4000 Da and lower bound of -150 Da, and a maximum number of allowed unknown modifications of 1. All databases were scrambled to generate decoys which were concatenated during the search. A list of 12 dynamic modifications were provided during the open modification search to reduce the number of unknown mass shifts. Downstream data analysis was performed with TopPICR.","fileCount":"825","fileSizeKB":"3379872692","spectra":"2059870","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:2 - \\\"Amidation.\\\";UNIMOD:5 - \\\"Carbamylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:425 - \\\"Dihydroxy.\\\"","keywords":"dementia;brain;FAIMS;top-down proteomics;intact protein;TopPIC","pi":[{"name":"Vladislav Petyuk","email":"vladislav.petyuk@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0cc67dac2ed74fd0b6ef69d6ae54d8aa","id":"3101"}, {"dataset":"MSV000093727","datasetNum":"93727","title":"Differential solubilization and top-down proteomics with FAIMS control experiments applied to mouse brain","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703564913000","created":"Dec. 25, 2023, 8:28 PM","description":"5-35 mg brain tissue plugs from mouse left or right hemisphere were homogenized on ice with a pellet pestle homogenizer in a 1.5 mL LoBind Eppendorf tube after addition of 8 uL hexafluoroisopropanol (HFIP) \/ mg tissue. Once tissue was fully disrupted, an equivolume amount of homogenization buffer (HB, consisting of 8 M urea, 10 mM ammonium bicarbonate (ABC), 10 mM tris(2-carboxyethyl)phosphine (TCEP), 2 mM EDTA) was added and then vortexed for 1 min, before separation into soluble (referred to as \"HFIP\" in the datasets) and insoluble (referred to as \"Urea\" in the datasets) fractions. Samples were analyzed using a Waters NanoACQUITY UPLC system with mobile phases consisting of 0.2% FA in H2O (Mobile Phase A) and 0.2% FA in ACN (Mobile Phase B). Both trapping-precolumn (200 um i.d., 5-cm length) and analytical column (100 um i.d., 50-cm length) were slurry-packed with C2 packing material (5 um and 3 um for trap\/analytical respectively, 300 A, Separation Methods Technology). Samples were loaded into a 10 uL loop, corresponding to 2.5 or 5 ug of loaded material and injected onto the trapping column with an isocratic flow of 1% B at 5 uL\/min over 15 min for desalting. Separation was performed with a 1% to 50% B gradient over 160 min at 300 nL\/min. For MS\/MS analysis of proteins, the NanoACQUITY system was coupled to a Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometer equipped with the FAIMS Pro interface. Source parameters included electrospray voltage of 2.2 kV, transfer capillary temperature of 275 C, and ion funnel RF amplitude of 30%. FAIMS was set to standard resolution without supplementary user-controlled carrier gas flow and a dispersion voltage (DV) of -5 kV (equivalent to a dispersion field of -33.3 kV\/cm), while the compensation voltage (CV) switched between three voltages (-50, -40, and -30) throughout data collection (referred to as \"internal CV stepping\"). The Fusion Lumos was set to \"Intact Protein\" application mode, and data was collected as full profile. Proteoform identification was performed with TopPIC version 1.5.4. Settings for TopPIC included a precursor window of 3 m\/z, mass error tolerance of 15 ppm, a proteoform cluster error tolerance of 0.8 Da, a mass shift upper bound of 4000 Da and lower bound of -150 Da, and a maximum number of allowed unknown modifications of 1. All databases were scrambled to generate decoys which were concatenated during the search. A list of 12 dynamic modifications were provided during the open modification search to reduce the number of unknown mass shifts. Downstream data analysis was performed with TopPICR.","fileCount":"228","fileSizeKB":"720428374","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:2 - \\\"Amidation.\\\";UNIMOD:5 - \\\"Carbamylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:425 - \\\"Dihydroxy.\\\"","keywords":"dementia;brain;FAIMS;top-down proteomics;intact protein","pi":[{"name":"Vladislav Petyuk","email":"vladislav.petyuk@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7abe1ef9c1104d3f902e71b0038d48d1","id":"3102"}, {"dataset":"MSV000093724","datasetNum":"93724","title":"Essential role of STAT5 tyrosine phosphorylation in vivo","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703347361000","created":"Dec. 23, 2023, 8:02 AM","description":"STAT5 proteins are vital for lymphocyte development and function. Tyrosine phosphorylation of a C-terminal tyrosine is the key event in cytokine activation of STAT5A and STAT5B. However, the role of STAT5 tyrosine phosphorylation has not been assessed in vivo. Here we generated Stat5a and Stat5b tyrosine mutant knock-in (KI) mice and found that these animals had greatly reduced CD8+ T cell numbers. These cells exhibited profoundly diminished proliferation in response to IL-2, correlating with greatly reduced IL-2-induced pRB and a block in the G1-->S phase transition. The mutant cells also exhibited decreased IL-2-mediated activation of pERK and pAKT, which can in part be attributed to diminished IL-2-induced expression of IL-2R-beta and IL-2R-gamma. Our findings highlight that the tyrosine phosphorylation of both STAT5A and STAT5B is essential for maximal IL-2 signaling and elucidate the molecular basis for achieving an optimal mitogenic effect of IL-2 on CD8+ T cells. [doi:10.25345\/C5833N851] [dataset license: CC0 1.0 Universal (CC0 1.0)]\n\n","fileCount":"13","fileSizeKB":"18813441","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Stat5, cytokine, IL-2, T cell, NK cell, tyrosine phosphorylation","pi":[{"name":"Warren Leonard","email":"leonardw@nhlbi.nih.gov","institution":"National Institute of Health, National Heart, Lung , and Blood Institute","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"687ab326b8bf4a068f6308c12cc75832","id":"3103"}, {"dataset":"MSV000093722","datasetNum":"93722","title":"Laser capture microdissected functional tissue units from kidney for top-down proteomic characterization using microPOTS","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703280282000","created":"Dec. 22, 2023, 1:24 PM","description":"Human kidney tissue obtained from Vanderbilt University Biomolecular Multimodal Imaging Center (BIOMIC) was laser capture microdissected onto microPOTS chips. Six replicates of 100,000 um2 from three distinct functional tissue units (glomeruli, tubules, and medullary rays) were acquired from a 10 um thick kidney section. Each microPOTS well had a diameter of 2.2 mm and was preloaded with 2 uL of DMSO as the capture liquid. DMSO was evaporated by heating the chip at 70C and protein extraction was performed by adding 2 uL lysis buffer in each well, containing 2.5 units\/uL benzonase nuclease, 2 mM MgCl2, 10 mM TCEP, 0.2% DDM and 4 M urea in 50 mM ABC. The mixture was incubated for 1 hr at 37C. Following incubation, the sample was acidified by adding 500 nL of 5% formic acid into each well and dried thoroughly in a vacuum chamber where the chips were stored at -20C until LC-MS\/MS analysis. Samples were analyzed with an Orbitrap Fusion Lumos mass spectrometer in intact protein mode and data was searched using TopPIC (version 1.4) before downstream analysis in R with the TopPICR R package","fileCount":"42","fileSizeKB":"303306313","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2 - \\\"Amidation.\\\";UNIMOD:5 - \\\"Carbamylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:425 - \\\"Dihydroxy.\\\"","keywords":"microPOTS;nanoPOTS;laser capture microdissection;HuBMAP;top-down proteomics;kidney","pi":[{"name":"Ljiljana Pasa-Tolic","email":"ljiljana.pasatolic@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f7afef33eea446d99f72f3220ef53a64","id":"3104"}, {"dataset":"MSV000093721","datasetNum":"93721","title":"UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER","user":"aordureau","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703264008000","created":"Dec. 22, 2023, 8:53 AM","description":"Supporting MS data for paper (doi: 10.1038\/s41586-024-07073-0) by DaRosa P.A., Penchev I. et al., titled \"UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER\". Index of MS supporting files uploaded: Related to Related to Fig. 1b, c (xb01004(UFM1), xb01005(SBP-UFM1): LFQ IP-MS (Unimod: 35; 4)). See also MSV000093510","fileCount":"3","fileSizeKB":"536749","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Label Free;UFM1;UFMylation","pi":[{"name":"Alban Ordureau","email":"OrdureaA@mskcc.org","institution":"Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0e530a15a2294bc99207c127f8896557","id":"3105"}, {"dataset":"MSV000093718","datasetNum":"93718","title":"Global phosphoproteomics for CRISPR\/Cas9 mediated PTPN22 Ser325 mutagenesis on Jurkat cells","user":"leighanarossitto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703212871000","created":"Dec. 21, 2023, 6:41 PM","description":"LQF of 3x FLAG PTPN22 WT Jurkat cells compared to S325A and S325E KI mutant Jurkat cells. WT or KI lines were stimulated with or without TCR engagement for 5 min.","fileCount":"25","fileSizeKB":"11989776","spectra":"0","psms":"194313","peptides":"45184","variants":"61590","proteins":"6705","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"PTPN22;Protein tyrosine kinase;Protein tyrosine phosphatase;T cell signaling;Phosphoproteomics;Jurkat cells","pi":[{"name":"David J Gonzalez","email":"djgonzalez@health.ucsd.edu","institution":"UCSD","country":"US"},{"name":"Nunzio Bottini","email":"nbottini@ucsd.edu","institution":"ACTRI","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048064","task":"15146bf0ee54420aa8f1b51ef170ee19","id":"3106"}, {"dataset":"MSV000093717","datasetNum":"93717","title":"Immunoprecipitated PTPN22 Phosphoproteomics from Jurkat Cells","user":"leighanarossitto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703211847000","created":"Dec. 21, 2023, 6:24 PM","description":"3x FLAG tagged PTPN22 were immunoprecipitated from Jurkat cells stimulated by TCR for 5min, and the proteins were eluted by FLAG peptides. This study aims to explore the phosphorylation sites on PTPN22 phosphatase, identifying two phosphorylation sites Ser325 and Ser449.","fileCount":"16","fileSizeKB":"2379885","spectra":"0","psms":"35190","peptides":"12000","variants":"14161","proteins":"2119","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"PTPN22;Protein tyrosine kinases;Protein tyrosine phosphatases;T cell signaling;IP-MS","pi":[{"name":"David J Gonzalez","email":"djgonzalez@health.ucsd.edu","institution":"UCSD","country":"US"},{"name":"Nunzio Bottini","email":"nbottini@ucsd.edu","institution":"ACTRI","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048062","task":"3c2f9f61437541df82eb516479676ba0","id":"3107"}, {"dataset":"MSV000093713","datasetNum":"93713","title":"The loss of the PDIM\/PGL virulence lipids causes differential secretion of ESX-1 sub-strates in Mycobacterium marinum","user":"mchampio","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703180735000","created":"Dec. 21, 2023, 9:45 AM","description":"Raw and processed files in support of manuscript\nThe loss of the PDIM\/PGL virulence lipids causes differential secretion of ESX-1 sub-strates in Mycobacterium marinum \n\nThe Virulence Lipid PDIM\/PGL is essential for optimal protein secretion in Mycobacte-rium marinum \n\nWT, PDIM and complement strains lysate and culture filtrate analysis of proteomes","fileCount":"5490","fileSizeKB":"258093029","spectra":"0","psms":"45049","peptides":"21446","variants":"28849","proteins":"2599","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium marinum M (NCBITaxon:216594)","instrument":"timsTOF Pro 2","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"PDIM;Mycobacteria;Acetylation;Secretion;Type VII;Bacteria","pi":[{"name":"Matthew Champion","email":"mchampio@nd.edu","institution":"University of Notre Dame","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048051","task":"8ab62ffefac34e1fa0ecf6ddf0d153bf","id":"3108"}, {"dataset":"MSV000093712","datasetNum":"93712","title":"Dark respiration optimizes photosynthesis carbon yield in cyanobacteria","user":"wangx98","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703177405000","created":"Dec. 21, 2023, 8:50 AM","description":"Cyanobacteria and plants experience daily diel light\/dark growth. Respiration in the dark supports survival of the photosynthetic cells by oxidizing storage compound fixed during the day. Dark respiration thus significantly lowers the overall photosynthetic carbon yield. Optimal dark respiration could minimize carbon loss and improve overall photosynthetic carbon yield. However, it is unclear how photosynthetic organisms best allocate carbon resources at night for dark survival and preparation for the reinitiation of carbon fixation reactions upon light exposure. We show in the cyanobacterium Synechococcus elongatus PCC 7942 that an integrative respiratory pathway in the dark helps allocate carbon resource for cell survival and preparation for photosynthesis reinitiation upon photoinduction. Optimization of dark respiration thus represents a unique strategy to enhance photosynthetic carbon yield and potential crop productivity.","fileCount":"337","fileSizeKB":"29408996","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechococcus elongatus PCC 7942 (NCBITaxon:1140)","instrument":"LTQ Orbitrap XL","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"photosynthesis;dark respiration;cyanobacteria","pi":[{"name":"Xin Wang","email":"wangx3@ufl.edu","institution":"University of Florida","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048049","task":"804bf7750d654412a844ab58357178aa","id":"3109"}, {"dataset":"MSV000093709","datasetNum":"93709","title":"Integrating mutliple datasets to identify protein ligand interactions in E.coli","user":"venkatesh04","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703173818000","created":"Dec. 21, 2023, 7:50 AM","description":"Integrating two chromatographies in a co-fractionation mass spectrometry approach improved protein-metabolite interactions mapping capabilities and revealed novel protein-ligand pairings in Escherichia coli.","fileCount":"18","fileSizeKB":"35461939","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"E.coli BW25113","instrument":"Orbitrap Exploris 480","modification":"oxidation [M]","keywords":"Escherichia coli, protein-metabolite interactions, lumichrome, dipeptides, omniTICC, PROMIS, CF-MS","pi":[{"name":"Venkatesh thirumalaikumar","email":"vpthirum@purdue.edu","institution":"Purdue University","country":"United States "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dcf2c1935ab7418e9711f04e44c3b21f","id":"3110"}, {"dataset":"MSV000093708","datasetNum":"93708","title":"AhyBURP source data submission","user":"Rolandoo1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703172794000","created":"Dec. 21, 2023, 7:33 AM","description":"Source data for Figure 4 and Figure 5 of manuscript \"An intramolecular macrocyclase in plant ribosomal peptide biosynthesis\", Lisa S. Mydy, Jordan Hungerford, Desnor N. Chigumba, Jamie R. Konwerski, Sarah C. Jantzi, Di Wang, Janet L. Smith, Roland D. Kersten. Please see manuscript for experimental details of datasets.","fileCount":"22","fileSizeKB":"3173693","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arachis hypogaea (NCBITaxon:3818)","instrument":"Orbitrap Fusion","modification":"MOD:00372 - \\\"A protein modification that effectively cross-links two L-tyrosine residues with a carbon-carbon bond to form 3'-(3'-L-tyrosinyl)-L-tyrosine.\\\"","keywords":"BURP domain, legumenin, lyciumin, AhyBURP, autocatalysis","pi":[{"name":"Lisa Mydy, Roland Kersten","email":"rkersten@umich.edu","institution":"University of Michigan, Ann Arbor","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc7d51c8c92f4984b6ef33a40058e07c","id":"3111"}, {"dataset":"MSV000093705","datasetNum":"93705","title":"Schreiber_2023_VS1_Exploring options for proximity-dependent biotinylation experiments","user":"Younlab_Toronto","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703171590000","created":"Dec. 21, 2023, 7:13 AM","description":"This dataset consists of 52 raw mass spectrometry files and associated peak lists and results files, acquired on a Thermo Orbitrap Exploris 480 operated in Data-Dependent Acquisition mode. Samples were generated by Karl Schreiber (clones were generated by Eileigh Kadijk and Karl Schreiber) and affinity purification and mass spectrometric acquisition were performed by Karl Schreiber. Analysis was performed by Karl Schreiber and Ji-Young Youn. The files are associated with a manuscript by Karl Schreiber et al. that evaluates different labeling enzymes and affinity resins for proximity-dependent biotinylation experiments. Ji-Young Youn is the corresponding author for the manuscript and should be contacted for questions regarding this dataset (jiyoung.youn@sickkids.ca). \n\nThis submission is associated with three Supplementary Files (in addition to this README file):\n\nTable I describes the composition of this dataset (sample information)\nTable II lists all the peptide identification evidence (per MSFragger)\nTable III lists the SAINTexpress interactions for all analyses performed","fileCount":"216","fileSizeKB":"102264321","spectra":"0","psms":"1970235","peptides":"98928","variants":"124262","proteins":"17455","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:00408 - \\\"A protein modification that effectively replaces a residue amino or imino hydrogen with an acetyl group.\\\"","keywords":"proximity-dependent biotinylation, BioID, miniTurbo, APEX2, TDP-43, TARDBP, Streptavidin Sepharose, MagResyn MS, SAINTexpress, proximal interactions","pi":[{"name":"Ji-Young Youn","email":"jiyoung.youn@sickkids.ca","institution":"Hospital for Sick Children","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD048043","task":"05fbac5be8f34774b25fc7c773cbe02f","id":"3112"}, {"dataset":"MSV000093703","datasetNum":"93703","title":"A chemoproteomics method for direct and comprehensive characterization of cysteine reversible oxidation","user":"xusenhan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703129702000","created":"Dec. 20, 2023, 7:35 PM","description":"Cysteine oxidation is a series of protein modifications caused by reactive oxygen species (ROS) in cells and can regulate protein functions and cellular activities. Comprehensive and site-specific characterization of the cysteine oxidation is critical for understanding the role of ROS regulating cellular events. Here we developed a chemoproteomics method to directly and systematically detect the reversible cysteine oxidation sites. Different from the commonly used methods for indirect detection of cysteine oxidation, this method allows for direct targeting of oxidized cysteine for MS analysis. The method was validated using small molecules containing oxidized cysteines and the whole cell lysate treated with the probe, demonstrating that it specifically targets reversible oxidized cysteines. In total, 3000-4000 proteins containing cysteine oxidation sites were identified from Jurkat, MCF7 and HEP G2 cells, respectively. Combining with multiplexed proteomics, we applied the method to quantify cysteine oxidation changes in the livers from mice fed with the high or low fat diet (HFD\/LFD). It was found that the overall cysteine oxidation in mouse liver was dramatically upregulated with HFD, and the upregulation is correlated with protein distribution, functions, and the flanking residues of the oxidation sites. Many biological processes critical in the pathology of fatty liver diseases are also significantly enriched among the oxidized proteins with higher abundance in the HFD samples, suggesting the potential regulatory role of cysteine oxidation in the diseases. Additionally, the method was applied to study the cysteine oxidation change in THP-1 cells with the lipopolysaccharide treatment, and among >15000 cysteine oxidation sites quantified in THP-1 cells, many of them were upregulated under the treatment. For the oxidized proteins with upregulated oxidation sites, they are associated with inflammation and immune response, indicating the potential role of cysteine oxidation in regulating cellular response to bacterial infection. This chemoproteomics method can be widely applied to comprehensively study cysteine oxidation events in various samples. ","fileCount":"133","fileSizeKB":"70791309","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite;Orbitrap Exploris 480","modification":"cysteine oxidation","keywords":"proteomics;protein modifications;Cysteine oxidation","pi":[{"name":"Ronghu Wu","email":"ronghu.wu@chemistry.gatech.edu","institution":"Georgia Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"167225dae97d47b8a990bd62db3a1a8e","id":"3113"}, {"dataset":"MSV000093700","datasetNum":"93700","title":"GNPS - Native metabolomics with E.coli CutA and Isosepiapterin","user":"Nike","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703069262000","created":"Dec. 20, 2023, 2:47 AM","description":"Native MS with E.coli CutA and Isosepiapterin to check for putative binding. 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The resultant striatal tissue was extracted, homogenized in a detergent-free buffer, digested, and analyzed with LC\/MS-MS.\n\n","fileCount":"33","fileSizeKB":"30603104","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"astrocytes, obsessive-compulsive disorder, neuroscience, striatum","pi":[{"name":"Baljit Khakh","email":"bkhakh@mednet.ucla.edu","institution":"UCLA","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"85fd4ee2f7b54238be6860ddb918b807","id":"3115"}, {"dataset":"MSV000093696","datasetNum":"93696","title":"Glioblastoma Extracellular Vesicles Modulate Immune PD-L1 Expression in Accessory Macrophages upon Radiotherapy","user":"whaas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703018962000","created":"Dec. 19, 2023, 12:49 PM","description":"The aim of the study was to investigate the effects of ionizing radiation on CT-2A cells at the protein level, proteomics analyses were performed on CT-2A cells irradiated with 5 Gy. To investigate the effect of glioma-secreted extracellular vesicles (EVs) on bone-marrow-derived macrophages (BMDM) at the protein level, BMDM were exposed to EVs for 48 hours.\nMultiplexed mass spectrometry-based proteomics was performed using TMTpro barcoding reagents and the SPS-MS3 method on an Orbitrap Lumos mass spectrometer.\nSamples were labeled as follows:\nCT-2A CTRL samples: CT2A_Cells_CTRL_1 (126), CT2A_Cells_CTRL_2 (127n)\nCT-2A IR samples: CT2A_Cells_IR_1 (127c), CT2A_Cells_IR_2 (128n)\nBMDM samples: Macrophage_CTRL_1 (128c), Macrophage_CTRL_2 (129n)\nBMDM+EV samples: Macrophage_Plus_EV_1 (130c), Macrophage_Plus_EV_2 (131n)\nBMDM+irEV samples: Macrophage_Plus_irEV_1 (131c), Macrophage_Plus_irEV_2 (132n)\n","fileCount":"13","fileSizeKB":"4267087","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"304.207146 (TMTpro16\\\/18), lysine, N-terminus, static;57.02146374 (IAA), cysteine, static;15.9949146221 (oxidation), methionine, variable","keywords":"Extracellular Vesicles, GBM, Radiation, PD-L1, Immunosuppression, Macrophages, TMTpro, Orbitrap Lumos, SPS-MS3","pi":[{"name":"Bakhos Tannous","email":"Bakhos.tannous@astrazeneca.com","institution":"Massachusetts General Hospital and Harvard Medical School (Present address: Early Oncology R&D, ICC, AstraZeneca, Waltham, MA02451, USA)","country":"USA"},{"name":"Koen Breyne","email":"kbreyne@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"USA"},{"name":"Wilhelm Haas","email":"whaas@mgh.harvard.edu","institution":"Massachusetts General Hospital and Harvard Medical School","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"adc6630ea9ac4ca4a0d83cd2682a0bcb","id":"3116"}, {"dataset":"MSV000093695","datasetNum":"93695","title":"GNPS - Synthetic confirmation of bile acid-amine conjugates from 'Microbially-catalyzed conjugation of GABA and tyramine to bile acids'","user":"mullowney","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703016932000","created":"Dec. 19, 2023, 12:15 PM","description":"UPLC-MS\/MS data used to confirm the retention times of bile acid conjugates to GABA and tyramine that were detected in microbial culture and human fecal samples. Synthesized conjugates included here are GABA-deoxycholic acid, tyramine-deoxycholic acid, GABA-cholic acid, tyramine-cholic acid, GABA-chenodeoxycholic acid, and tyramine-chenodeoxycholic acid. Data of biological samples (B. fragilis P207 spiked with DCA, healthy human donor 11 feces, patient 207 v12 feces) from the same UPLCMS\/MS sequence is included for comparison and validation. All using positive ionization.","fileCount":"37","fileSizeKB":"1355771","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacteroides fragilis P207","instrument":"Orbitrap IQ-X (Thermo Scientific instrument model)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"bile acid;bile acid amidate;conjugated bile acid;GABA;tyramine","pi":[{"name":"Sean Crosson","email":"crosson4@msu.edu","institution":"Michigan State University","country":"United States "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9f92053a821f48018fc39b35206fda6f","id":"3117"}, {"dataset":"MSV000093694","datasetNum":"93694","title":"GNPS - IP-MS\/MS of chaperone pulldown of the HigBAC system during lambda and escape lambda infection","user":"cdoering","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703004888000","created":"Dec. 19, 2023, 8:54 AM","description":"Pulldown on the chaperone component of the HigBAC toxin-antitoxin-chaperone system during phage infection. Infection done with both phage lambda and an escape lambda that can escape defense by HigBAC.","fileCount":"13","fileSizeKB":"4","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Escherichia virus Lambda (NCBITaxon:10710)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lambda infection;toxin-antitoxin-chaperone systems;IP-MS\/MS","pi":[{"name":"Vasili Hauryliuk","email":"vasili.hauryliuk@med.lu.se","institution":"Lund University","country":"Sweden"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e85b3fb6ae254b148bfa155eb22f2b16","id":"3118"}, {"dataset":"MSV000093693","datasetNum":"93693","title":"Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703004165000","created":"Dec. 19, 2023, 8:42 AM","description":"Whole proteome analysis of iNeurons treated with bortezomib or bafilomycin.","fileCount":"46","fileSizeKB":"217360296","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"iNeurons;Bortezomib;Bafilomycin;Whole proteome","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047953","task":"30ed7f9b6e6f41c78387938c9723ddda","id":"3119"}, {"dataset":"MSV000093692","datasetNum":"93692","title":"GNPS - IP-MS\/MS of chaperone pulldown of the CmdTAC system during T4 infection","user":"cdoering","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703003706000","created":"Dec. 19, 2023, 8:35 AM","description":"Spectra from an IP-MS\/MS experiment to identify binding partners for the phage defense system CmdTAC. Done during infection with the bacteriophage T4 (NCBITaxon: 2681598)\r\n","fileCount":"12","fileSizeKB":"63","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562);Escherichia phage T4","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"IP-MS\/MS;phage;toxin-antitoxin systems","pi":[{"name":"Michael Laub","email":"laub@mit.edu","institution":"Massachusetts Institute of Technology","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3db6cb01552b4a17a55651fa5c75c128","id":"3120"}, {"dataset":"MSV000093691","datasetNum":"93691","title":"Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1703000889000","created":"Dec. 19, 2023, 7:48 AM","description":"Ubiquitylation enrichment in iNeurons treated with Bortezomib and Bafilomycin","fileCount":"45","fileSizeKB":"118623680","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Ubiquitylation;iNeurons;PTM;Bortezomib;Bafilomycin","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047952","task":"6e8f288dbda14f90b3fb0c3d4ff10ea6","id":"3121"}, {"dataset":"MSV000093690","datasetNum":"93690","title":"Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702999563000","created":"Dec. 19, 2023, 7:26 AM","description":"Whole proteome (TMT) of Mouse brains from young and old animals.","fileCount":"39","fileSizeKB":"24745772","spectra":"528797","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - 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\\\"Acetylation.\\\";UNIMOD:6 - \\\"Iodoacetic acid derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Acetylation;Mouse;Brain;Aging;PTM","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047947","task":"e2489c8ad70541d492c4ff2be5f9f75e","id":"3123"}, {"dataset":"MSV000093687","datasetNum":"93687","title":"Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702993506000","created":"Dec. 19, 2023, 5:45 AM","description":"Characterization of phosphorylated peptides during Mouse brain aging.","fileCount":"23","fileSizeKB":"47078227","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:6 - \\\"Iodoacetic acid derivative.\\\"","keywords":"PTM;Phosphorylation;Brain;Mouse;Aging","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047945","task":"43679ee2de454849a228b4581e16afb2","id":"3124"}, {"dataset":"MSV000093686","datasetNum":"93686","title":"Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain","user":"ProteomicsCF_FLI","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702990657000","created":"Dec. 19, 2023, 4:57 AM","description":"Characterization of ubiquitylation in Mouse brain during aging.","fileCount":"29","fileSizeKB":"45261272","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";MOD:00492 - \\\"A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of glycylglycine, the two glycine residues left after tryptic digestion of ubiquitin.\\\"","keywords":"Mouse;Brain;Aging;PTM;Ubiquitylation","pi":[{"name":"Alessandro Ori","email":"alessandro.ori@leibniz-fli.de","institution":"Leibniz Institute on Aging Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047940","task":"496224681f404e568b66e3692741158d","id":"3125"}, {"dataset":"MSV000093684","datasetNum":"93684","title":"Investigating the Impacts of Sphingomyelinases on Extracellular Vesicle Cargo Sorting","user":"Monod","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702933474000","created":"Dec. 18, 2023, 1:04 PM","description":"The biogenesis of extracellular vesicles (EVs) is a regulated process, driven by mechanisms at specific subcellular milieus. Sphingomyelinases (SMases), which metabolize sphingomyelin in membranes, play a role in EV biogenesis. Their metabolic product, ceramide, induces invaginations at the endosome or blebbing from the plasma membrane, both important in EV generation. Here, we sought to evaluate the impact of SMase inhibition on EV protein and RNA cargoes. For this, we treated human MCF7 cells with the neutral SMase (NSM) inhibitor GW4869 or the acid SMase (ASM) inhibitor FTY720. EVs were then purified from the conditioned media of control or inhibitor-treated cells and characterized by a variety of approaches, including LC-MS\/MS and RNA-sequencing. SMase inhibition resulted in morphological and phenotypic changes in the heterogeneous EV population. Strikingly, NSM inhibition resulted in a depletion of nanoparticles, as well as a decrease in the RNA and protein content of EVs, with a marked reduction in endosomal, spliceosomal, and translation-related proteins. Furthermore, we observed a reduction in the overall RNA-binding proteins (RBPs) in EVs released by cells treated with the NSM-inhibitor. In contrast, the ASM-inhibitor treatment, which appears to reduce plasma membrane-derived vesicles, elicited an inverse response, leading to an increase in RBP and associated machineries within the released EV population. RNA sequencing of these EV revealed changes in the RNA biotypes composition, with an increase in protein coding transcripts. Interestingly, ASM-inhibitor resulting EVs induced increased cell migration and protein translation in recipient MCF10A cells. These results suggest that SMase-dependent vesiculation represents a major route of RBP and RNA trafficking outside the cell, via endosomal pathways.","fileCount":"40","fileSizeKB":"72056585","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Extracellular vesicle;Neutral sphingomyelinase;Acid sphingomyelinase;GW4869;FTY720;RNA-binding proteins;Sphingolipids;Ceramide;EV biogenesis;ASmase;NSmase;RNA sequencing","pi":[{"name":"Eric L'Ecuyer","email":"Eric.Lecuyer@ircm.qc.ca","institution":"Institut de Recherche Clinique de Montreal","country":"Canada"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c12ec5c7f18246c4bc0b0b02a1a3939a","id":"3126"}, {"dataset":"MSV000093683","datasetNum":"93683","title":"Zika Virus NS1 Drives Tunneling Nanotube Formation for Mitochondrial Transfer, Enhanced Survival, Interferon Evasion, and Stealth Transmission in Trophoblasts ","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702923419000","created":"Dec. 18, 2023, 10:16 AM","description":"Zika virus (ZIKV) infection continues to pose a significant public health concern due to limited available preventive measures and treatments. ZIKV is unique among flaviviruses in its vertical transmission capacity (i.e., transmission from mother to fetus) yet the underlying mechanisms remain incompletely understood. Here, we show that both African and Asian lineages of ZIKV induce tunneling nanotubes (TNTs) in placental trophoblasts and multiple other mammalian cell types. Amongst investigated flaviviruses, only ZIKV strains trigger TNTs. We show that ZIKV-induced TNTs facilitate transfer of viral particles, proteins, and RNA to neighboring uninfected cells. ZIKV TNT formation is driven exclusively via its non-structural protein 1 (NS1); specifically, the N-terminal region (50 aa) of membrane-bound NS1 is necessary and sufficient for triggering TNT formation in host cells. Using affinity purification-mass spectrometry of cells infected with wild-type NS1 or non-TNT forming NS1 (pNS1deltaTNT) proteins, we found mitochondrial proteins are dominant NS1-interacting partners, consistent with the elevated mitochondrial mass we observed in infected trophoblasts. We demonstrate that mitochondria are siphoned via TNTs from healthy to ZIKV-infected cells, both homotypically and heterotypically, and inhibition of mitochondrial respiration reduced viral replication in trophoblast cells. Finally, ZIKV strains lacking TNT capabilities due to mutant NS1 elicited a robust antiviral Interferon lambda 1\/2\/3 response, indicating ZIKV's TNT-mediated trafficking also allows ZIKV cell-cell transmission that is camouflaged from host defenses. Together, our findings identify a new stealth mechanism that ZIKV employs for intercellular spread among placental trophoblasts, evasion of antiviral interferon response, and the hijacking of mitochondria to augment its propagation and survival. Discerning the mechanisms of ZIKV intercellular strategies offers a basis for novel therapeutic developments targeting these interactions to limit its dissemination.","fileCount":"47","fileSizeKB":"15067852","spectra":"295903","psms":"216379","peptides":"65380","variants":"92323","proteins":"11801","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Zika virus (NCBITaxon:64320);Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"zika virus;TNT-mediated trafficking ;tunneling nanotubes;non-structural protein 1 (NS1)","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047909","task":"8748e2c3cc4b42289cb8baaf580b8747","id":"3127"}, {"dataset":"MSV000093682","datasetNum":"93682","title":"Analyses of Pseudoexfoliation Aqueous Humor Proteome in Homo sapiens","user":"sbhattacharya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702916074000","created":"Dec. 18, 2023, 8:14 AM","description":"Pseudoexfoliation syndrome (PEX) is a systemic disorder that manifests as a fluffy, proteinaceous fibrillar material throughout the body. In the eye, such deposits result in glaucoma (PEXG), due to impeding aqueous humor outflow. When a patient presents acute glaucoma, it is necessary to remove some of the aqueous fluid within the eye to relief pain and pressure. This label free proteomics dataset was collected from human donors during cataract surgery. The aqueous humor was collected during essential ophthalmic procedures that allowed paracentesis after obtaining informed consents from human subjects without collecting identifiers, but all disease and medication history were collected. The sample collection included non-glaucomatous controls (CTL-GC), those with pseudoexfoliation syndrome (PEX-GC), and synthesized GC-Globulin pure protein (GC-Pure). Approximately 50-120 ul volume of AH was collected by paracentesis and stored in -80C immediately upon acquisition until analysis. Protein extraction was carried out by homogenization of the tissue in extraction buffer (TEAB, NaCl and SDS). Protein amounts were estimated and normalized to 10 ug across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. Untargeted liquid chromatography-mass spectrometry was performed on an Easy nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10. Each sample was run three separate times.\n\nRaw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The human proteome was downloaded from UniProt and used as the target database for protein identification. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, and carbamidomethylation. The normalization was set to total peptide amount and confidence to low.","fileCount":"86","fileSizeKB":"103156055","spectra":"0","psms":"387349","peptides":"106943","variants":"126281","proteins":"40856","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Axon Regeneration, PEX, Pseudoexfoliation, Proteomics, Label Free, Aqueous Humor, Human","pi":[{"name":"Sanjoy Bhattacharya","email":"sbhattacharya@med.miami.edu","institution":"University of Miami","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047906","task":"0f861c92a5a048a4b6a080dea1023d60","id":"3128"}, {"dataset":"MSV000093681","datasetNum":"93681","title":"Proteomic analysis of unconcentrated exovesicle-depleted cell culture medium of Norway spruce","user":"mohijafari","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702890397000","created":"Dec. 18, 2023, 1:06 AM","description":"Exovesicle-enriched fraction was isolated from the culture medium of tissue-cultured cells of Norway spruce during extracellular lignin formation by an ultracentrifugation-based protocol. From the remaining, now exovesicle-depleted culture medium, 11.8 ul of the medium was prepared for proteomic analysis.","fileCount":"20","fileSizeKB":"13313518","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Picea abies (NCBITaxon:3329)","instrument":"LTQ Orbitrap","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Norway spruce;culture medium;cell culture;exovesicles;proteomics;Picea abies","pi":[{"name":"Anna Happonen","email":"anna.happonen@luke.fi","institution":"Natural Resources Institute Finland","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047895","task":"6ff4e7067e334ec6a379f6ecc7d4254b","id":"3129"}, {"dataset":"MSV000093678","datasetNum":"93678","title":"GNPS IFAS sample AM recorded on Dec 2023 ","user":"amitGNPS","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702789303000","created":"Dec. 16, 2023, 9:01 PM","description":"The sample is submitted for the analysis of the GNPS study on the basis of molecular networking systems.","fileCount":"3","fileSizeKB":"150003","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Clavibacter nebraskensis strain 61-1","instrument":"TSQ Altis","modification":"N\\\/A","keywords":"Sugar modification, Alkyl chain identification, Natural products","pi":[{"name":"Yousong Ding","email":"YDing@ufl.edu","institution":"University of Florida","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4fbbc32c9bf04564a26585cec727de3a","id":"3130"}, {"dataset":"MSV000093677","datasetNum":"93677","title":"Development and application of GlycanDIA workflow for glycomic analysis","user":"xie753951","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702773168000","created":"Dec. 16, 2023, 4:32 PM","description":"Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat of cells called the glycocalyx. The aberrant changes in glycosylation have been linked to the initiation and progression of many diseases. Thus, while the significance of glycosylation is well established, a lack of methods to characterize glycans has hindered the ability to understand their biological functions. Mass spectrometry (MS)-based methods have generally been at the core of most glycan profiling efforts; however, modern data-independent acquisition (DIA) has not been benchmarked for analyzing glycans. Herein, we developed a DIA-based glycomic workflow, termed GlycanDIA, to identify and quantify glycans with high sensitivity and accuracy. The GlycanDIA workflow combined higher energy collisional dissociation (HCD)-MS\/MS and staggered windows for glycomic analysis, which facilitates the sensitivity in identification and the accuracy in quantification compared to conventional data-dependent acquisition (DDA)-based glycomics. To facilitate the application, we also developed a generic search engine, GlycanDIA Finder, incorporating an iterative decoy searching for confident glycan identification and quantification from DIA data. The results showed GlycanDIA can distinguish glycan composition and isomers from N-glycans, O-glycans, and human milk oligosaccharides (HMOs), while it also reveals information on low-abundant modified glycans. With the improved sensitivity, we performed experiments to profile N-glycans from RNA samples, which have been underrepresented due to their low abundance. Using this integrative workflow to unravel the N-glycan profile in cellular and tissue glycoRNA samples, we found that RNA-glycans have specific forms as compared to protein-glycans and are also tissue-specific differences, suggesting distinct functions in biological processes. Overall, GlycanDIA can provide comprehensive information for glycan identification and quantification, enabling researchers to obtain in-depth and refined details on the biological roles of glycosylation.","fileCount":"80","fileSizeKB":"48326448","spectra":"2931129","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Glycomics;N-Glycan;O-Glycan;HMO;GlycoRNA","pi":[{"name":"Benjamin A. Garcia","email":"bgarci@mail.med.upenn.edu","institution":"Department of Biochemistry and Biophysics, University of Pennsylvania","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9f5160f9b4574db9a9abde9d922fcb5d","id":"3131"}, {"dataset":"MSV000093676","datasetNum":"93676","title":"GNPS - Temporal Dynamics of Cyanobacterial Bloom Community Composition and Toxin Production from Urban Lakes","user":"mxb1224","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702758698000","created":"Dec. 16, 2023, 12:31 PM","description":"These data are raw mass spec files and corresponding mzXML files for time series mass spec data from three urban lakes at Roger Williams Park in Providence, RI. Data files are described by lake location (Pleasure, Polo, Cunliff) and date of sample collection. The Microcystis _Cells file is a positive control of a cultivated strain from the UTEX culture collection (M. aeruginosa UTEX #LB2385) - a known microcystin-LR producer. Information on LC-MS\/MS method can be found in the published work.","fileCount":"93","fileSizeKB":"5520307","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Cyanobacteria (NCBITaxon:1117)","instrument":"LTQ XL","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Harmful Algal Blooms, cyanoHABs, metabolomics, cyanotoxins","pi":[{"name":"Matt Bertin","email":"mxb1224@case.edu","institution":"Case Western Reserve University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b14280ba02a7442b91462c7e9b918d4f","id":"3132"}, {"dataset":"MSV000093675","datasetNum":"93675","title":"TcSERPIN_an_inhibitor_that interacts_with_cocoa_defense_proteins_and_has_biotechnological_potential_against_human_pathogens","user":"yulimora","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702733046000","created":"Dec. 16, 2023, 5:24 AM","description":"The objective of this study was to characterize a serpin from Theobroma cacao, called TcSERPIN, to identify its endogenous targets and determine its function and biotechnological potential. The protease trap containing immobilized rTcSERPIN captured endogenous defense proteins from cocoa extracts that are related to metabolic pathways, stress and defense.","fileCount":"303","fileSizeKB":"590571","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Theobroma cacao (NCBITaxon:3641)","instrument":"6545 Q-TOF LC\\\/MS","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:359 - \\\"Proline oxidation to pyroglutamic acid.\\\"","keywords":"Serpin;Theobroma cacao;Protease inhibitor","pi":[{"name":"Akyla Maria Martins Alves","email":"akylamma@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Andria dos Santos Freitas","email":"andria.sfreitas@yahoo.com.br","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Ariana Silva Santos","email":"ana.silva0491@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Brenda Concei\uFFFD\uFFFDo Guimar\uFFFDes Santana","email":"brenda.c.g.santana@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Bruno Silva Andrade","email":"bandrade@uesb.edu.br","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Carlos Priminho Pirovani","email":"pirovanicp@gmail.com","institution":"State University of Santa Cruz","country":"Brazil"},{"name":"Geiseane Velozo Amaral geiseanevelozo@gmail.com","email":"geiseanevelozo@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Irma Yuliana Mora-Ocampo ","email":"yuliproteomica@gmail.com","institution":"State University of Santa Cruz","country":"Brazil"},{"name":"Keilane Silva Farias","email":"keilaneuesc@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Maria Lu\uFFFDza do Carmo Santos","email":"mluizadocarmo@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"},{"name":"Maria Zugaib","email":"mariazugaib@hotmail.com","institution":"Universidade Estadual de Santa Cruz (UESC), Brazil","country":"Brazil"},{"name":"Monaliza Macedo Ferreira","email":"monalizamacedo2@gmail.com","institution":"Universidade Estadual de Santa Cruz (UESC)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cc5a6f331b8c4d9983c4eab0f627b691","id":"3133"}, {"dataset":"MSV000093674","datasetNum":"93674","title":"Cooperation Between PRMT1 and PRMT6 Drives Lung Cancer Health Disparities Among Black\/African American Men","user":"mcc_proteomics1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702679583000","created":"Dec. 15, 2023, 2:33 PM","description":"SUMMARY Non-Hispanic Black\/African American (Black\/AA) men in the United States have disproportionally higher incidence and mortality rates of lung cancer compared to non-Hispanic White (NHW) men. Biological factors are believed to play critical roles in driving the disparities. Nevertheless, large-scale genomic studies fail to identify significant somatic differences in lung cancer driver genes contributing to the disparities. Elevated expression of protein arginine methyltransferases (PRMTs) correlating with poorer prognosis is observed in many cancer types. Here, we observed a higher PRMT6 expression in lung cancer of Black\/AA men compared to NHW men. PRMT6 formed a heteromer complex with PRMT1 to catalyze arginine methylation of interleukin enhancer-binding factor 2 essential for cell proliferation. Disrupting PRMT1\/PRMT6 heteromer complex by a competitive peptide reduced cell proliferation in non-small cell lung cancer cell lines and lung cancer patient-derived organoids. This work implicates that PRMT1\/PRMT6 heteromer complex contributes to poorer lung cancer outcomes in Black\/AA men vs. NHW men that could serve as a target to eliminate cancer health disparities.","fileCount":"6","fileSizeKB":"499367","spectra":"0","psms":"8374","peptides":"512","variants":"740","proteins":"133","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\"","keywords":"ILF2","pi":[{"name":"Charles Lyons","email":"mccproteomics@vcu.edu","institution":"VCU","country":"US"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"580c32c0483b437091c6f9c224a4f428","id":"3134"}, {"dataset":"MSV000093673","datasetNum":"93673","title":"Proteomic evaluation of decellularization of porcine auricular cartilage","user":"brucepu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702674561000","created":"Dec. 15, 2023, 1:09 PM","description":"This dataset represents protein profiles of porcine ear cartilage before and after decellularization.","fileCount":"5","fileSizeKB":"1318364","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sus scrofa domesticus (NCBITaxon:9825)","instrument":"LTQ Velos","modification":"proline hydroxylation;lysine hydroxylation","keywords":"porcine, cartilage, decellularization","pi":[{"name":"Julia Thom Oxford","email":"joxford@boisestate.edu","institution":"Boise State University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7134600b63b24d18833e332e2a08c824","id":"3135"}, {"dataset":"MSV000093672","datasetNum":"93672","title":"SCarP: proteome heterogeneity characterization of primary mouse cardiomyocytes","user":"bineka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702669218000","created":"Dec. 15, 2023, 11:40 AM","description":"Cardiac myocyte heterogeneity has been acknowledged based on ion channel expression, cellular electrophysiology and through transcriptomics, but the exploration of individual cardiomyocytes at the board proteome-wide level has remained challenging. We developed an entire analytical pipeline to assess the cell heterogeneity of adult primary cardiomyocytes isolated from mouse hearts. Over 700 single cell proteomes were isolated from 4 mice hearts. Each single cell image was captured by the cellenONE sorter interface and evaluated for morphological features of apoptotic cells, i.e.: hypercontracted cell shape. This imaging analysis allowed us to retain 270 rod-shaped cardiac cells for downstream single cell proteome sample processing and analysis on Bruker timsTOF SCP mass spectrometer. Final dataset UMAP dimension reduction and clustering analysis yielded 3 cardiomyocyte cell sub-populations that displayed differential: i) expression of Myh7 and Myh7b, ii) carbon metabolism signatures and iii) distribution of 7 proteins involved in calcium signaling. Single cardiomyocyte protemes demonstrated potential differences related to the metabolism and calcium ion handling between those sub-populations and could bring new insights for cardiology studies on mice.","fileCount":"20878","fileSizeKB":"1238461946","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF SCP","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Single cell proteomics;mass spectrometry;cardiomyocyte;heart;myosin;mouse","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047860","task":"8502d24aac5c4da78d06598ef301ec2b","id":"3136"}, {"dataset":"MSV000093671","datasetNum":"93671","title":"Native mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination","user":"liuweij1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702580822000","created":"Dec. 14, 2023, 11:07 AM","description":"This dataset contains mass spectra of GPCR complex analyzed by ensemble measurement and Direct Mass Technology mode.","fileCount":"6","fileSizeKB":"1513951","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"GPCR","instrument":"Q Exactive UHMR","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"GPCR, native MS, Direct Mass Technology mode","pi":[{"name":"Weijing Liu","email":"weijing.liu@thermofisher.com","institution":"Thermo Fisher Scientific","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9f5367d6256b453b976b1ee48c204e29","id":"3137"}, {"dataset":"MSV000093670","datasetNum":"93670","title":"Proteomic analysis of Breast cancer spheroids responder and non-responder to Trastuzumab","user":"DavidePerico","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702576959000","created":"Dec. 14, 2023, 10:02 AM","description":"Proteomic analysis of breast cancer spheroids obtained from BT-474 cell line to characterize Trastuzumab resistance mechanism. Four conditions were examined: responder and non-responder spheroids before and after a 15-days treatment with Trastuzumab (RS_0, RS_15, nRS_0 and nRS_15).","fileCount":"28","fileSizeKB":"38322943","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 120","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"LC-MS\/MS;Breast cancer;Trastuzumab;Proteomics","pi":[{"name":"DAVIDE PERICO","email":"davide.perico@itb.cnr.it","institution":"ITB-CNR","country":"Italia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ef29f20a454f42e491466a46f4fc0940","id":"3138"}, {"dataset":"MSV000093669","datasetNum":"93669","title":"A protein-proximity screen reveals that Ebola virus co-opts the mRNA decapping complex through the scaffold protein EDC4","user":"uma_aryal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702570892000","created":"Dec. 14, 2023, 8:21 AM","description":"Understanding the molecular interactions of host cells with Ebola virus (EBOV) is integral for further therapeutic development of antivirals. We performed a proximity-dependent protein interaction screen for six of seven EBOV proteins to characterize the EBOV-host interactome. Using network analysis, putative EBOV interacting proteins were mapped to a human protein interactome. We overlayed viral protein interactions onto the host network. Within this map, several known EBOV-host protein interactions were identified, as well as several cell processes, such as RNA processing, previously implicated in EBOV replication. Furthermore, this interactome revealed novel interactions between EBOV proteins and host proteins arranged in functional complexes. As proof of this concept, we characterized the interaction between EBOV VP35 and the mRNA decapping complex, which regulates mRNA turnover in host cells. Our protein-protein interaction data demonstrate that VP35 engages multiple components of this complex by binding binds the scaffold protein EDC4. Inhibiting expression of mRNA decapping complex components EDC4, EDC3, or DCP2 inhibited viral replication by reducing early viral RNA synthesis. Our approach examining EBOV-host protein interactions in conjunction with network analysis reveals how EBOV interacts with entire cellular machines as opposed to singular cell proteins to promote its replication.","fileCount":"53","fileSizeKB":"80893137","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ebolavirus (NCBITaxon:186536)","instrument":"Q Exactive HF;Orbitrap Fusion Lumos","modification":"Oxidation [M]","keywords":"Ebola virus, proximity labeling, mRNA decaping complex, Scafold Protein ","pi":[{"name":"Douglas J. 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This project aimed at identification of protein interactors of Duxbl. Following IP of flag-tagged exogenous Duxbl or EV, proteins were trypsin digested with S-traps. Following IP of endogenous Duxbl or IP with non-specific IgG, proteins were subjected to gel separation and in-gel trypsin digestion. All pulldowns were performed in biological replicate. Samples were run on either a Fusion tribrid (exogenous) or an Exploris 480 hydbrid (endogenous). Data were searched in PD 2.4 using the mouse database from Uniprot.","fileCount":"66","fileSizeKB":"58033103","spectra":"0","psms":"66482","peptides":"8049","variants":"9608","proteins":"1632","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion;Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Duxbl;development;interactome","pi":[{"name":"Lisa Jenkins","email":"jenkinsl@mail.nih.gov","institution":"NCI, NIH","country":"United States"},{"name":"Sergio Ruiz","email":"sergio.ruizmacias@nih.gov","institution":"NCI, NIH","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047807","task":"f464d44eb3d5480689afbf43aec9366a","id":"3141"}, {"dataset":"MSV000093661","datasetNum":"93661","title":"SUMO2\/3 IP of chromatin samples from WT and RNF4 knockout B cells","user":"sleat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702503346000","created":"Dec. 13, 2023, 1:35 PM","description":"SUMO2\/3 IP of chromatin samples from WT and RNF4 knockout B cells","fileCount":"32","fileSizeKB":"11200663","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"mouse;brain;RNF4","pi":[{"name":"Samuel Bunting","email":"bunting@cabm.rutgers.edu","institution":"Rutgers, the State University of NJ","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD047803","task":"cb3e3d18dd3e4277a3601a6f3752f5d5","id":"3142"}, {"dataset":"MSV000093660","datasetNum":"93660","title":"iPOND analysis of samples from WT and RNF4 knockout B cells","user":"sleat","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702502385000","created":"Dec. 13, 2023, 1:19 PM","description":"iPOND analysis of samples from WT and RNF4 knockout B cells","fileCount":"32","fileSizeKB":"12213325","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"mouse;brain;RNF4","pi":[{"name":"Samuel Bunting","email":"bunting@cabm.rutgers.edu","institution":"Rutgers, the State University of NJ","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD047801","task":"38e7dd3ac7a74d80b85db52e596e2299","id":"3143"}, {"dataset":"MSV000093659","datasetNum":"93659","title":"Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics","user":"stephan_eckert","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702499694000","created":"Dec. 13, 2023, 12:34 PM","description":"Proteomics is making important contributions to drug discovery - from target deconvolution to mechanism of action (MoA) elucidation and the identification of biomarkers of drug response. Here, we introduce decryptE, a proteome-wide approach that measures the full dose-response characteristics of drug-induced protein expression changes which informs cellular drug MoA. Assaying 144 clinical drugs and research compounds against 8,000 proteins resulted in >1 million dose-response curves that can be interactively explored online in ProteomicsDB and a custom-built ShinyApp. Analysis of the collective data provided molecular explanations for known phenotypic drug effects and uncovered novel aspects of the MoAs of human medicines. Most notable, HDAC inhibitors potently and strongly down-regulated the T-cell receptor complex resulting in impaired human T-cell activation in-vitro and ex-vivo. This not only offers a rational explanation for the efficacy of HDAC inhibitors in certain lymphomas and autoimmune diseases but also their poor performance in treating solid tumors.","fileCount":"13485","fileSizeKB":"3322521568","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Escherichia coli (NCBITaxon:562);Pseudomonas aeruginosa (NCBITaxon:287);Mus musculus (NCBITaxon:10090);Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Orbitrap Eclipse;Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\"","keywords":"FAIMS;micro-flow liquid chromatography;drug screen;drugs;decryptE;mode of action;dose-response;protein expression profiles;primary T cells;HDAC inhibitors;HDAC;proteomics","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Technical University of Munich (TUM)","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD047799","task":"70cd42693c7f4d4da2cf466a0832e87d","id":"3144"}, {"dataset":"MSV000093658","datasetNum":"93658","title":"G1 Length Dictates Heterochromatin Landscape","user":"FHproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702499020000","created":"Dec. 13, 2023, 12:23 PM","description":"Overall, this paper demonstrated that the speed of the cell cycle determines the level of H3K27me3 in serum-grown murine embryonic stem cells, with extended G1 phase leading to increased global H3K27me3 levels and accelerated cell cycle leading to decreased H3K27me3 levels. This MassIVE entry contains mass spectrometry files that measured H3K27me3 levels using propionic anhydride derivatization methods.","fileCount":"8","fileSizeKB":"6474443","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion","modification":"UNIMOD:37 - \\\"Tri-Methylation.\\\"","keywords":"trimethylation, histone, H3, H3K27, cell cycle, chromatin","pi":[{"name":"Srinivas Ramachandran","email":"srinivas.ramachandran@cuanschutz.edu","institution":"University of Colorado Anschutz Medical Campus","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d3a626c8679f4fa5bdc6b1f4ca269848","id":"3145"}, {"dataset":"MSV000093654","datasetNum":"93654","title":"Dataset Accompanying \"Proteomic comparison of the organic matrices from parietal and base plate of the acorn barnacle Amphibalanus amphitrite\"","user":"jhervey4","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702438914000","created":"Dec. 12, 2023, 7:41 PM","description":"ABSTRACT: Acorn barnacles are efficient colonizers on a wide variety of marine surfaces. As they proliferate on critical infrastructure, their settlement and growth have deleterious effects on performance. To address acorn barnacle biofouling, research has focused on the settlement and adhesion processes with the goal of informing the development of novel coatings. This effort has resulted in the discovery and characterization of several proteins found at the adhesive substrate interface, i.e. cement proteins, and a deepened understanding of the function and composition of the biomaterials within this region. While the adhesive properties at the interface are affected by the interaction between the proteins, substrate, and mechanics of the calcified base plate, little attention has been given to the interaction between the proteins and the cuticular material present at the substrate interface. Here, the proteome of the organic matrix isolated from the base plate of the acorn barnacle Amphibalanus amphitrite is compared with the chitinous and proteinaceous matrix embedded within A. amphitrite parietal plates. The objective was to gain an understanding of how the basal organic matrix may be specialized for adhesion via an in-depth comparative proteome analysis. In general, the majority of proteins identified in the parietal matrix were also found in the basal organic matrix, including nearly all those grouped in classes of cement proteins, enzymes and pheromones. However, the parietal organic matrix was enriched with cuticle-associated proteins, of which ~30% of those identified were unique to the parietal region. In contrast, ~30-40% of the protease inhibitors, enzymes, and pheromones identified in the basal organic matrix were unique to this region. Not unexpectedly, nearly 50% of the cement proteins identified in the basal region were significantly distinct from those found in the parietal region. The wider variety of identified proteins in the basal organic matrix indicates a greater diversity of biological function in the vicinity of the substrate interface where several processes related to adhesion, cuticle formation, and expansion of the base synchronize to play a key role in organism survival.","fileCount":"43","fileSizeKB":"33552388","spectra":"0","psms":"50901","peptides":"2895","variants":"6814","proteins":"1195","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Amphibalanus amphitrite","instrument":"Orbitrap Fusion Lumos","modification":"oxidation of M;deamidation of N, Q","keywords":"Amphibalanus amphitrite;cement protein;mass spectrometry;cuticle;chitin binding","pi":[{"name":"J Hervey","email":"judson.hervey@nrl.navy.mil","institution":"NRL","country":"USA"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"PXD047775","task":"76327b8b8dcf4084b6c885f18c19b608","id":"3146"}, {"dataset":"MSV000093653","datasetNum":"93653","title":"GNPS - Raw data for manuscript : ","user":"aliagh81","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702434961000","created":"Dec. 12, 2023, 6:36 PM","description":"Metabolic dysfunction-associated steatotic liver disease (MASLD) affects one third of the global population. Understanding metabolic pathways involved can provide insights into disease progression and treatment. Untargeted metabolomics of livers from mice with early-stage steatosis uncovered decreased methylated metabolites, suggesting altered one-carbon metabolism. The levels of glycine, a central component of one-carbon metabolism, were lower in mice with hepatic steatosis, consistent with clinical evidence. Stable-isotope tracing demonstrated that increased serine synthesis from glycine via reverse serine hydroxymethyltransferase (SHMT) is the underlying cause for decreased glycine in steatotic livers. Consequently, limited glycine availability in steatotic livers impaired glutathione synthesis under acetaminophen-induced oxidative stress, enhancing acute hepatotoxicity. Glycine supplementation or hepatocyte-specific \r\nablation of the mitochondrial SHMT2 isoform in mice with hepatic steatosis mitigated \r\nacetaminophen-induced hepatotoxicity by supporting de novo glutathione synthesis. Thus, early metabolic changes in MASLD that limit glycine availability sensitize mice to xenobiotics even at the reversible stage of this disease. ","fileCount":"417","fileSizeKB":"48222959","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240;Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"MASLD;Glycine;acetaminophen hepatotoxicity;GSH;xenobiotic;one carbon metabolism;SHMT2","pi":[{"name":"Eyal Gottlieb","email":"egottlieb@mdanderson.org","institution":"University of Texas MD Anderson Cancer Center","country":"United States"},{"name":"Inbal Mor","email":"inbal.mor123@gmail.ac.il","institution":"Technion - Israel Institute of Technology","country":"Israel"},{"name":"Oren Rom","email":"oren.rom@lsuhs.edu","institution":"Louisiana State University Health Sciences Center-Shreveport","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8b18c552fc9f40448c5f4acf26ed071e","id":"3147"}, {"dataset":"MSV000093650","datasetNum":"93650","title":"Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly","user":"brettsp1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702407344000","created":"Dec. 12, 2023, 10:55 AM","description":"Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide VPS, matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Single-cell force spectroscopy revealed that proteins critical for biofilm formation, OmpU, the matrix proteins RbmA, RbmC, Bap1, and VPS, contribute to cell-surface adhesion forces at differing efficiency, with VPS showing the highest efficiency whereas Bap1 showing the lowest efficiency. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may provide new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of V. cholerae.","fileCount":"13","fileSizeKB":"178247946","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Vibrio cholerae (NCBITaxon:666)","instrument":"timsTOF Pro 2;Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"OmpU;biofilm matrix assembly","pi":[{"name":"Fitnat H. 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The automation does not only allow higher sample numbers to be processed in parallel, but also improves reproducibility and lowers the minimal sample input. Furthermore, we combined automated sample processing with shorter liquid chromatography gradients and data-independent acquisition to increase analysis throughput and enable reproducible protein quantitation across a large number of samples. We successfully applied this workflow to optimise the detection of proteasome substrates by proximity-dependent labelling.","fileCount":"15","fileSizeKB":"31529333","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"BioID, proximity labelling, mass spectrometry, automation, high throughput","pi":[{"name":"Therese Dau","email":"therese.dau@leibniz-fli.de","institution":"Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, ","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047757","task":"16ef22479977433d93558e338a2f1e4c","id":"3149"}, {"dataset":"MSV000093645","datasetNum":"93645","title":"Characterization of YlxR\/Ssr1238, a conserved RNA binding protein in a model cyanobacterium","user":"Stholen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702383433000","created":"Dec. 12, 2023, 4:17 AM","description":"Throughout the tree of life RNA-binding proteins play important roles in the regulation of gene expression and RNA metabolism, but they are only poorly characterized in cyanobacteria. Here, we characterized the protein Ssr1238 from the model cyanobacterium Synechocystis sp. PCC 6803, which was predicted as a potential RNA-binding protein. Ssr1238 is a potential homolog of the protein YlxR from Bacillus subtilis and is encoded in a syntenic region within the nusA-ssr1238-infB operon. Co-immunoprecipitation of proteins followed by MS analysis and sequencing of UV-cross-linked co-immunoprecipitated RNA samples identified potential interaction partners of Ssr1238. The most highly enriched transcript was the RNase P RNA, while RnpA, the protein component of RNase P was among the most highly enriched proteins, consistent with recent findings that YlxR proteins can influence the enzymatic activity of RNase P. The data further suggest that Ssr1238 interacts with the 3 region of gene ssl3177, encoding a rare lipoprotein homolog and with the precursor transcript of the initiator tRNAfMet and the group I intron in it. Thus, Ssr1238 may play additional roles in the initiation of translation and cell division. The data also show a strong connection to the RNA maturation and modification system indicated by co-precipitation of riboendonuclease E, RNA methyltransferase Sll1967, the A-adding tRNA nucleotidyltransferase Sll1253 and queuine tRNA-ribosyltransferase, as well as enolase. Our results are consistent with recent findings that the B. subtilis YlxR protein functions as an RNase P modulator (RnpM), extend its proposed role to the phylum cyanobacteria and suggest additional functionalities.","fileCount":"22","fileSizeKB":"6398362","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Synechocystis sp. PCC 6803 (NCBITaxon:1148)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanobacteria, gene expression, photosynthesis, Synechocystis sp. PCC 6803, RNA binding proteins, RNase P","pi":[{"name":"Wolfgang R. 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","fileCount":"1088","fileSizeKB":"668694567","spectra":"9544369","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus;Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS\/MS;Human immune cell;Proteomic profiling;CD4+T cell;CD8+T cell;NK cell;B cell;Daudi;Jurkat;Stimulated Jurkat;Molt-4;Ramos;PBMC;THP-1","pi":[{"name":"Hophil Min","email":"mhophil@kist.re.kr","institution":"KIST","country":"South Korea"},{"name":"Hyeon-Jeong Lee","email":"hjl@kist.re.kr","institution":"KIST","country":"South Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047742","task":"adb633d3623344c0b03c933bc963b1e4","id":"3151"}, {"dataset":"MSV000093641","datasetNum":"93641","title":"Genome-guided isolation of Fervidibacter sacchari, an aerobic, hyperthermophilic polysaccharide-degrading specialist","user":"gabrig","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702347936000","created":"Dec. 11, 2023, 6:25 PM","description":"Few aerobic hyperthermophiles degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic hyperthermophile, Fervidibacter sacchari, which was originally ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides as sole carbon sources from 65-87.5 Celsius and expresses 190 carbohydrate-active enzymes according to RNA-Seq and proteomics, including 31 with unusual glycoside hydrolase 177 or 179 domains.","fileCount":"3","fileSizeKB":"7457013","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fervidibacter sacchari;Calditenuis;data comes from the G-10 lab culture;other associated microorganisms","instrument":"timsTOF Pro","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"aerobic, hyperthermophilae, polysaccharide-degrading","pi":[{"name":"Brian P. Hedlund","email":"brian.hedlund@unlv.edu","institution":"University of Nevada","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047732","task":"c4115bc81d584c77a217ef174c8fa6ce","id":"3152"}, {"dataset":"MSV000093639","datasetNum":"93639","title":"Low input proteomics on FABP7 hi\/low mammary luminal progenitor cells","user":"mrwaas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702331912000","created":"Dec. 11, 2023, 1:58 PM","description":"Low input proteomics on FABP7 hi\/low mammary luminal progenitor cells isolated from human patient samples ","fileCount":"18","fileSizeKB":"37009207","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"mammary;progenitor;luminal","pi":[{"name":"Dr. Thomas Kislinger","email":"thomas.kislinger@utoronto.ca","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b42e3dd0117c4df49b6ee560a09151c9","id":"3153"}, {"dataset":"MSV000093637","datasetNum":"93637","title":"Extracellular Domains of CAR Reprogram T Cell Metabolism Without Antigen Stimulation","user":"aliyalakhani","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702331632000","created":"Dec. 11, 2023, 1:53 PM","description":"Phosphopeptides of CARs in 14g2a-based anti-GD2, Leu16 anti-CD20, rituximab anti-CD20, and RFR-LCDR anti-CD20 CAR-T cells without antigen stimulation","fileCount":"9","fileSizeKB":"5288154","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"CAR-T cells;phosphoproteomics","pi":[{"name":"Junyoung O. Park","email":"jop@ucla.edu","institution":"University of California, Los Angeles","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ab1708b9ae434f6082da533fcf27870a","id":"3154"}, {"dataset":"MSV000093636","datasetNum":"93636","title":"Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips","user":"bbudnik","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702326867000","created":"Dec. 11, 2023, 12:34 PM","description":"Modulation of mucus production by the human endo- and ecto-cervical epithelium by steroid hormones and associated interactions with commensal microbiome play a central role in the physiology and pathophysiology of the female reproductive tract. However, most of our knowledge about these interactions is based on results from animal studies or in vitro models that fail to faithfully mimic the mucosal environment of the human cervix. Here we describe microfluidic organ-on-a-chip (Organ Chip) models of the human cervical mucosa that recreate the cervical epithelial-stromal interface with a functional epithelial barrier and produce abundant mucus that has compositional, biophysical, and hormone-responsive properties similar to the living cervix. Application of continuous fluid flow to chips lined primary human cervical epithelial cells from a commercial source that contained a mixture of primary human ecto- and endo-cervical epithelial cells promoted preferential expression of the ecto-cervical phenotype, whereas use of periodic flow including periods of stasis induced endo-cervical specialization. When the periodic flow Cervix Chips were co-cultured with living Lactobacillus crispatus and Gardnerella vaginalis bacterial communities to respectively mimic the effects of human host interactions with optimal (healthy) or non-optimal (dysbiotic) microbiome associated with an ascending infection in the female reproductive tract, significant differences in tissue innate immune responses, barrier function, cell viability and protein profile, and mucus composition were detected reminiscent of those observed in vivo. Thus, these Organ Chip models of human cervix provide a physiologically relevant experimental in vitro model to study cervical mucus physiology and its role in human host-microbiome interactions as well as a potential preclinical testbed for development of therapeutic interventions to enhance women's health. ","fileCount":"6","fileSizeKB":"1984463","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Gardnerella vaginalis (NCBITaxon:2702);Lactobacillus (NCBITaxon:1578)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"organ-on-chip, human cervix, microbiome, bacterial vaginosis","pi":[{"name":"Don Ingber","email":"Don.Ingber@wyss.Harvard.edu","institution":"Wyss Institute for Biologically Inspired Engineering at Harvard University ","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"d088dda43de948879be16868356e9bbf","id":"3155"}, {"dataset":"MSV000093634","datasetNum":"93634","title":"GNPS - Ancestral allele of DNA polymerase gamma modifies antiviral tolerance","user":"zhaialek","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702314468000","created":"Dec. 11, 2023, 9:07 AM","description":"Mitochondria are arising as critical modulators of antiviral tolerance by releasing mtDNA\/mtRNA fragments to cytoplasm upon infection, activating virus sensors and type-I interferon response. The relevance of these mechanisms for mitochondrial diseases remains understudied. Here, we investigated mitochondrial recessive ataxia syndrome (MIRAS), caused by a common European founder mutation in DNA polymerase gamma (POLG1). The patients homozygous for the MIRAS variant p.W748S show exceptionally variable ages-of-onset and symptoms, indicating unknown modifying factors contributing to disease manifestation. We report that the mitochondrial DNA (mtDNA) replicase POLG1 has a role in antiviral defence mechanisms to double-stranded DNA and positive-strand RNA virus infections (HSV-1, TBEV, SARS-CoV-2) and its p.W748S variant dampens innate immune responses. Our patient and knock-in mouse data show that p.W748S compromises mtDNA replisome stability, causing mtDNA depletion, aggravated by virus infection. Low mtDNA and mtRNA release to cytoplasm and slow interferon response in MIRAS allow an early replicative advantage for viruses, leading to augmented pro-inflammatory response, subacute loss of GABAergic neurons, liver inflammation and necrosis. A population databank of ~300,000 Finns demonstrates enrichment of immunodeficient traits in p.W748S carriers. Our evidence suggests that POLG1 defects compromise antiviral tolerance, triggering epilepsy and liver disease. The finding has important implications to mitochondrial disease spectrum, including epilepsy, ataxia, and parkinsonism. In this metabolomic dataset: To investigate the in vivo response of MIRAS to viral infection, we generated a MIRAS-knock-in mouse model and subjected the mice to TBEV infection. These animals carry a homozygous knock-in mutation and the accompanying polymorphic variant homologous to the human ancestral MIRAS allele (p.W726S+E1121G in mice and p.W748S+E1143G in humans). We performed metabolomic analyses on the mouse brain (cerebral cortex) isolated from the control (wildtype) and MIRAS mice at 4 days post TBEV infection (n=5 mice per condition).","fileCount":"12","fileSizeKB":"171631","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"6550 iFunnel Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mitochondria;viral infection;MIRAS;metabolomics;epilepsy","pi":[{"name":"Anu Suomalainen (Wartiovaara)","email":"anu.wartiovaara@helsinki.fi","institution":"Stem Cell and Metabolism Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland, Helsinki University Hospital, HUS Diagnostics, Helsinki, Finland","country":"Finland"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c3e438e74afa473a81ecd6e3fa68b824","id":"3156"}, {"dataset":"MSV000093633","datasetNum":"93633","title":"Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate","user":"eachapman2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702313466000","created":"Dec. 11, 2023, 8:51 AM","description":"Native top-down mass spectrometry is a powerful structural biology tool that can localize post-translational modifications, explore ligand-binding interactions, and elucidate the three-dimensional structure of proteins and protein complexes in the gas-phase. Fourier-transform ion cyclotron resonance-MS offers distinct capabilities for nTDMS, owing to its ultra-high resolving power, mass accuracy, and robust fragmentation techniques. Previous nTDMS studies using FTICR have mainly applied to over-expressed recombinant proteins and protein complexes. Here, we report the first nTDMS study that directly analyzes human heart tissue lysate by direct infusion FTICR-MS without prior chromatographic separation strategies. We have achieved comprehensive nTDMS characterization of cardiac contractile proteins that play critical roles in heart contraction and relaxation. Specifically, our results reveal structural insights into ventricular myosin light chain 2, ventricular myosin light chain 1, and alpha-tropomyosin in the sarcomere, the basic contractile unit of cardiac muscle. Furthermore, we localize the calcium binding domain in MLC-2v. In summary, our nTDMS platform extends the application of FTICR-MS to directly characterize the structure, PTMs, and metal-binding of endogenous proteins from heart tissue lysate without prior separation methods. ","fileCount":"317","fileSizeKB":"1045969","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"FTICR","modification":"UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Native top-down;cardiac;FTICR;endogenous;structural biology","pi":[{"name":"Ying Ge","email":"ying.ge@wisc.edu","institution":"University of Wisconsin - Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047719","task":"d57cd244c72e4813a6b7dc2a05702247","id":"3157"}, {"dataset":"MSV000093632","datasetNum":"93632","title":"Lu_C16orf72_APMS_U2OS_P36_Elite_VS38","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702313382000","created":"Dec. 11, 2023, 8:49 AM","description":"This dataset consists of 6 raw MS files and associated peak lists and results files, acquired on Orbitrap Elite mass spectrometer operated in Data Dependent Acquisition mode. \nSamples were generated by YiQing Lu. BioID and Mass spectrometry acquisition was performed by Zhen-Yuan Lin. Analysis was performed by YiQing Lu, Anne-Claude Gingras, and Daniel Schramek. \nThe files are associated with a manuscript submitted for publication by YiQing Lu et al. The main goal of this paper was to identify novel interactors of wild-type and p53 mutants commonly found in cancer. This dataset profiles the interactomes of C16orf72 in U2-OS cells.\nDaniel Schramek is the corresponding author of the manuscript (schramek@lunenfeld.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 3 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence (as per iProphet)\nTable 3 lists the SAINTexpress interactions\n","fileCount":"31","fileSizeKB":"4658969","spectra":"0","psms":"82590","peptides":"22281","variants":"26336","proteins":"23609","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Affinity purification;Protein-protein interaction;C16orf72","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047718","task":"2e53ee23fb2842089e1e2e65f8dbad02","id":"3158"}, {"dataset":"MSV000093630","datasetNum":"93630","title":"Lu_C16orf72_APMS_293_P36_Elite_VS37","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702312174000","created":"Dec. 11, 2023, 8:29 AM","description":"This dataset consists of 6 raw MS files and associated peak lists and results files, acquired on Orbitrap Elite mass spectrometer operated in Data Dependent Acquisition mode. \nSamples were generated by YiQing Lu. BioID and Mass spectrometry acquisition was performed by Zhen-Yuan Lin. Analysis was performed by YiQing Lu, Anne-Claude Gingras, and Daniel Schramek. \nThe files are associated with a manuscript submitted for publication by YiQing Lu et al. The main goal of this paper was to identify novel interactors of wild-type and p53 mutants commonly found in cancer. This dataset profiles the interactomes of C16orf72 in HEK293 cells.\nD\nDaniel Schramek is the corresponding author of the manuscript (schramek@lunenfeld.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 3 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence (as per iProphet)\nTable 3 lists the SAINTexpress interactions\n","fileCount":"31","fileSizeKB":"5020204","spectra":"0","psms":"84113","peptides":"23541","variants":"28013","proteins":"24593","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Elite","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Affinity purification;C16orf72;protein-protein interaction","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047717","task":"33a6b17744c543c4a4f7f8e65f715c2e","id":"3159"}, {"dataset":"MSV000093629","datasetNum":"93629","title":"LCMS-Metabolomic Profiling and Genome Mining of Delftia lacustris DSMZ 21246 Revealed Four New Delftibactin Metallophores","user":"Mohammed86","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702309415000","created":"Dec. 11, 2023, 7:43 AM","description":"This dataset encompasses the metabolomic profile of Delftia lacustris DSMZ 21246 cultivated on DMS (iron-limited defined medium). Additionally, as a duplicate, 50% ACN SPE fractions obtained from both high and low supplementation experiments have been incorporated. The dataset also comprises the HPLC-purified fractions of the bacterium grown under identical conditions. Lastly, the 50% ACN SPE fractions resulting from the interaction of compound 1 with iron, gold, and copper have been included.","fileCount":"32","fileSizeKB":"1112402","spectra":"11616","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Delftia lacustris (NCBITaxon:558537)","instrument":"6530C Q-TOF LC\\\/MS (Agilent instrument model)","modification":"NA","keywords":"Delftia lacustris, metabolomics, genomics, metallophore, delftibactins","pi":[{"name":"Paul Boudreau","email":"boudreau@olemiss.edu","institution":"University of Mississippi - School of Pharmacy","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"82eb17cf6cf944f1b9e631512019ad03","id":"3160"}, {"dataset":"MSV000093628","datasetNum":"93628","title":"Lu_TP53stability_BioID_P103_6600_VS50","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702308053000","created":"Dec. 11, 2023, 7:20 AM","description":"This dataset consists of 20 raw MS files and associated peak lists and results files, acquired on AB Sciex TripleTOF 6600 mass spectrometer operated in Data Dependent Acquisition mode. \nSamples were generated by YiQing Lu. BioID and Mass spectrometry acquisition was performed by Zhen-Yuan Lin. Analysis was performed by YiQing Lu, Anne-Claude Gingras, and Daniel Schramek. \nThe files are associated with a manuscript submitted for publication by YiQing Lu et al. The main goal of this paper was to identify novel interactors of wild-type and p53 mutants commonly found in cancer. This dataset profiles the interactomes of novel p53 interactors (CCDC6 and FBXO42)\nDaniel Schramek is the corresponding author of the manuscript (schramek@lunenfeld.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 3 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence (as per iProphet)\nTable 3 lists the SAINTexpress interactions\n","fileCount":"107","fileSizeKB":"56187419","spectra":"0","psms":"523634","peptides":"68868","variants":"80859","proteins":"41199","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;Proximity-dependent biotinylation;TP53;CCDC6;FBXO48","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047710","task":"bac6b3b54bab4e7ca9b1f5135fc8a2e8","id":"3161"}, {"dataset":"MSV000093627","datasetNum":"93627","title":"GNPS - 20231211_public_raw_data_invivo_sildenafil_metabolite","user":"xat007","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702289047000","created":"Dec. 11, 2023, 2:04 AM","description":"sildenafil oral dosing to rat and mouse, plasma analysis data for in vivo metabolite ID. 48h used as blank plasma. + 's' added prefix each raw data.","fileCount":"21","fileSizeKB":"986159","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"rat;mouse","instrument":"6530A Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sildenafil;in vivo;oral administration;rat;mouse","pi":[{"name":"Junsang Yu","email":"wowxat@naver.com","institution":"Hanyang University","country":"South Korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3b1f38b806594626b10c9eda4196f439","id":"3162"}, {"dataset":"MSV000093625","datasetNum":"93625","title":"Small-scale Serial Size Exclusion Chromatography (s3SEC) for High Sensitivity Top-down Proteomics of Large Proteoforms","user":"htrogers","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702248981000","created":"Dec. 10, 2023, 2:56 PM","description":"Mass spectrometry data for \"Small-scale Serial Size Exclusion Chromatography (s3SEC) for High Sensitivity Top-down Proteomics of Large Proteoforms\"","fileCount":"4839","fileSizeKB":"213434585","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"maXis II;nanoACQUITY UPLC","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\"","keywords":"serial size exclusion chromatography;top-down proteomics;high sensitivity;mass spectrometry;1 mg tissue","pi":[{"name":"Ying Ge","email":"ge2@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047680","task":"9fbc17bc97bd48869e12cd89e1101cbd","id":"3163"}, {"dataset":"MSV000093624","datasetNum":"93624","title":"Phosphoproteomics of dried blood collected on Mitra devices","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702222929000","created":"Dec. 10, 2023, 7:42 AM","description":"Venous blood was collected in Li-heparin or EDTA blood tubes and loaded onto 20 uL Mitra devices or separated to plasma as detailed in metadata. Samples were denatured in 5.5% SDC, reduced and alkylated, and digested with TPCK-trypsin followed by acid precipitation. 1 mg of filtered precipitates were enriched for phosphopeptides using TiO. Data was acquied using nanoLC, Evosep One or SPE-ZipChip. Data was acquired by DIA (Exploris 480 or TimsTOF Pro 2) or LFQ-DDA. DIA data was analyzed with Spectronaut 18 and DDA with Skyline.","fileCount":"198","fileSizeKB":"175384966","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Exploris 240;timsTOF Pro 2","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"phosphorylation;data-independent acquisition","pi":[{"name":"Matthew W. Foster","email":"mwfoster@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD047676","task":"4a6d8b9748ca49879355d5d56a66aa33","id":"3164"}, {"dataset":"MSV000093623","datasetNum":"93623","title":"Identification of ubiquitin interactors in Legionella pneumophila using ubiquitin activity-based probes","user":"zhan3248","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702184191000","created":"Dec. 9, 2023, 8:56 PM","description":"In this experiments, we used several ubiquitin activity-based probes (Ub-Prg, Ub-VME, and Ub-VS) to covalently capture ubiquitin-interacting proteins in Legionella pneumophila. These enriched interactome were analyzed by LC-MS\/MS to identify Legionella effectors uniquely captured by the probes.","fileCount":"470","fileSizeKB":"6912550","spectra":"0","psms":"8033","peptides":"2399","variants":"3193","proteins":"456","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Legionella pneumophila subsp. pneumophila Lp02 (NCBITaxon:1080311)","instrument":"Q Exactive HF","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"ubiquitin;Legionella","pi":[{"name":"Chittaranjan Das","email":"cdas@purdue.edu","institution":"Purdue University","country":"United States"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"","task":"8852af185d2b4b1b88655514998f2e40","id":"3165"}, {"dataset":"MSV000093622","datasetNum":"93622","title":"Top-Down Proteomic Analysis of Limited Samples Using Porous Layer Open Tubular Columns and High-Field Asymmetric Ion Mobility Spectrometry Coupled to Mass Spectrometry","user":"mgregus","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702175151000","created":"Dec. 9, 2023, 6:25 PM","description":"Here we explored the potential of a novel platform based on ultra-low flow porous layer open tubular (PLOT) columns and high-field asymmetric waveform ion mobility spectrometry (FAIMS) interfaced with an ultrasensitive mass spectrometry (MS)-based technology in top-down proteomic analysis of a low number of mammalian cells.","fileCount":"45","fileSizeKB":"17764858","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS;PLOT column;ultra-low flow LC-MS;top-down proteomics;FAIMS","pi":[{"name":"Alexander R Ivanov","email":"a.ivanov@northeastern.edu","institution":"Northeastern University, Boston, MA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0f30c9091b9a42b3be0843f893132d31","id":"3166"}, {"dataset":"MSV000093621","datasetNum":"93621","title":"GNPS - Development and Application of a Collision Cross Section Database for the Detection of Quaternary Ammonium Compounds and Their Phase I Hepatic Metabolites in Humans","user":"libinxulab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702160352000","created":"Dec. 9, 2023, 2:19 PM","description":"LC-IM-MS\/MS analysis of human liver microsome (HLM; +\/- NADPH) quaternary ammonium compound (QAC) incubation extracts. 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One organism with particular development is Dictyostelium discoideum, during which it transitions from free-living unicellular to multicellular. Previously the transcriptome has been thoroughly studied during multicellular development, however the proteome and its correlation to the transcriptome during this transition is not fully understood.\nIn this study, for the first time, paired transcriptomics and proteomics was performed in a time series during aggregative multicellularity. From the analysis, the majority of transcripts were identified as differentially expressed, and we could quantify roughly a third of the proteome during early multicellular development. The proteome and transcriptome correlate relatively highly during steady-state, however this decreases as soon as multicellular aggregation is initiated. Correlation is particularly low at the gene-level during development. We find that dynamically regulated mRNA often leads to linear up- or downregulation of the protein, and that there is a time lag of approximately 2 to 4 hours between mRNA and protein. \n","fileCount":"69","fileSizeKB":"39757018","spectra":"0","psms":"378864","peptides":"35841","variants":"43032","proteins":"4856","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Dictyostelium discoideum (NCBITaxon:44689)","instrument":"Q Exactive GC Orbitrap","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:121 - \\\"Ubiquitinylation residue.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Multi-omics;Transcriptomics;Proteomics;mRNA-protein correlation;Aggregative multicellularity;Amoebozoa;Dictyostelium discoideum","pi":[{"name":"Fredrik Soderbom","email":"fredrik.soderbom@icm.uu.se","institution":"Uppsala University","country":"Sweden"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD047669","task":"754f249893ca42cea0bc1c0d2196a49b","id":"3168"}, {"dataset":"MSV000093618","datasetNum":"93618","title":"GNPS - Feline fecal samples (quantification of polyamine conjugated to bile acids)","user":"helenamrusso","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702133183000","created":"Dec. 9, 2023, 6:46 AM","description":"Fecal samples from felines extracted with 50:50 MeOH:H2O and chromatographed using a Phenomenex polar C18 column. MS\/MS data was acquired on a QExactive Orbitrap in positive ionization mode. Quantification of polyamines conjugated to bile acids was performed (cholyl-putrescine, cholyl-cadaverine, cholyl-N-acetyl-putrescine), in addition to taurocholic acid and glycocholic acid.","fileCount":"265","fileSizeKB":"35926122","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Panthera leo (NCBITaxon:9689);Leptailurus serval (NCBITaxon:61405);Acinonyx jubatus (NCBITaxon:32536);Panthera onca (NCBITaxon:9690);Herpailurus yagouaroundi;Panthera tigris (NCBITaxon:9694)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"felines;Polyamine bile acids;fecal","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c0cdee0201c94f03a63ee3ea09b43925","id":"3169"}, {"dataset":"MSV000093615","datasetNum":"93615","title":"Proteomics of dried blood collected on Mitra devices","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702096561000","created":"Dec. 8, 2023, 8:36 PM","description":"Venous blood was collected in Li-heparin or EDTA blood tubes and loaded onto 20 uL Mitra devices or separated to plasma as detailed in metadata. Samples were denatured in 5.5% SDC, reduced and alkylated, and digested with TPCK-trypsin followed by acid precipitation. Filtered precipitated were analyzed by direct injection microflow-LC using a Waters ACQUITY, 1 mm x 150 mm ACQUITY Premier column at 100 uL\/min with post-column DMSO and solvent divert. MS\/MS used an Exploris 480 with staggered\/overlapping DIA acquistion. Demultiplexing was performed using HTRMS converter (Biognosys) and data was analyzed with Spectronaut 18 (Biognosys).","fileCount":"227","fileSizeKB":"221781176","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"whole blood;microsampling;microflow;data-indepndent acquistion;plasma","pi":[{"name":"Matthew W. Foster","email":"mwfoster@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD047666","task":"cf28a9f7320f493abd200745a2ca04e5","id":"3170"}, {"dataset":"MSV000093614","datasetNum":"93614","title":"GC-MS of 4 species of plant used in Amazonia medicine recipes","user":"F4ss0","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702082081000","created":"Dec. 8, 2023, 4:34 PM","description":"GC-MS of 4 species of plant (A. rigidum, C. guianensis, M. laevis and P. sagotianum) used in Amazonia medicine recipes.","fileCount":"80","fileSizeKB":"2719224","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspidosperma rigidum;Couroupita guianensis (NCBITaxon:66684);Maytenus laevis;Protium sagotianum (NCBITaxon:246856)","instrument":"GCMS-QP2020NX","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"A. rigidum;C. guianensis;M. laevis;P. sagotianum;Amazonian medicinal plants;Mass Spectrometry;Liquid-Chromatography;Gas-Chromatography;Biological activity","pi":[{"name":"Jefferson Vladimir Pastu\uFFFDa Fasso","email":"vladimir.fasso@gmail.com","institution":"IKIAM Amazon Regional University","country":"Ecuador"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"50bb6e865ca64dfab28252ac2c127508","id":"3171"}, {"dataset":"MSV000093613","datasetNum":"93613","title":"Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer","user":"coonlabs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702077010000","created":"Dec. 8, 2023, 3:10 PM","description":"Contains files from manuscript titled 'Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer'. Includes mouse and human phosphoproteomics with Orbitrap Astral and mouse proteomics with Orbitrap Eclipse.","fileCount":"958","fileSizeKB":"1420497736","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse;Orbitrap Astral","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Phosphoproteome;DIA phosphoproteomics;Mouse Tissues;HEK293T","pi":[{"name":"Joshua J Coon","email":"coon@wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bda6396ce50547bdaac0deccdb110bd5","id":"3172"}, {"dataset":"MSV000093612","datasetNum":"93612","title":"Protein Kinase C alpha (PRKCA) CRISPR in HCC827 Phospho-proteomics","user":"MSadeghi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702068907000","created":"Dec. 8, 2023, 12:55 PM","description":"Cell Line: HCC827 Empty Vector and PKRCA CRISPR \nLabel: Labeled ARG10LYS8 (Kit: Cat# A33973)\nFile Description: P1, P2, P3 are the independent biological replicates.","fileCount":"56","fileSizeKB":"42046304","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"HCC827;Protein Kinase C alpha CRISPR;PRKCA CRISPR;NSCLC;PKC","pi":[{"name":"Yusuf A. 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Here we developed a novel spontaneously indefinite prostate cancer cell line UCDCaP and its paired castration-resistant line UCDCaP-CR, which exhibits neural lineage plasticity and high levels of N-Myc protein expression. Through rapid immunoprecipitation mass spectrometry assay, we revealed that heat shock protein 70, HSP70 is a top partner for N-Myc. HSP70 is known to function in protein folding and it also coordinates with the E3 ubiquitin ligase, STIP1 homology and U-box containing protein 1, STUB1, to regulate oncoprotein degradation. We find that HSP70 binds a conserved SELILKR motif and prevents the access of STUB1 on N-Myc possibly through steric hindrance. When HSP70 dwell time on N-Myc is increased by the conformational change of HSP70, STUB1 is in close proximity with N-Myc and becomes functional to promote N-Myc ubiquitination on the K416 and K419 sites of the bHLH-LZ domain and form the poly ubiquitination chains linked by the K11 and K63 sites. 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Samples were reduced with 20 mM dithiothreitol, followed by 20 min alkylation with 50 mM iodoacetamide. The alkylated proteins underwent three washes with 200 uL of 8 M Urea in 0.1 M Ammonium Bicarbonate (ABC) and were subsequently equilibrated three times with 0.1 M ABC prior to trypsin digestion. Proteins were digested using Trypsin at an enzyme: protein ratio of 1:50 in 50 uL of 0.1 M ABC buffer at 37C overnight. The resulting digested peptides were collected by centrifugation at 14,000 g for 20 min, followed by two elutions with 50 uL of 50 mM ABC and one elution with 50 uL of 0.5 M NaCl. The eluted peptides were desalted using C18 columns and were dried. The digested proteins were then reconstituted in a 30 uL solution of 5% acetonitrile and 0.1% formic acid buffer for LC-MS analysis.","fileCount":"18","fileSizeKB":"9798477","spectra":"0","psms":"138292","peptides":"65573","variants":"82584","proteins":"62489","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa PAO1 (NCBITaxon:208964)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pseudomonas aeruginosa;aerobic metabolism;respiratory chain;NQR;bc1 complex;SDH;urinary tract infection;metabolic activation;target identification","pi":[{"name":"Oscar Juarez","email":"ojuarez@iit.edu","institution":"Illinois Institute of Technology","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047660","task":"7184a7a931fe4a08b7f4bdb03c4cbc84","id":"3175"}, {"dataset":"MSV000093609","datasetNum":"93609","title":"GNPS - LC-MS\/MS of 4 species of plant used in Amazonia medicine recipes","user":"F4ss0","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702061655000","created":"Dec. 8, 2023, 10:54 AM","description":"LC-MS\/MS of 4 species of plant (A. rigidum, C. guianensis, M. laevis and P. sagotianum) used in Amazonia medicine recipes.","fileCount":"1025","fileSizeKB":"7620444","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Aspidosperma rigidum;Couroupita guianensis (NCBITaxon:66684);Maytenus laevis;Protium sagotianum (NCBITaxon:246856)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"A. rigidum;C. guianensis;M. laevis;P. sagotianum;Amazonian medicinal plants","pi":[{"name":"Jefferson Vladimir Pastu\uFFFDa Fasso","email":"vladimir.fasso@gmail.com","institution":"IKIAM Amazon Regional University","country":"Ecuador"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"25dbc907bfa14ef5ace83696d0388cf7","id":"3176"}, {"dataset":"MSV000093608","datasetNum":"93608","title":"Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics","user":"ychang123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702059572000","created":"Dec. 8, 2023, 10:19 AM","description":"Lysine deacetylase inhibitors (KDACis) are approved for cutaneous T-cell lymphoma (CTCL) and multiple myeloma. Nevertheless, their mechanisms of action (MoA) remain elusive. To characterize the MoA of these drugs in more detail, we systematically measured dose-dependent changes in protein expression, acetylation, and phosphorylation in response to 21 clinical and pre-clinical KDACis. MV4-11 cells were treated for 6 h with vehicle control and 10 increasing doses of the respective drug (from 100 pM to 30 mM). PTM-carrying and unmodified peptides were analyzed separately by liquid chromatography tandem mass spectrometry (LC-MS\/MS) for peptide and protein identification and quantification. Furthermore, time-dependent experiments were carried out for Vorinostat and Panobinostat at their respective pEC50 concentrations from the cell viability data. In an independent experiment, the subcellular proteomes of Panobinostat-treated cells were measured.","fileCount":"1363","fileSizeKB":"317136213","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse;Orbitrap Fusion Lumos","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"HDACs;Lysine deacetylase inhibitors;Acetylome;Phosphoproteome;Proteomic pharmacology;Chemical proteomics;Dose-dependent response","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD047659","task":"08840ee1bc2a49f8b1d4a80275c1f7ed","id":"3177"}, {"dataset":"MSV000093605","datasetNum":"93605","title":"Heart proteomics of pathological atrial enlargement associated with atrial fibrillation","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1702005896000","created":"Dec. 7, 2023, 7:24 PM","description":"Atrial fibrillation (AF) remains challenging to prevent and treat. It is associated with increased rates of heart failure, stroke and neurological decline. A key feature of AF is atrial enlargement. However, not all atrial enlargement progresses to pathology and AF. \nIn the current study, we characterized mouse atria from a 1) pathological model (cardiac-specific transgenic (Tg) that develops dilated cardiomyopathy [DCM] and AF due to reduced protective signalling [PI3K]; DCM-dnPI3K), and a 2) physiological model (cardiac-specific Tg with an enlarged heart due to increased insulin-like growth factor 1 receptor; IGF1R). Atrial enlargement in the DCM-dnPI3K Tg, but not IGF1R Tg, was associated with atrial dysfunction, fibrosis and a heart failure gene expression pattern. Proteomics analysis identified proteins and pathways that were differentially regulated in pathological and physiological atrial enlargement, and provides a resource to study potential drug targets for AF.","fileCount":"29","fileSizeKB":"27011433","spectra":"1291747","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF-X","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"heart;Atrial fibrillation;atrial enlargement;drug targets","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047631","task":"fc9e1326a5b741cd8a74ba37dfe90d69","id":"3178"}, {"dataset":"MSV000093604","datasetNum":"93604","title":"GNPS - Symbiont Mapping Project Orbicella Faveolata","user":"jdeutsch79","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701984127000","created":"Dec. 7, 2023, 1:22 PM","description":"This metabolomics dataset was acquired on individual coral colonies of Orbicella faveolata. 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Pan-PI3K inhibitors thus generate substantial adverse effects, a reality that has plagued drug development against this target class. We present here evidence that a high affinity binding module with the capacity to target all class I PI3K isoforms can facilitate selective degradation of the most frequently mutated class I isoform, PI3Ka, when incorporated into a cereblon-targeted (CRBN) degrader. A systematic proteomics study guided the fine tuning of molecular features to optimize degrader selectivity and potency. Our work resulted in the creation of WJ112-14, a PI3Ka-specific nanomolar degrader that should serve as an important research tool for studying PI3K biology. Given the toxicities observed in the clinic with unselective PI3Ka inhibitors, the results here offer a new approach toward selectively targeting this frequently mutated oncogenic driver.","fileCount":"226","fileSizeKB":"143766223","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"PI3Ka, degrader","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047599","task":"6966d3b21f954155a94190f9d2c0b0b7","id":"3185"}, {"dataset":"MSV000093593","datasetNum":"93593","title":"ARID3C acts as a regulator of monocyte to macrophage differentiation interacting with NPM1","user":"gmltn1541","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701933645000","created":"Dec. 6, 2023, 11:20 PM","description":"IP-MS raw data for halo negative control and ARID3C.\n","fileCount":"7","fileSizeKB":"2396976","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"IP-MS","pi":[{"name":"Je-Yoel Cho","email":"jeycho@snu.ac.kr","institution":"Seoul National University","country":"Korea, Republic of"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c82d864a7a24a7eb8afc824744a7e88","id":"3186"}, {"dataset":"MSV000093592","datasetNum":"93592","title":"Neuronal_Notch_Exosome_YZWang_2023_Cell_Reports","user":"jeffsavas","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701928404000","created":"Dec. 6, 2023, 9:53 PM","description":"Summary\nExtracellular vesicles (EVs) facilitate intercellular communication by transferring cargo between cells in a variety of tissues. However, how EVs achieve cell type-specific intercellular communication is still largely unknown. We found that Notch1 and Notch2 proteins are expressed on the surface of neuronal EVs that have been generated in response to neuronal excitatory synaptic activity. Notch ligands bind these EVs on the neuronal plasma membrane, trigger their internalization, activate the Notch signaling pathway, and drive the expression of Notch target genes. The generation of these neuronal EVs requires the ESCRT-associated protein Alix. Adult Alix conditional knockout mice have reduced hippocampal Notch signaling activation and glutamatergic synaptic protein expression. Thus, EVs facilitate neuron to neuron communication via the Notch receptor-ligand system in the brain.\n","fileCount":"216","fileSizeKB":"116559225","spectra":"0","psms":"439203","peptides":"84102","variants":"84102","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Rattus rattus (NCBITaxon:10117)","instrument":"Orbitrap Fusion","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"Exosome,Alix,Neuron,Notch","pi":[{"name":"Jeffrey N. Savas, PhD","email":"jeffrey.savas@northwestern.edu","institution":"Department of Neurology Northwestern University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047597","task":"50acc1d7e2694135b19df30ef1a82161","id":"3187"}, {"dataset":"MSV000093591","datasetNum":"93591","title":"GNPS - Dataset Creation from GNPS Molcular Networking - d18527df6be44fc498f3c700cd4d0643","user":"t_sritharan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701926381000","created":"Dec. 6, 2023, 9:19 PM","description":"GNPS molecular networking analysis of 176- soil-derived fungi permitted a rapid prioritization of the fungus Penicillium shearii CMB-STF067 as a source of antibacterial active xanthoquinodin class of compounds, jugiones A-D. ","fileCount":"5915","fileSizeKB":"1291840","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858);Soil samples","instrument":"6545 Quadrupole Time-of-Flight ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"soil fungus, GNPS, New South Wales, Austarlia","pi":[{"name":"Prof. Robert J. 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Capon","email":"r.capon@uq.edu.au","institution":"IMB, The University of Queensland","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a8234245cf1f4e8a82be997c44676646","id":"3190"}, {"dataset":"MSV000093587","datasetNum":"93587","title":"Developmental Exposure to a Perfluorooctanesulfonic acid, Perfluorooctanoic acid, Perfluorohexanesulfonic Mixture Alters the Neonatal Lung Proteome","user":"sadegh123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701886695000","created":"Dec. 6, 2023, 10:18 AM","description":"This study aimed to assess PFAS distribution and lung proteome changes in CD-1 offspring after gestational and lactational exposure to PFOS, PFOA, PFHxS, or a PFAS mix. A secondary aim was to evaluate how maternal exposure to a high fat diet (HFD) affected the latter endpoints. Pregnant CD-1 mice received PFOA, PFOS, PFHxS (1 mg\/kg), a PFAS mix (1 mg\/kg each), or vehicle. Dams were fed standard diet (SD) or high fat diet (HFD), and PFAS were administered from gestation day 1 to postnatal day 20. At PND 21, lung PFAS concentration was measured using LC-MS\/MS, and proteomic analysis was conducted. Results from LC-MS\/MS analysis showed a significant overall difference in PFOS, PFOA, and PFHxS levels and the treatment groups with PFHxS concentration were significantly higher compared to PFOS and PFOA. Proteomic analysis determined female pups exposed to maternal HFD Mix (Mix HFD female) and PFOS (PFOS HFD female) had the most differentially expressed proteins followed by PFOS SD male, Mix SD female, and Mix SD male. Canonical pathways like EIF2 signaling, mTOR signaling, and mitochondrial dysfunction were differentially modulated. This study provides insights into PFAS distribution, the molecular mechanism, biomarkers on the neonatal lung in animal models following perinatal exposure.","fileCount":"272","fileSizeKB":"1243530813","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"ABSciex Triple TOF5600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Lung PFAS Mixture Prenatal exposure","pi":[{"name":"Angela Slitt","email":"angela_slitt@uri.edu","institution":"University of Rhode Island","country":"United states"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4305b2a3ac524453a7121aedbf4206db","id":"3191"}, {"dataset":"MSV000093586","datasetNum":"93586","title":"Detection of 187AA by mass spectrometry","user":"huzhijuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701876378000","created":"Dec. 6, 2023, 7:26 AM","description":"Identification of 187AA unique peptides by mass spectrometry and detection of 187AA by mass spectrometry in human cells (GZF2-iPSC, GZF2-hep, 293T, SK-hep1, ESC-derived cardiomyocytes, Hep-G2 and Hela).","fileCount":"16","fileSizeKB":"4000521","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Q Exactive Plus","modification":"none","keywords":"187AA MS","pi":[{"name":"xingguo liu","email":"liu_xingguo@gibh.ac.cn","institution":"Guangzhou Institutes of Biomedicine and Health Chinese Academy of Science","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1d18bac5ad1e4872b601d7e168eceee0","id":"3192"}, {"dataset":"MSV000093584","datasetNum":"93584","title":"A splice-site variant in MADD affects hormone expression in pancreatic b-cells and pituitary gonadotropes","user":"XIOLIU","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701865302000","created":"Dec. 6, 2023, 4:21 AM","description":"MADD is a multifunctional protein regulating activation and localization of small GTP-binding proteins RAB3 and RAB27, MAPK-signaling and cell survival. Polymorphisms in MADD locus have been associated with glycemic traits, but patients with bi-allelic variants in MADD manifest complex syndrome affecting nervous, endocrine, exocrine and hematological systems. We created relevant cell lines for AP-MS and BioID to examine the protein interactome of MADD to clarify how this mutation could leading the syndrome.","fileCount":"13","fileSizeKB":"3176000","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Thermo Scientific Orbitrap Elite MS","modification":"No","keywords":"MADD","pi":[{"name":"Markku Varjosalo","email":"markku.varjosalo@helsinki.fi","institution":"University of Helsinki","country":"Finland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"026f727d5029498988b2d9f9eb150c9a","id":"3193"}, {"dataset":"MSV000093583","datasetNum":"93583","title":"Extracellular vesicles from pancreatic cancer cells activate mast cells which in turn promote tumor cell proliferation and establish a tumor-supportive microenvironment ","user":"Wszymanski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701854421000","created":"Dec. 6, 2023, 1:20 AM","description":"Background and aim: Recent studies reveal a critical role of tumor cell-released extracellular vesicles (EVs) in pancreatic cancer progression. Driver genes directing EV function, the EV-recipient cells, as well as their cellular response to EV uptake remain, however, to be identified. To address this, we investigated the role of the EV biogenesis regulator Bcl-2-associated-anthanogene6 (BAG6)for cancer progression. \nMethods: We used a cre recombinase\/loxP-based reporter system in combination with single-cell RNA sequencing to monitor in vivo EV uptake and tumor microenvironment (TME) changes in preclinical mouse models for pancreatic ductal adenocarcinoma (PDAC) in a Bag6 pro- or deficient background. In vivo data were validated using mouse and human organoids, as well aspatient samples. \nResults: Bag6-deficient subcutaneous and orthotopic PDAC tumors showed accelerated tumor growth dependent on EV release. Mechanistically, this was attributed to mast cell (MC) activation via EV-associate IL33. Activated MCs promoted tumor cell proliferation and altered the composition of the TME affecting fibroblast polarization and immune cell infiltration. Tumor cell proliferation and TME remodeling were mediated via the MC secretome containing high levels of PDGF and CD73. In patients, BAG6 gene expression and protein serum level correlated with survival and low MC infiltration indicating clinical relevance. \nConclusion: The study revealed a tumor-suppressing activity of BAG6 in PDAC, unknown up to now. Bag6-deficiency allowed the release of Evs-associated IL33 which shaped the composition of the TME via MC activation causing aggressive tumor growth. MC depletion using Imatinib diminished tumor growth providing a scientific rationale for the evaluation of Imatinib treatment of patients stratified for low BAG6 expression and high MC infiltration. ","fileCount":"794","fileSizeKB":"83277582","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"timsTOF Pro","modification":"UNIMOD:366 - \\\"Deamidation in presence of O18.\\\";MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. Remap to MOD:01060.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"extracellular vesicles;mouse;pancreatic cancer;TimsTof Pro;DDA;Bag6","pi":[{"name":"Elke Pogge von Strandmann","email":"poggevon@staff.uni-marburg.de","institution":" Institute for Tumor Immunology, Philipps-University Marburg","country":"Germany"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD047563","task":"bb2f353fc3e74f94a207aaa7495ece70","id":"3194"}, {"dataset":"MSV000093581","datasetNum":"93581","title":"Comparison of glioblastoma cell culture platforms based on transcriptional similarity with paired tissue","user":"khj232","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701850122000","created":"Dec. 6, 2023, 12:08 AM","description":"In this study, we isolated GBM TSs and extracellular matrices (ECM) from tissues obtained from newly diagnosed IDH1 wild-type GBM patients, and cultured GBM TSs on five different culture platforms: (1) ordinary TS culture liquid media (LM), (2) collagen-based three-dimensional (3D) matrix, (3) patient normal ECM-based 3D matrix, (4) patient tumor ECM-based 3D matrix, and (5) mouse brain. To evaluate each culture platform, we obtained transcriptome data of all cultured GBM TSs using microarrays. The LM platform exhibited the most similar transcriptional program to paired tissues based on the four aspects, including GBM genes, stemness- and invasiveness-related genes, transcription factor activity, and canonical signaling pathways. GBM TSs can be cultured via an easy-to-handle, cost-efficient, and time-saving LM platform while preserving the transcriptional program of the originating tissues without supplementing artificially manipulated or patient-derived ECM or embedding into the mouse brain to imitate the tumor microenvironment of brain. In addition to applications in basic cancer research, GBM TSs cultured in LM may also serve as patient avatars in drug screening and pre-clinical evaluation of targeted therapy, and may function as a standardized and clinically relevant model for precision medicine owing to its scalability and reproducibility.","fileCount":"34","fileSizeKB":"10447661","spectra":"0","psms":"207262","peptides":"31295","variants":"35170","proteins":"3976","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"cell culture platform;transcriptional program","pi":[{"name":"Pilnam Kim","email":"pkim@kaist.ac.kr","institution":"Korea Advanced Institute of Science and Technology","country":"Republic of Korea"},{"name":"Seok-Gu Kang","email":"seokgu9@gmail.com","institution":"Yonsei University College of Medicine","country":"Republic of Korea"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047560","task":"8b08f6c7747043feb8978673ad13f36c","id":"3195"}, {"dataset":"MSV000093580","datasetNum":"93580","title":"Detection of 187AA by mass spectrometry","user":"huzhijuan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701848564000","created":"Dec. 5, 2023, 11:42 PM","description":"Identification of 187AA unique peptides by mass spectrometry and detection of 187AA by mass spectrometry in eight human cells (GZF2-iPSC, GZF2-hep, 293T, SK-hep1, ESC-derived cardiomyocytes, Hep-G2, QSG-7701 and Hela).","fileCount":"17","fileSizeKB":"4533932","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Q Exactive Plus","modification":"None","keywords":"187AA","pi":[{"name":"xingguo liu","email":"liu_xingguo@gibh.ac.cn","institution":"Guangzhou Institutes of Biomedicine and Health Chinese Academy of Science","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"60288f0a1e0d4472b30849c2a77bcd1f","id":"3196"}, {"dataset":"MSV000093578","datasetNum":"93578","title":"Interactions between sea snails and trematodes: analysis of metabolomes","user":"egor_repkin","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701811727000","created":"Dec. 5, 2023, 1:28 PM","description":"This work is devoted to the analysis of parasite-host interactions at the metabolome level. We analyzed the metabolome of two species of molluscs, Littorina saxatilis and L. obtusata, healthy and infected with trematodes Microphallus pygmaeus.\nFor analysis of the mollusc metabolome, snail soft tissues (without hepatopancreas and operculum) were separated and fixed individually in 100% methanol. Five to eight biological replicates per each group of comparison were collected (53 samples in total). \nTo analyse the parasite metabolome, we used daughter sporocysts with metacercariae of M. pygmaeus purified from host tissues in filtered sea water (0.2 mkm filters, Merck). Parasite tissues were fixed in 100% methanol. Six to eight biological replicates per each group of comparison were collected (28 samples in total). The prepared material was fixed and then frozen initially at -20oC and later at -80oC until use.\nMetabolomic data were obtained using nontargeted GC-MS (gas-chromatography mass spectrometry)-based profiling of the trimethylsilyl derivatives. Shortly: the frozen tissues were homogenised, centrifuged, afterwards the supernatants were vacuum-dried and dissolved in pyridine (Merck) containing 1 mg\/ml of an internal standard (nC23, Sigma-Aldrich). The silylation agent (N,O-bis(trimethylsilyl)-trifluoroacetamide with 1% trimethylsilyl chloride, Sigma-Aldrich) was added to each sample before the analysis. The analysis was carried out on a gas chromatograph with a time-of-flight mass spectrometer Pegasus 4D GCxGC-TOF MS (Leco). \nChromatographic separation was performed in Zorbax DB-5 columns ((5%-phenyl)-methylpolysiloxane; length 30 m, inner diameter 0.25 mm, film thickness 0.25 mkm; Agilent Technologies). Analysis method: evaporator temperature 250oC; starting temperature 70oC; gradient 6oC\/min; final temperature 320oC; helium carrier gas, flow rate 1 ml\/min. Mass spectrometry: detection frequency 10 spectra\/sec in the mass range 50-800Da. ","fileCount":"90","fileSizeKB":"4268226","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Littorina saxatilis (NCBITaxon:31220);Littorina obtusata (NCBITaxon:31218);Microphallus pygmaeus (NCBITaxon:862625)","instrument":"Pegasus 4D GCxGC-TOF MS (Leco)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"molecular parasitology, host-parasite interactions, metabolomics, GC-MS ","pi":[{"name":"Egor A. Repkin","email":"erepkin53@gmail.com","institution":"Saint-Petersburg State University","country":"Russia"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"867323ed45434680a2ab57d3d3b91be5","id":"3197"}, {"dataset":"MSV000093577","datasetNum":"93577","title":"Analysis of p53 independent functions of the Mdm2 MdmX complex using data independent acquisition based profiling","user":"cuproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701809377000","created":"Dec. 5, 2023, 12:49 PM","description":"We utilized data independent acquisition (DIA) to study the poorly understood biology of Mdm2 and MdmX in a p53 null context. Mdm2 and MdmX form a E3 ligase complex that has as its most well studied function the negative regulation of the tumor suppressor p53, however, it is also known to interact with many other proteins in a p53 independent manner. In this work, small molecule and siRNA-based technology were used to modify Mdm2\/Mdmx activity in a human non small cell lung carcinoma cell line lacking p53 expression. Study of the proteome of these cells helped identify biological processes where Mdm2 and MdmX may be playing role in a p53 independent manner. Proteins from H1299 cells, treated with the drug MEL23, siRNA against Mdm2 or MdmX were analyzed. Protein ontology and function were analyzed demonstrating which pathways are affected by modulation of the proteins that originate the complex. Insights on how those functions are dependent on the activity of the complex could also be proposed based on comparison among the three groups of samples. We selected a potential target from the DIA analysis and validated it by immunoblotting and qPCR demonstrating a new interaction partner of the Mdm2 MdmX complex in human cells.","fileCount":"87","fileSizeKB":"271439190","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"cancer;data independent acquisition;label-free proteomics;Mdm2;MdmX;p53 independent functions","pi":[{"name":"Carol Prives","email":"clp3@columbia.edu","institution":"Columbia University","country":"United States"},{"name":"Lewis M. Brown","email":"lb2425@columbia.edu","institution":"Columbia University","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"d0394be715c64bd1ac3d0b15c14ff1c4","id":"3198"}, {"dataset":"MSV000093576","datasetNum":"93576","title":"AP-MS analyses of Halo- Sin3 complex subunits stably expressed in 293T cells.","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701807950000","created":"Dec. 5, 2023, 12:25 PM","description":"Sin3 complex subunits tagged with an N-terminal Halo affinity tag were stably expressed in Flp-In-293 cells. The resulting lysates were used to capture Sin3 associated proteins. Purified protein complexes were identified by AP-MS.","fileCount":"1641","fileSizeKB":"105223563","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"SAP25;Sin3 complex;Halo tag","pi":[{"name":"Laurence Florens","email":"laf@stowers.org","institution":"The Stowers Institute for Medical Research","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"04441b42daeb44458f978541cc639685","id":"3199"}, {"dataset":"MSV000093575","datasetNum":"93575","title":"GNPS - P. fluorescens in CAA with Iron Infusion and High pH","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701802631000","created":"Dec. 5, 2023, 10:57 AM","description":"Pseudomonas fluorescens were cultured in casamino acids media and analyzed on LC\/MS with an iron infusion and high pH.","fileCount":"33","fileSizeKB":"1738081","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pseudomonas;fluorescens;casamino acids","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9b44381297b34f309935697cc67543b5","id":"3200"}, {"dataset":"MSV000093574","datasetNum":"93574","title":"GNPS - P. fluorescens in Succinate Minimal Media","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701802071000","created":"Dec. 5, 2023, 10:47 AM","description":"Pseudomonas fluorescens was cultured in succinate minimal media and analyzed for metabolites.","fileCount":"41","fileSizeKB":"2147201","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pseudomonas fluorescens;succinate","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a8fedb3595404fed8cc1921dfefab928","id":"3201"}, {"dataset":"MSV000093573","datasetNum":"93573","title":"Multiplexed Proteomics Analysis of Zebrafish Embryos at Early Developmental Stages","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701799872000","created":"Dec. 5, 2023, 10:11 AM","description":"Sample Preparation | Four biological replicate of 25 dechorionated, but non-deyolked, zebrafish embryos were collected at 4 time points of embryonic development: 1-cell stage (0-hpf, hour post fertilization), 2-hph, 4-hpf, and 6-hpf. All 16 pooled embryo samples were lysed independently by adding 100 ul of Mammalian lysis buffer and 1x Protease Inhibitor cocktail.\nDigestion | Samples were reduced and alkylated with TCEP and 2-chloroacetamide. Six volumes of pre-chilled acetone were added, and the precipitation was let to proceed overnight. The precipitated proteins were dissolved in 100 ul of 50 mM TEAB, mass spectrometry grade trypsin (Promega Gold) was added at 1:40 w\/w and the digestion was let to proceed at 37oC overnight. Pierce fluorometric peptide assay was performed on 10 ul of each digested sample. \nTandem Mass Tag (TMT) Labeling | 20 ul of anhydrous acetonitrile were added to each of the 0.5mg TMTpro 16plex reagents. For each sample, 20 ug of peptides were measured out and adjusted to 100 ul with 100 mM TEAB, then mixed with the TMT reagents. The replicate samples for each of the time points were labeled for 1 hr with TMTpro-126, 127N, 127C, -128N (0-hpf, replicates 1-4); 128C, 129N, 129C, 130C (2-hpf, 1-4); 130C, 131N, 131C, 132N (4-hpf, 1-4), 132C, 133N, 133C, 134N (6-hpf, 1-4), respectively. After checking labeling efficiency (>99%), 30 ul each of the 16 differentially labeled samples were combined in a new tube and the resulting volume was reduced using a SpeedVac concentrator to less than 10 ul.\nHigh pH Reverse Phase Fractionation | 300 ul of the TMT-labeled peptide mixture (in 0.1% TFA) were loaded onto a Pierce high pH fractionation cartridge placed on a 2.0 ml sample tube. After centrifuging at 3000 x g for 2 minutes, the eluate was collected as the flow-through fraction. The loaded cartridge was placed on a new sample tube, washed with 300 ul of ddH20, and the eluate collected as wash fraction. An additional round of washing was performed using 300 ul of 5% acetonitrile in 0.1% TFA to remove unreacted TMT reagent. A total of 9 HpH RP fractions (E1-E9) were collected by sequential elution in new sample tubes using 300 ul of 10%, 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 50%, and 80% acetonitrile in 0.1% TFA. Dried samples were resolubilized in 44 ul of buffer A (5% acetonitrile in 0.1% formic acid, FA) before LC-MS analysis.\nMultiplexed Mass Spectrometry Analysis | TMT-labeled peptides were analyzed on an Orbitrap Eclipse Tribrid Mass Spectrometer with a FAIMS Pro interface, equipped with a Nanospray Flex Ion Source, and coupled to a Dionex UltiMate 3000 RSCLnano System. Peptides were loaded on an Acclaim PepMap 100 C18 trap cartridge (0.3 mm i.d., 5 mm length) with the U3000 loading pump via the autosampler. A 75 um i.d. analytical microcapillary column was packed in-house with 250 mm of 1.9 um ReproSil-Pur C18-AQ resin (Dr. Masch). The Orbitrap Eclipse was set up to run the TMT-SPS-MS3 method with three FAIMS compensation voltages (CV) at -40V, -55V, and -70V and a cycle time of 1 sec. Briefly, peptides were scanned from 400-1600 m\/z in the Orbitrap at 120,000 resolving power before MS2 fragmentation by CID at 35% NCE and detection in the ion trap set to turbo detection. Dynamic exclusion was enabled for 45s. Real time search (RTS) was performed during the ddMS2 IT CID step against a non-redundant Danio rerio sequence database downloaded from UniProtKB 2021-03 and complemented with common contaminants. Carbamidomethyl and TMTpro16plex (304.2071 Da on Kn) were searched statically, while methionine oxidation was searched as a variable modification. Synchronous precursor scanning (SPS) selected the top 10 MS2 peptides for TMT reporter ion detection in the Orbitrap using HCD fragmentation at 65% NCE at 50,000 resolving power. In addition, RTS was also set up to reject further fragmentation of peptides mapping to contaminants and yolk proteins using an exclusion list with the keywords Contaminant, Phosvitin, and Vitellogenin.\nMS\/MS Data Processing | The LC\/MSn dataset was searched using Proteome Discoverer 2.4 against the same protein database used for RTS. SEQUEST-HT implemented through Proteome Discoverer was set up as: precursor ion mass tolerance 10 ppm, fragment mass tolerance 0.6 Dalton, up to two missed cleavage sites, static modification of cysteine, and lysine and peptide N-termini with TMT tag (+229.163 Da) and dynamic oxidation of methionine. Results were filtered to a 1% FDR at peptides levels using Percolator through Proteome Discoverer. MS3 spectra were processed to extract intensity for each reporter ion. Proteins were quantified by summing reporter ion intensities across all matching PSMs.","fileCount":"15","fileSizeKB":"27262497","spectra":"0","psms":"21720","peptides":"8675","variants":"10352","proteins":"2559","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"Embryo Development;Maternally Inherited;TMT-labeling","pi":[{"name":"Laurence Florens","email":"laf@stowers.org","institution":"The Stowers Institute for Medical Research","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047541","task":"b787d9c16d9c4f1da3b00b5b6d83299e","id":"3202"}, {"dataset":"MSV000093572","datasetNum":"93572","title":"Quantitative proteomics of Axon Regeneration in Xenopus laevis: A closer look at the Tectum, Retina, Chiasm, and Optic Nerve.","user":"sbhattacharya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701794617000","created":"Dec. 5, 2023, 8:43 AM","description":"In this labeled quantitative proteomics dataset, we profile the proteomic changes in the tectum, retina, chiasm, and optic nerve in transgenic lines of 1 year old Xenopus laevis Tg(islet2bgfp). The frogs had monocular surgery of either a left optic crush injury (crush) or sham surgery (sham) and the matching controls of uninjured optic nerves were collected as a control factor. The Tg(islet2bgfp) frogs were allowed to recover for 12 and 27 days post optic nerve crush before euthanasia and tissue collection. Protein extraction was carried by homogenization of the tissue in extraction buffer (TEAB, NaCl, SDS) via Precellys. During extraction, three internal peptide standards were spiked to measure extraction efficiency. Protein amounts were estimated and normalized across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. TMT (Tandem Mass Tag) labelling was carried out using 6 sets of 17 tags from a 18plex TMT kit for quantification. The samples were fractionated into 9 fractions using Pierce High pH Reversed-Phase Peptide Fractionation Kit (Thermo Scientific). After fractionation and drying of all peptide samples, each TMT sample was spiked with two additional isobarically labelled peptides to be used as an ionization control and cross-sample quantification standard. The combination internal peptides were used to compare and normalize against a future axon regeneration cohort. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10.\n\nAfter animals were euthanized, optic nerves were collected by dissection. There were six experimental conditions and six biological replicates per tissue for a total of 102 samples. Protein extraction was carried out by homogenizing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic peptide standards were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 48uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 50ug\/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin.\nAll samples were labelled using 6 sets of 17 tags from a 18plex TMT (Tandem Mass Tag) kit for quantification. After combination and drying of all peptide samples, each combined TMT sample was spiked with two additional peptide standards containing isobaric labels. The final concentration of the post extraction peptides was 54uM per plex or 324uM for all six plex's. These standards were spiked in directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards serve as a normalization method that may be used to compare protein abundance data across multiple datasets.\n\nRaw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The frog proteome was downloaded from UniProt and used as the target database for protein identification. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. The Normalization was set to total peptide amount and confidence to low.","fileCount":"218","fileSizeKB":"277144748","spectra":"0","psms":"240526","peptides":"145772","variants":"163576","proteins":"47560","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xenopus laevis (NCBITaxon:8355)","instrument":"Q Exactive","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Axon Regeneration, Quantitative Proteomics, African clawed frog, Standardization, TMT Labeling","pi":[{"name":"Sanjoy Bhattacharya","email":"sbhattacharya@med.miami.edu","institution":"University of Miami","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047540","task":"1f7282f56177437f8de5a91ccc4f5221","id":"3203"}, {"dataset":"MSV000093571","datasetNum":"93571","title":"GNPS - 20231123_ChemProp2_Non-targeted Metabolomics of Xenobiotic Biotransformations using synthetic gut bacterial community","user":"bciap01","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701780027000","created":"Dec. 5, 2023, 4:40 AM","description":"ChemProp2 Dataset: Investigating potential biotransformations with a panel of 45 Drugs on Synthetic Community (Com20) to elucidate Drug-Microbiome-Host Dynamics","fileCount":"842","fileSizeKB":"77450983","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"sythetic community","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"com20;gut bacteria;chemprop2","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f7b88e938ad14fa6954d3c9deb9aa5f5","id":"3204"}, {"dataset":"MSV000093570","datasetNum":"93570","title":"GNPS - Transition metal (W, Mo) stress response strategies of leguminous plants (Glycine max) and their symbiotic partners (B. japonicum)","user":"JPreiner","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701779627000","created":"Dec. 5, 2023, 4:33 AM","description":"Tungsten (W) and molybdenum (Mo) are economically important transition elements residing in the chromium group of the periodic table. Due to a myriad of industrial applications, ranging from household appliances to war-ammunition and high-tech products, they are increasingly discharged into the environment. However, little is known about their eco-toxicology. While molybdenum is an important micronutrient and serves as co-factor in various key enzymes of microbes, plants and other higher lifeforms, W-enzymes are only found in some archaea and bacteria. Due to their chemical similarities regarding structure, atomic radii and electron configuration, it is proposed that molybdenum ions bound to co-factors of enzymes can be substituted by tungsten. In plants it has been repeatedly demonstrated that tungsten renders the four molybdoenzymes (nitrate reductase, aldehyde oxidase, xanthine dehydrogenase and sulfite oxidase), functionless if incorporated instead of molybednum. In addition, the rhizobial molybdoenzyme, nitrogenase, was found to retain its function even if tungsten is incorporated into the enzyme.\r\n\r\nAlthough it has been shown that both transition metals can be phytotoxic when occurring in excess concentrations, knowledge about their effect on plant metabolic processes is still limited. Due to preliminary experimental data obtained for W, we believe that the two transition metals interfere with integral metabolic pathways, especially phosphorous and nitrogen dependent processes. Additionally, it has already been shown that symbiotically grown leguminous plants respond differently to tungsten toxicity than their non-symbiotically grown counterparts. Still, our understanding of the mechanisms behind the molecular response to tungsten toxicity and similarities to molybdenum metabolism remains limited. We aim to comprehensively understand the molecular mechanisms behind phytotoxicity and stress response induced by excess tungsten and molybdenum as well as possible stress alleviation through Rhizobium symbiosis. \r\n\r\nIn order to uncover the mechanisms that govern toxicity of Mo and W in plants as well as to identify possible benefits of bacterial symbiosis, soybean plants inoculated with Bradyrhizobium japonicum and a surface sterilized non-symbiotic control supplied with nitrate (10mM KNO3) were grown in a semi hydroponic setup for three weeks, until nodules were formed and symbiosis was fully established. After these three weeks, three different metal treatments (control, 0.5 mM tungsten and 0.5 mM molybdenum) for were applied for two weeks and subsequently harvested for metabolomic and proteomic analysis.\r\n","fileCount":"98","fileSizeKB":"83111592","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Glycine max (NCBITaxon:3847)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"soy bean;heavy metals;tungsten;molybendum;rhizobia;symbiosis;abiotic stress","pi":[{"name":"Julian Preiner","email":"julian.preiner@univie.ac.at","institution":"University of Vienna","country":"Vienna"},{"name":"Stefanie Wienkoop","email":"stefanie.wienkoop@univie.ac.at","institution":"Univiersity of Vienna","country":"Vienna"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047532","task":"83c312c03b1a4bcb9756c18475857d37","id":"3205"}, {"dataset":"MSV000093569","datasetNum":"93569","title":"GNPS - Dataset Creation from GNPS Molcular Networking - f884a88d38134c69bb951be15ffc9f9d","user":"rboiteau","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701774965000","created":"Dec. 5, 2023, 3:16 AM","description":"LESA analysis of natural Trichodesmium colonies from the Red sea and laboratory cultured Trichodesmium IMS101 colonies.","fileCount":"42","fileSizeKB":"2330230","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trichodesmium sp. (NCBITaxon:1207)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LESA;Trichodesmium colonies","pi":[{"name":"Rene Boiteau","email":"rboiteau@umn.edu","institution":"University of Minnesota","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b5bd9f575e304fcba802d7f897f19934","id":"3206"}, {"dataset":"MSV000093567","datasetNum":"93567","title":"5HT - Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3","user":"ccms","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701734096000","created":"Dec. 4, 2023, 3:54 PM","description":"we provide evidence for a new class of histone posttranslational modification (PTM): serotonylation.","fileCount":"31","fileSizeKB":"13932132","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;Q Exactive","modification":"PRIDE:0000398","keywords":"Posttranslational modification; Ptm; Serotonylation.","pi":[{"name":"Ian Maze","email":"ian.maze@mssm.edu","institution":"Mount Sinai School of Medicine","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD008106","task":"f798a9de0aa84f2596e2d33834f21478","id":"3207"}, {"dataset":"MSV000093565","datasetNum":"93565","title":"GNPS - P. fluorescens Iron Infusion in CAA","user":"aronlabshared","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701731559000","created":"Dec. 4, 2023, 3:12 PM","description":"Pseudomonas fluorescens was cultured in casamino acid media in varying iron conditions.","fileCount":"26","fileSizeKB":"1194712","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas fluorescens (NCBITaxon:294)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"pseudomonas;fluorescens;casamino acids;CAA","pi":[{"name":"Allegra Aron ","email":"allerga.aron@du.edu","institution":"University of Denver","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f4d69137e9574d4699b195bb4aa92866","id":"3208"}, {"dataset":"MSV000093564","datasetNum":"93564","title":"Mass spectrometric profiling of lysine malonylation in CRISPRi 562 cells lines to investigate malonylation activity of lysine acetyltransferases","user":"JoannaBons","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701731390000","created":"Dec. 4, 2023, 3:09 PM","description":"Lysine malonylation is a protein posttranslational modification with potentially broad biological impact. We present a protocol to generate stable gene knockdown K562 cell lines through lentiviral infection of a CRISPRi system followed by lysine malonylation measurement using mass spectrometry (MS). We detail gRNA vector cloning, lentiviral infection, cell line purification, protein digestion, malonyllysine enrichment, desalting, and MS acquisition and analysis. This protocol can be applied for CRISPRa cell line generation and lysine malonylation profiling in tissues, with slight changes.","fileCount":"76","fileSizeKB":"233144117","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MOD:01893 - \\\"A protein modification that effectively converts an L-lysine residue to N6-malonyl-L-lysine.\\\"","keywords":"Malonylation;Data-independent acquisition (DIA);Post-translational modifications;Lysine acetyltransferases;Stable gene knockdown K562 cell lines ","pi":[{"name":"Birgit Schilling","email":"bschilling@buckinstitute.org","institution":"Buck Institute","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD047514","task":"72d533028f8b4cbfb97d1608db803c0f","id":"3209"}, {"dataset":"MSV000093562","datasetNum":"93562","title":"Comparison of glycopeptide to released glycan abundances and the influence of glycopeptide charge state on N-linked glycosylation of IgG antibodies","user":"glycopep_2023","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701725059000","created":"Dec. 4, 2023, 1:24 PM","description":"We report the comparison of mass-spectral-based abundances of tryptic glycopeptides with fluorescence abundances of released labeled glycans, both derived from therapeutic monoclonal antibodies. These proteins were selected for their very high purities, which assures the origin of all observed released glycans. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances over a dynamic range of 500. The primary glycoforms derived from Rituximab, NISTmAb, Evolocumab, and Infliximab were high mannose and biantennary complex galactosylated and fucosylated and, in some cases, sialylated N-glycans. Except for Evolucumab, in-source ions derived from the loss of HexNAc or HexNAc and hexose sugars to HexNAc(4)Hex(4)Fuc(1) glycoform are prominent for other therapeutic IgGs. After excluding in-source fragmentation of glycopeptide ions from the results, a linear correlation was observed between fluorescently labeled N-glycan and glycopeptide abundances across all mAb samples over a dynamic range of 500. Different charge states of human IgG-derived glycopeptides containing a wider variety of abundant attached glycans were also investigated closely to examine the effect of charge state on ion abundances. These results confirmed and refined results for the therapeutic proteins, clearly revealing a linear dependence of relative glycopeptide abundance on the mass of the glycan, with higher charge states favoring higher mass glycans. Overall, our findings indicate that the mass-spectrometry-based bottom-up approach can provide results as accurate as those of glycan release studies while revealing the origin of each attached glycan. These site-specific relative abundances are conveniently displayed and compared using previously described Glycopeptide Abundance Distribution Spectra GADS representations.","fileCount":"97","fileSizeKB":"62955549","spectra":"1342636","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"Orbitrap Fusion Lumos;timsTOF Pro 2","modification":"glycans;glycopeptides","keywords":"glycoproteomics;glycomics;mass spectrometry","pi":[{"name":"Concepcion Remoroza","email":"concepcion.remoroza@nist.gov","institution":"NIST","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047513","task":"f6add7efb1fe4cdbb7f41731c75b082c","id":"3210"}, {"dataset":"MSV000093556","datasetNum":"93556","title":"Rapid Discovery of Antitumor Substances from Marine Fungi Based on UPLC-Q-TOF-MS","user":"1234512345","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701511130000","created":"Dec. 2, 2023, 1:58 AM","description":"The research results of this paper show that the directional separation method combined with UPLC-QTOF-MS \/ MS technology and GNPS, ACD and other network identification methods can effectively solve the above problems, and quickly and effectively find antitumor active substances from a large number of marine fungal samples cultured by OSMAC strategy.","fileCount":"7","fileSizeKB":"794583","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fungi (NCBITaxon:4751)","instrument":"UPLC-QTOF-MS\\\/MS","modification":"no","keywords":"OSMAC strategy;UPLC-QTOF-MS\/MS","pi":[{"name":"Yuting Wu","email":"13142319312@163.com","institution":"Huaqiao University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dfd2c032fc9543fbbb2f57d30a1a5cff","id":"3211"}, {"dataset":"MSV000093555","datasetNum":"93555","title":"Rapid Discovery of Antitumor Substances from Marine Fungi Based on OSMAC Strategy and UPLC-Q-TOF-MS","user":"1234512345","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701507457000","created":"Dec. 2, 2023, 12:57 AM","description":"Six marine fungal strains (P-WZ-2, P-WZ-3-2, P-WZ-4, P-WZ-5, P341) with significant changes in cancer cell inhibition induced by the OSMAC strategy were analysed by UPLC-QTOF-MS\/MS. The ACD \/ MS Structure ID Suite software was used to predict the possible structures with inhibitory effects on cancer cells.","fileCount":"13","fileSizeKB":"2030544","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fungi (NCBITaxon:4751)","instrument":"6545 LC\\\/QTOF and a 1290 Infinity LC system Agilent Technologies","modification":"NO","keywords":"the secondary metabolites; fungal strains;OSMAC strategy","pi":[{"name":"Yuting Wu","email":"13142319312@163.com","institution":"Huaqiao University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"400bf2a37616427e845454565bc77a78","id":"3212"}, {"dataset":"MSV000093554","datasetNum":"93554","title":"Unveiling the Neuroprotective Potential of Nobiletin in human Neural Progenitor Cells (hNPCs)","user":"abpant","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701505327000","created":"Dec. 2, 2023, 12:22 AM","description":"The data belongs to the proteomic analysis of human neural progenitor cells exposed to sodium arsinate and treated with Nobielin.","fileCount":"54","fileSizeKB":"59744828","spectra":"0","psms":"186729","peptides":"10863","variants":"16757","proteins":"2234","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Neural Proginator cells (NPCs);Nobiletin ;Proteomics ","pi":[{"name":"Professor AB Pant ","email":"abpant@iitr.res.in","institution":"CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh","country":"India"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD047456","task":"23530b31ada8427a8bdc362c040bde05","id":"3213"}, {"dataset":"MSV000093553","datasetNum":"93553","title":"AP-MS analyses of Halo-SAP25 transiently expressed in 293T cells.","user":"simrproteomics","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701459654000","created":"Dec. 1, 2023, 11:40 AM","description":"Different versions (full length and various mutants) of SAP25 tagged with an N-terminal Halo affinity tag were expressed in 293T cells. The resulting lysates were used to capture SAP25 associated proteins. Purified protein complexes were identified by AP-MS.","fileCount":"1151","fileSizeKB":"79334545","spectra":"0","psms":"568360","peptides":"19972","variants":"26297","proteins":"6027","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"SAP25;Sin3 complex;Halo tag","pi":[{"name":"Laurence Florens","email":"laf@stowers.org","institution":"The Stowers Institute for Medical Research","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD047452","task":"f8fb3ed0e9f74eda99348bed1295523b","id":"3214"}, {"dataset":"MSV000093550","datasetNum":"93550","title":"Mapping the anti-cancer activity of alpha-connexin carboxyl-terminal (aCT1) peptide in resistant HER2+ breast cancer","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701447505000","created":"Dec. 1, 2023, 8:18 AM","description":"Connexin 43 (Cx43) is a protein encoded by the GJA1 gene and is a component of cell membrane structures called gap junctions, which facilitate intercellular communication. Prior evidence indicates that elevated GJA1 expression in the HER2-positive (HER2+) subtype of breast cancer is associated with poor prognosis. Prior evidence also suggests that HER2+ breast cancers that have become refractory to HER2 targeted agents have a loss of Cx43 gap junction intercellular communication (GJIC). In this study, a Cx43 targeted agent called alpha-connexin carboxyl-terminal peptide (aCT1) is examined to determine whether GJIC can be rescued in refractory HER2+ breast cancer cells. A proposed mechanism of action for aCT1 is binding to the tight junction protein Zonal Occludens-1 (ZO-1). However, the true scope of activity for aCT1 has not been explored. In this study, proteomic analysis is used to determine the breadth of aCT1 interacting proteins. The NanoString nCounter Breast Cancer 360 panel was also used to examine the effect of aCT1 on cancer signaling in HER2+ breast cancer cells. Findings from this study show a dynamic range of binding partners for aCT1, many of which regulate gene expression and RNA biology. nCounter analysis shows that a number of pathways are significantly impacted by aCT1 including upregulation of apoptotic factors, leading to the prediction and demonstration that aCT1 can boost the cell death effects of cisplatin and lapatinib in HER2+ breast cancer cells that have become resistant to HER2 targeted agents.","fileCount":"14","fileSizeKB":"15368023","spectra":"0","psms":"157095","peptides":"25818","variants":"34920","proteins":"2638","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Connexin 43;breast cancer;HER2;gap junction","pi":[{"name":"Amber L. 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We here use secretome and cell-surface proteomics to show that the loss of IER3IP1 or expression of the pathogenic p.L78P-mutation causes ER retention of selective cell-surface receptors and secreted proteins involved in neuronal migration. This correlates with distension of ER membranes and increased lysosomal activity. Trafficking of the cargo receptor ERGIC53 and of KDEL-receptor 2 are impaired, the latter causing the aberrant secretion of ER-localized chaperones. In utero knock-down of IER3IP1 in brains of mouse embryos displays a morphological phenotype of newborn neurons. Taken together, our data provide hints on how the loss or mutation of a 10 kDa small ER-membrane protein can cause a fatal syndrome.","fileCount":"73","fileSizeKB":"395545692","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"endoplasmic reticulum, COPII, anterograde transport, microcephaly, diabetes, axon pathfinding, cortical development","pi":[{"name":"Christoph Kaether","email":"Christoph.Kaether@leibniz-fli.de","institution":"Leibniz Institute on Aging, Fritz Lipmann Institute (FLI)","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047434","task":"62d9b5e5353b4a599767f74a069e1e78","id":"3216"}, {"dataset":"MSV000093543","datasetNum":"93543","title":"Targeting Spermidine Metabolism Decreases Leukemia Stem Cell Function through Reduction in KAT7 Protein Levels","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701377866000","created":"Nov. 30, 2023, 12:57 PM","description":"MOLM13 whole cell lysates processed with S-Trap and digested with trypsin.","fileCount":"47","fileSizeKB":"28866201","spectra":"0","psms":"728661","peptides":"104725","variants":"163342","proteins":"30106","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Whole cell, trypsin, MOLM13, DENspm","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047414","task":"4cbf8b147a13416ba803701c92ecba61","id":"3217"}, {"dataset":"MSV000093542","datasetNum":"93542","title":"Alkyne-probe pull-down in LAPC4-CR cells","user":"gcraven13","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701340867000","created":"Nov. 30, 2023, 2:41 AM","description":"LAPC4-CR cells were treated with alkyne-probe or DMSO for 2 h in triplicate, lysed and conjugated with biotin-picolyl-azide. 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This disconnect is particularly apparent in cancer entities such as sarcomas for which the oncogenic drivers are often not clear. To investigate more systematically how the cellular proteotypes of sarcoma cells shape their response to molecularly targeted drugs, we profiled the proteomes and phosphoproteomes of 17 sarcoma cell lines and screened the same cells against 150 cancer drugs. The resulting 2,550 phenotypic drug profiles revealed distinct drug responses and the cellular activity landscapes derived from deep (phospho)proteomes (9-10,000 proteins and 10-27,000 phosphorylation sites per cell line) enabled several lines of analysis. For instance, connecting the (phospho)proteomic data with drug responses revealed known and novel mechanisms of action (MoAs) of kinase inhibitors and identified markers of drug sensitivity or resistance. All data is publically accessible via an interactive web application that enables exploration of this rich molecular resource for better understanding active signalling pathways in sarcoma cells, identifying treatment response predictors, and revealing novel MoA of clinical KIs.","fileCount":"365","fileSizeKB":"145304940","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";MOD:00696 - \\\"A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate').\\\";MOD:00425 - \\\"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\\\";MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";MOD:00397 - \\\"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\\\"","keywords":"phosphoproteomics;kinase inhibitor;sarcoma;drug response;proteotype","pi":[{"name":"Bernhard Kuster","email":"kuster@tum.de","institution":"Chair of Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046959","task":"5dfc5fd562644bb1925b229bb84cb469","id":"3223"}, {"dataset":"MSV000093532","datasetNum":"93532","title":"Broad-specificity enzymes enable fast and cost-effective digestion for in-depth proteomics and precise label free quantitation","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701263705000","created":"Nov. 29, 2023, 5:15 AM","description":"We have devised fast and robust SP3- and STRAP-based protocols for the broad-specificity proteases subtilisin, proteinase K, and thermolysin. All three enzymes are remarkably fast, producing near-complete digests in 1-5 min, and cost 200-1000x less than proteomics-grade trypsin. Using FragPipe resolved a major challenge by drastically reducing the duration of the required \"unspecific\" searches.\n\nIn-depth analyses of proteinase K, subtilisin, thermolysin Jurkat digests identified 7374, 8178, 8752 unique proteins with average sequence coverages of 21%, 29%, 37%, including tens of thousands of amino acids not reported in the PeptideAtlas database spanning over 2400 experiments. While we could not identify distinct cleavage patterns, machine learning could distinguish true protease products from random cleavages, potentially enabling the prediction of cleavage products.\n\n2D runs: 20 high-pH RP-HPLC fractions analyzed by DDA LC-MS\/MS mode on a timsTOF Pro2, with Evosep; 15 SPD method, 200 ng peptide loaded on-column.\n\nSTRAP vs SP3: each digest prepared in triplicate with SP3 and STRAP, respectiveyl-- analyzed by DDA nano-LC-MS\/MS on an Orbitrap Exploris 480, 87 min gradient, 750 ng peptide loaded on-column.\n","fileCount":"1402","fileSizeKB":"323488149","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;timsTOF Pro 2","modification":"C+57.021","keywords":"machine learning;label free quantitation;high speed;alternate broad proteases","pi":[{"name":"Rene Zahedi","email":"rene.zahedi@umanitoba.ca","institution":"University of Manitoba","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"356bff1941ad4b1691f068e8951959f6","id":"3224"}, {"dataset":"MSV000093530","datasetNum":"93530","title":"Lipidomics datasets of human cirrhotic liver","user":"zhall1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701258445000","created":"Nov. 29, 2023, 3:47 AM","description":"Mass spectrometry-based lipidomics datasets of cirrhotic liver tissue from patients with advanced steatotic liver disease (SLD; N=20) compared with background liver tissue (N=32) from patients with colorectal metastases to the liver (CRLM) or focal nodular hyperplasia (FNH). 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We submit two datasets investigating peptides modified by itaconate. Experiment001 contains data obtained from endogenous itaconate producing WT or itaconate incompetent Irg1-\/- Bone marrow-derived macrophages stimulated with LPS for 24h. The second dataset from Experiment002 contains data obtained from WT Bone marrow-derived macrophages treated with media or 5 mM itaconic acid for 16h. 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The extract was fractionated by centrifugation into a supernatant and pellet. Labels 126, 127, 128 are supernatant replicates and labels 129, 130, 131 are pellet replicates.\n\nSamples 994350_F1-8: Using recombinant purified mEGFP-tagged MED1-IDR we reconstituted condensates in a soluble nuclear extract isolated from U2OS cells. The extract was fractionated by centrifugation into a supernatant and pellet. Labels 126, 127, 128 are supernatant replicates and labels 129, 130, 131 are pellet replicates.\n\nFor the proximity biotinylation method, we used SILAC (Lys-6, Arg-6) in the media of cells expressing the control while both FUS-IDR and MED1-IDR cells were grown in natural isotope conditions. Cells were subject to the biotinylation protocol followed by nuclear extract preparation. Light and heavy extracts were mixed at a 1:1 ratio followed by streptavidin pulldown, stringent washing, and elution. Two independent replicates of SILAC data were collected for both FUS-IDR (QEX2_1011001 and ECL1_1073837) and MED1-IDR (QEX2_996337 and ECL1_1078014). \n","fileCount":"41","fileSizeKB":"57946732","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF;Orbitrap Fusion Lumos;Orbitrap Eclipse","modification":"UNIMOD:188 - \\\"13C(6) Silac label.\\\"","keywords":"biomolecular condensates;intrinsically disordered regions;selective partitioning;IDR specificity","pi":[{"name":"Benjamin Sabari","email":"Benjamin.sabari@utsoutwhestern.edu","institution":"UT Southwestern Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a3164ed1135f40a78ef141f785711e6f","id":"3231"}, {"dataset":"MSV000093519","datasetNum":"93519","title":"MS-based Proteomics Analysis of Cerebrospinal Fluid from Niemann-Pick type C Disease Patients","user":"sebastianevw","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701188027000","created":"Nov. 28, 2023, 8:13 AM","description":"MS-based proteomics dataset of CSF from NPC patients","fileCount":"3766","fileSizeKB":"1572292116","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Niemann-Pick Type C Disease;proteomics","pi":[{"name":"Forbes D. 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Following addition of iRT standards (Biognosys), the low molecular weight proteome (peptidome) was isolated from 100uL patient K3EDTA plasma using TCA precipitation, cleaned up by solid phase extraction on Waters Oasis HLB 96-well plates, and peptide concentrations estimated by A205nm on a Nanodrop. Peptides were separated by nanoUPLC on Proxeon 1000 thermostated at 50oC prior to nanoelectrospray into an Orbitrap ELITE. High resolution MS1 (240,000) were collected in the FT and MS2 were collected by ITMS. Data were analyzed by PEAKS Studio for de novo database analysis and PTM imputation. 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Optic Nerve crush was performed 2 weeks post AAV injections at three times points (0, 7, 14 days post injury) and collected for proteomics analysis. \nA protein extraction was carried out by homogenization of the tissue in extraction buffer (TEAB, NaCl and SDS). During extraction, three internal peptide standards, named as Regen III, were spiked to measure extraction efficiency. Protein amounts were estimated and normalized across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. TMT (Tandem Mass Tag) labelling was carried out using 1 sets of 18 tags from a 18plex TMT kit for quantification. After combination and drying of all peptide samples, each TMT sample was spiked with two additional isobarically labelled human peptides to be used as an ionization control and cross-sample quantification standard (Regen II). Overall, Regen V standards (refers to a combination of Regen III and Regen II, for extraction and ionization normalization) were used to compare and normalize against any future axon regeneration sample cohort. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10.\n\nAfter animals were euthanized, optic nerves were collected by dissection. There were 6 experimental conditions and three biological replicates for each condition for a total of 18 nerves. Protein extraction was carried out by homogenizing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic bacterial peptide standards (Regen III) were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 18uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 50ug\/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin.\nAll samples were labelled using 1 set of 18 tags from a 18plex TMT (Tandem Mass Tag) kit for quantification. After combination and drying of all peptide samples, the samples were fractionated via Pierce High pH Reversed-Phase Peptide Fractionation Kit (Thermo Fisher). Each combined TMT sample was spiked with two additional human peptide standards containing isobaric labels (Regen II). The final concentration of Regen II was 54uM. These standards were spiked in directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards, known as Regen V (Regen III + Regen II), serve as a normalization method that may be used to compare protein abundance data across multiple datasets.\n\nRaw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The mouse proteome was downloaded from UniProt and used as the target database for protein identification. Two additional local databases were created. One contains the Regen V internal standard peptide sequences, and the other contains BSA peptide sequences. The identification of the Regen V and BSA standards was run in a separate Proteome Discoverer workflow targeted to identify the internal standards separately from experimental proteins. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. Post translational modifications of the Regen II, (biotin, carbon-13 and nitrogen-15) were added during this step to ensure correct identification of the modified standards. 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Briefly, the sample was first trapped on a Symmetry C18 20 mm x 180 um trapping column (5 ul\/min at 99.9\/0.1 v\/v water\/acetonitrile), after which the analytical separation was performed using a 1.8 um Acquity HSS T3 C18 75 um x 250 mm column (Waters Corp.) with a 90-min linear gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 400 nanoliters\/minute (nL\/min) with a column temperature of 55C. Data collection on the Fusion Lumos mass spectrometer was performed for three difference compensation voltages (-40v, -60v, -80v). Within each CV, a data-dependent acquisition (DDA) mode of acquisition with a r 120,000 (m\/z 200) full MS scan from m\/z 375 - 1500 with a target AGC value of 4e5 ions was performed. MS\/MS scans were acquired in the Orbitrap at r 50,000 ( m\/z 200) from m\/z 100 with a target AGC value of 1e5 and max fill time of 35 ms. The total cycle time for each CV was 1s, with total cycle times of 3 sec between like full MS scans. A 20s dynamic exclusion was employed to increase depth of coverage. The total analysis cycle time for each sample injection was approximately 2 hours. 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","fileCount":"27","fileSizeKB":"31962339","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana (NCBITaxon:3702)","instrument":"Q Exactive;Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis;CLASSY","pi":[{"name":"James Wohlschlegel","email":"jwohl@ucla.edu","institution":"UCLA","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f64fd033852c480e8716587da67b5983","id":"3249"}, {"dataset":"MSV000093499","datasetNum":"93499","title":"GNPS - Mass spectral library for glycation products derived from amino acids","user":"Yingfei","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1701034899000","created":"Nov. 26, 2023, 1:41 PM","description":"The non-enzymatic reaction between amino acids (AAs) and reducing sugars, also known as the Maillard reaction (MR), is the primary source of free glycation products in vivo and in vitro. The limited number of MS\/MS records for glycation products (GPs) in public libraries hinders the annotation and investigation of non-enzymatic glycation. To address this issue, we present a mass spectral library containing experimental MS\/MS spectra of diverse GPs from model systems. Based on the conceptional reaction processes and structural characteristics of products, we classified GPs into common glycation products (CGPs) and modified AAs (MAAs). A workflow for annotating GPs was established based on the structural and fragmentation patterns of each GP type. The final spectral library contains 157 CGPs, 499 MAAs, and 2426 GP spectra with synthetic model system information, retention time, precursor m\/z, MS\/MS, and annotations. Our GPs library can serve as an online resource to quickly screen possible GPs in an untargeted metabolomics workflow, further with the model system as a practical synthesis method to confirm their identity.","fileCount":"2","fileSizeKB":"2923","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"chemical reactions","instrument":"maXis","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"non-enzymatic glycation;Maillard model system;glycation product annotation","pi":[{"name":"Philippe Schmitt-Kopplin","email":"philippe.schmittkopplin@helmholtz-munich.de","institution":"Helmholtz Munich - Research Unit Analytical Biogeochemistry","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bc87a0bf01974c52827dcff165b5173b","id":"3250"}, {"dataset":"MSV000093498","datasetNum":"93498","title":"GNPS - Brittonodoxa subpinnata Insoluble extract","user":"Wilton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700954189000","created":"Nov. 25, 2023, 3:16 PM","description":"The plant leaves were incubated (twice) at room temperature in NaCl solution (1M, 5 mL) for 15 min each, in methanol (5 mL), then in methanol-chloroform (1:1, 5 mL) twice for 30 min, and finally washed with methanol (5 mL). After each incubation, the supernatant was discarded.\r\nThe residue was dried in the open air and submitted to alkaline hydrolysis for 18 h at room temperature and in absence of light using NaOH (1M, 50 mL g-1). The alkaline extract was filtered and acidified with HCl until pH 3 and filtered again. The extract was submitted to the same process of cleanup with SPE described above, but the column was washed with ultrapure water and methanol 5% before elution using 10 mL of methanol.","fileCount":"74","fileSizeKB":"11466317","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brittonodoxa subpinnata","instrument":"LC-MS low-resolution (Thermo-Fischer)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Moss, LC-MS, Cell-wall extract","pi":[{"name":"Wilton Ricardo Sala-Carvalho","email":"wiltonsala@hotmail.com","institution":"Universidade de Sao Paulo","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1946858f53b74a48b193660506ac27f4","id":"3251"}, {"dataset":"MSV000093497","datasetNum":"93497","title":"GNPS - Brittonodoxa subpinnata soluble extract","user":"Wilton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700949862000","created":"Nov. 25, 2023, 2:04 PM","description":"For HPLC-MS2 analysis, 50 mg of plant material was extracted with 5 mL of 80% methanol. The supernatant was collected and submitted to a cleanup process through a C18 SPE by activating the column with methanol and equilibrating it with ultrapure water. The extract was loaded into the column and eluted with 5 mL of the following solvents: ultrapure water, followed by 25% methanol, 50% methanol, and washed with methanol. The fractions were joined, transferred to a tube, and vacuum dried.","fileCount":"77","fileSizeKB":"8719371","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brittonodoxa subpinnata","instrument":"HPLC-MS ESI low resolution (Thermo-Fischer)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LC-MS, Mosses, Intracelular compounds","pi":[{"name":"Wilton Ricardo Sala-Carvalho","email":"wiltonsala@hotmail.com","institution":"Universidade de Sao Paulo","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fa46caae090741f2b7b48fe508005e1e","id":"3252"}, {"dataset":"MSV000093496","datasetNum":"93496","title":"GNPS - Brittonodoxa subpinnata non-polar extract","user":"Wilton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700945241000","created":"Nov. 25, 2023, 12:47 PM","description":"For GC-MS analysis, plant material was extracted as following: 50 mg of frozen material was crushed and extracted with 700 uL of pre-cooled methanol (-20oC). Were added 60 uL of adonitol (0.2 mg mL-1, internal standard), with the mixture being centrifuged (10 min at 11000 g) and the supernatant transferred to glasses tubes to add chloroform (375 uL at -20oC) and ultrapure water (750 uL at 4oC), with the polar and non-polar phases being collected separately. The non-polar phase was derivatized with 50 uL of pyridine and 50 uL of BSTFA (N,O-bis-(trimethylsilyl)-trifluoroacetamide) for 1 h at 70oC; 5 uL of tridecanoic acid (2 mg mL-1) was used as internal standard.\r\nThe non-polar phase was analyzed by GC-MS equipped with an HP5-MS capillary column (30 m, 0.25 mm, 0.25 um). An initial column temperature was adjusted to 100oC for 5 min, and increasing at a rate of 5oC min-1 to a final temperature of 320oC, with a total run time of 49 min. 1 uL of injection volume with helium as a carrier gas. In both analyses a blank was injected in each 15 samples.\r\n","fileCount":"73","fileSizeKB":"982945","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brittonodoxa subpinnata","instrument":"GC-MS (Agilent 6850 Network GC System \\\/Agilent 5975C VL MSD) ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mosses, non-polar extract, GC-MS","pi":[{"name":"Wilton Ricardo Sala-Carvalho","email":"wiltonsala@hotmail.com","institution":"Universidade de Sao Paulo","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"381df7d0fd114923bb004c129c61be59","id":"3253"}, {"dataset":"MSV000093495","datasetNum":"93495","title":"GNPS - Brittonodoxa subpinnata polar extracts","user":"Wilton","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700944038000","created":"Nov. 25, 2023, 12:27 PM","description":"For GC-MS analysis, plant material was extracted as following: 50 mg of frozen material was crushed and extracted with 700 uL of pre-cooled methanol (-20oC). Were added 60 uL of adonitol (0.2 mg mL-1, internal standard), with the mixture being centrifuged (10 min at 11000 g) and the supernatant transferred to glasses tubes to add chloroform (375 uL at -20oC) and ultrapure water (750 uL at 4oC), with the polar and non-polar phases being collected separately.\r\nThe polar phase was derivatized using methoxyamine hydrochloride (20 mg mL-1 in pyridine; 28 uL, for two hours at 37oC) and 48 uL of MSTFA (N-Methyl-N-(trimethylsilyl) trifluoroacetamide) for 30 min at 37oC.\r\nSamples were injected (1 uL) into a gas chromatograph (6850 Network GC System - Agilent) coupled to a mass spectrometer (Agilent 5975C VL MSD) (GC-MS) equipped with the VF-5ms column (30 m, 0.25 mm, 0.25 um) and a pre-column (0.25 mm, 10 m). The initial column temperature was adjusted to 70oC for 5 min, increasing at a rate of 5oC min-1 to a final temperature of 295oC, with a total run time of 50 min, with Helium as the carrier gas.\r\n","fileCount":"73","fileSizeKB":"474244","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brittonodoxa subpinnata","instrument":"GC-MS (Agilent 6850 Network GC System \\\/Agilent 5975C VL MSD)","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mosses, polar extract, GC-MS","pi":[{"name":"Wilton Ricardo Sala-Carvalho","email":"wiltonsala@hotmail.com","institution":"Universidade de Sao Paulo","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"de3e8d212e8f429c9048add0bef55972","id":"3254"}, {"dataset":"MSV000093494","datasetNum":"93494","title":"nPOP_ProtocolPaper_Dataset_celllines","user":"andrewleduc95","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700942227000","created":"Nov. 25, 2023, 11:57 AM","description":"WM989, u937, and CPAF cell lines run on the timsTOF Ultra. 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The raw files submitted are described in the metafile included, but in brief, they are categorized as data generation (i.e., bottom-up in-solution enzymatic digestion), native gel separation followed by digestion, non-reducing room temperature (NRT) gel separation followed by digestion, middle-down, non-reducing, and isobaric resolution. 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Laiban, Tanay, Rizal Province. Research supported by The Forest Foundation Philippines under the Dr. Perry S. Ong Fellowship Program. ","fileCount":"59","fileSizeKB":"7708594","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Apis cerana (NCBITaxon:7461);Apis dorsata breviligula (NCBITaxon:655644);Tetragonula (NCBITaxon:398144);Pterocarpus indicus (NCBITaxon:100170)","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"forest honey","pi":[{"name":"Hiyas A. Junio, Ph.D.","email":"hajunio@up.edu.ph","institution":"Institute of Chemistry, University of the Philippines Diliman","country":"Quezon City"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"da9ceada1ac740d389bd4fe5e6b2753f","id":"3259"}, {"dataset":"MSV000093475","datasetNum":"93475","title":"GNPS_Aviwe Alternaria alternata P02PL2","user":"SizweM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700776368000","created":"Nov. 23, 2023, 1:52 PM","description":"Untargeted metabolomics of Alternaria alternata P02PL2, Matandela Aviwe MSc 2023","fileCount":"26","fileSizeKB":"1371139","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Alternaria alternata (NCBITaxon:5599)","instrument":"LCMS-9030","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Untargeted Metabolomics;Alternaria alternata;Endophytic fungi","pi":[{"name":"Sizwe Ndlovu","email":"msizwe@uj.ac.za","institution":"Fungal Functional Genomics RG, University of Johannesburg","country":"South Africa"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"d13d75f8cab244bc973922c0915cf534","id":"3260"}, {"dataset":"MSV000093474","datasetNum":"93474","title":"GNPS_Metabolomic_Profiling_Guadua_Species_Positive","user":"chitival","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700764959000","created":"Nov. 23, 2023, 10:42 AM","description":"Metabolomic profile analysis of 30 samples of plant extracts from different Bamboo species belonging to the genus Guadua Kunth using LC-MS-QTOF (+) in three different collosion energies.","fileCount":"125","fileSizeKB":"53795690","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Guadua (NCBITaxon:38692)","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Metabolomic profiling, Bamboo, Guadua, and Natural products","pi":[{"name":"Luis Carlos Chitiva Chitiva","email":"chitival@javeriana.edu.co","institution":"Pontificia Universidad Javeriana","country":"Bogota"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cafc7c03ad674517b83666ec38154dd3","id":"3263"}, {"dataset":"MSV000093469","datasetNum":"93469","title":"GNPS - 20231122 ReFrame drug reupload separate file name for pos and neg ionization","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700701397000","created":"Nov. 22, 2023, 5:03 PM","description":"MS\/MS analysis of standards in ReFrame drug library. Positive and negative analysis have different file names.","fileCount":"656","fileSizeKB":"20561157","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"NA","instrument":"Q Exactive","modification":"NA","keywords":"ReFrame;drug;library","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ab8fae3917a7452da1a49ecee22ee592","id":"3264"}, {"dataset":"MSV000093468","datasetNum":"93468","title":"Towards an ultimate solution for peptide retention time prediction: the effect of column temperature on separation selectivity","user":"vspicer1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700681758000","created":"Nov. 22, 2023, 11:35 AM","description":"The effect of the column temperature on the selectivity of reversed-phase peptide separation in standard separation settings applied in bottom-up proteomics has been evaluated. Tryptic digests of A549, MCF7, Jurkat and HCT116 human cells in non-labeled and TMT-labeled formats have been analyzed by 1D LC-MS\/MS at four different column temperature settings: 25, 35, 45 and 55 C. \n\nTo increase the size of retention datasets available for retention time prediction modelling, 2D LC-MS\/MS acquisitions were also performed on a Jurkat digest (both non-labeled and TMT-modified). The first dimension separation featured high pH RPLC separation (XTerra, 1x100 mm column, pH 10, 2 % per minute acetonitrile gradient). \n\nFourteen (non-labeled) and eighteen (TMT) concatenated fractions were analyzed using RPLC-MS settings identical to that of the 1D experiments.\n\nThe second dimension of RP chromatographic separation employed the Thermo Fisher Scientific EASY Spray column (PepMap, RSLC C18, 2mm, 100-angstrom, 75mm x 50cm), operated at four temperatures with a gradient of 1% to 50% B (A: 100% water, B: 80:20 ACN: water, both containing 0.1% formic acid) in 107 min, followed by a 1 min rapid increase to 100%B and 12 minute wash. \n\nThe total acquisition time for each sample\/fraction was 120 min.","fileCount":"161","fileSizeKB":"154229039","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:739 - \\\"Native Tandem Mass Tag.\\\"","keywords":"peptide separation;temperature impact;predictive modeling;machine learning;chromatography fundmanetal studies","pi":[{"name":"Oleg Krokhin","email":"oleg.krokhine@umanitoba.ca","institution":"University of Manitoba","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5d4707d32c15467daa6051fce37b2f27","id":"3265"}, {"dataset":"MSV000093466","datasetNum":"93466","title":"Protection of beta cells against pro-inflammatory cytokine stress by GDF15-ERBB2 signaling","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700677574000","created":"Nov. 22, 2023, 10:26 AM","description":"TMT-labeled proteomic data from human islets treated with or without GDF15 for 24 h followed by cytokine (IL1beta & IFNgamma) treatment for 24 h. There are 4 biological replicates. Islets were collected and dissolved in 50 mM NH4HCO3 containing 8 M urea, digested with trypsin and labeled with a 16-plex TMT kit. Peptides were multiplexed, fractionated by high pH reverse phase chromatography, and analyzed by LC-MS\/MS on an Acquity M-Class Nano UHPLC system connected to a Q-Exactive mass spectrometer. LC-MS\/MS data were processed with MaxQuant, by searching against a human SwissProt database (2017-04-12 with 20,198 proteins). The default settings for precursor and fragment mass tolerance were used. Peptide searching was performed with specific trypsin digestion with a maximum of two missed cleavage sites. Carbamidomethylation of cysteine was set as a fixed modification; acetylation of protein N-terminus and oxidation of methionine residues were set as variable modifications. The false discovery rate (FDR) was set to 1% at the protein and peptide levels. The dataset was log2 transformed, and sample level quality control was performed to ensure that all of the samples had data of high enough quality for analyses. With no sample-level issues identified, the data was normalized to total abundance. Statistical analyses utilized a standard Analysis of Variance (ANOVA) model.","fileCount":"50","fileSizeKB":"31625442","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"GDF15;ERBB2;HER2","pi":[{"name":"Ernesto S. Nakayasu","email":"ernesto.nakayasu@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e95b888428624770bbf6ebf6826bae82","id":"3266"}, {"dataset":"MSV000093465","datasetNum":"93465","title":"Quantitative proteomics with Regen V standardization in axon regeneration of Xenopus Laevis.","user":"sbhattacharya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700675612000","created":"Nov. 22, 2023, 9:53 AM","description":"In this labeled quantitative proteomics dataset we profile the proteomic changes in a transgenic line of 1 year old Xenopus laevis Tg(islet2bgfp) frogs that were left untreated (naive) or had a monocular surgery of either a left optic crush injury (crush) or a sham surgery. Matching controls of uninjured optic nerves were also collected for a control factor. The Tg(islet2bgfp) frogs were allowed to recover for 12 and 27 days post optic nerve crush before euthanasia and optic nerve collection. A protein extraction was carried by homogenization of the tissue in extraction buffer (TEAB, NaCl, SDS) via Precellys. During extraction, three internal peptide standards, named as Regen III, were spiked to measure extraction efficiency. Protein amounts were estimated and normalized across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. TMT (Tandem Mass Tag) labelling was carried out using 3 sets of 13 tags from a 16plex TMT kit for quantification. The samples were fractionated into 8 fractions using Pierce High pH Reversed-Phase Peptide Fractionation Kit (Thermo Scientific). After fractionation and drying of all peptide samples, each TMT sample was spiked with two additional isobarically labelled human peptides to be used as an ionization control and cross-sample quantification standard (Regen II). The combination of Regen III and Regen II (Regen V) were used to compare and normalize against a future axon regeneration cohort. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10.\n\nAfter animals were euthanized, optic nerves were collected by dissection. There were six experimental conditions and six biological replicates for each condition for a total of 36 nerves. Protein extraction was carried out by homogenizing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic bacterial peptide standards (Regen III) were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 48uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 50ug\/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin.\nPrior to labelling, three samples of mass spec grade pre-digested bovine serum albumin (BSA) were prepared at a concentration of 150pmol. These samples were included to account for differences in labelling efficiency between TMT batches. Three TMT batches were used to label the 36 experimental conditions, so three additional standards were prepared to be used for normalization. All samples, including the three BSA standards, were labelled using 3 sets of 13 tags from a 16plex TMT (Tandem Mass Tag) kit for quantification. Each BSA standard was labelled with a different tag. After combination and drying of all peptide samples, each combined TMT sample (including one BSA-labelled standard) was spiked with two additional human peptide standards containing isobaric labels (Regen II). The final concentration of Regen II was 54uM. These standards were spiked in directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards, known as Regen V (Regen III + Regen II), serve as a normalization method that may be used to compare protein abundance data across multiple datasets.\n\nRaw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The mouse proteome was downloaded from UniProt and used as the target database for protein identification. Two additional local databases were created. One containing the Regen V internal standard peptide sequences, and the other containing BSA peptide sequences. The identification of the Regen V and BSA standards was run in a separate Proteome Discoverer workflow targeted to identify the internal standards separately from experimental proteins. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. Post translational modifications of the Regen II, (biotin, carbon-13 and nitrogen-15) were added during this step to ensure correct identification of the modified standards. The Normalization was set to total peptide amount and confidence to low.","fileCount":"98","fileSizeKB":"142983162","spectra":"0","psms":"73083","peptides":"46307","variants":"48606","proteins":"24888","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xenopus laevis (NCBITaxon:8355)","instrument":"Q Exactive","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Axon Regeneration, Quantitative Proteomics, TMT Labels, Optic Nerve, African Clawed Frog","pi":[{"name":"Sanjoy Bhattacharya","email":"sbhattacharya@med.miami.edu","institution":"University of Miami","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047176","task":"d9f1d6f696b34112a2fd4876721fc868","id":"3267"}, {"dataset":"MSV000093464","datasetNum":"93464","title":"GNPS_Korean_Medicinal_Plants_reprocess_ENPKG","user":"pmallard","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700674315000","created":"Nov. 22, 2023, 9:31 AM","description":"ENPKG reprocess of files of https:\/\/doi.org\/doi:10.25345\/C5SB50","fileCount":"338","fileSizeKB":"92311","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Viridiplantae (NCBITaxon:33090)","instrument":"Xevo G2 Q-Tof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ENPKG;medicinal plants;Korea","pi":[{"name":"Pierre-Marie Allard","email":"pierre-marie.allard@unifr.ch","institution":"COMMONS Lab - University of Fribourg","country":"Suisse"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6651db00ebfa41b08e45ffec3eafd990","id":"3268"}, {"dataset":"MSV000093463","datasetNum":"93463","title":"GNPS - Senegal Mangrove spcecies Raw data extract","user":"khadime","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700670999000","created":"Nov. 22, 2023, 8:36 AM","description":"senegal mangrove mangrove\r\nraw extract : ethanol and water\r\n","fileCount":"3","fileSizeKB":"45722","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"senegal mangrove species","instrument":"6510 Quadrupole Time-of-Flight LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Senegal Mangrove","pi":[{"name":"GAYE","email":"cheikhouna.gaye@etu.univ-amu.fr","institution":"Aix-Marseille University","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b7b62cf0c8234d5eb2d6a14fc1ce9ff7","id":"3269"}, {"dataset":"MSV000093458","datasetNum":"93458","title":"GNPS - LC-MSe Data from the Berries and Roots of 60 Panax ginseng Genotypes","user":"kbkang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700660776000","created":"Nov. 22, 2023, 5:46 AM","description":"LC-MSe data acquired from the berry and root extracts of 60 different Panax ginseng genotypes, grown in an identical research farm. Details will be updated when the manuscript is published.","fileCount":"1924","fileSizeKB":"45074522","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Panax ginseng (NCBITaxon:4054)","instrument":"Xevo G2 Q-Tof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Panax ginseng;Accessions;Berries;Roots","pi":[{"name":"Kyo Bin Kang ","email":"kbkang@sookmyung.ac.kr","institution":"Sookmyung Women's University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"98f07b08ba69400896a1b1685e61ee52","id":"3270"}, {"dataset":"MSV000093457","datasetNum":"93457","title":"Structure-function analysis of the cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens","user":"klemens_froehlich","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700659942000","created":"Nov. 22, 2023, 5:32 AM","description":"Here, we analyzed a single protein: \nQ7CWD9 AGRFC Beta glucan biosynthesis protein","fileCount":"29","fileSizeKB":"868564","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Agrobacterium fabrum str. C58 (NCBITaxon:176299)","instrument":"Q Exactive HF","modification":"UNIMOD:144 - \\\"Hex3.\\\"","keywords":"open search","pi":[{"name":"Jaroslaw Sedzicki","email":"jaroslaw.sedzicki@unibas.ch","institution":"Uni Basel","country":"Switzerland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"09d72590d36e45f891af923505b43187","id":"3271"}, {"dataset":"MSV000093456","datasetNum":"93456","title":"Ttttttttttttttttttttttttttttttttttttttteszt15","user":"KecskemetiGabor2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700638414000","created":"Nov. 21, 2023, 11:33 PM","description":"aaaaaaaaaaaaaaaaaaaazzzzzzzzzzzzzzzzzzztttttttttttttttttttttttaaaaaaaaaaaaaaa","fileCount":"35","fileSizeKB":"20666560","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lc-ms","pi":[{"name":"Kecskemeti Gabor","email":"kecskemeti.gabor8907@gmail.com","institution":"University of Szeged","country":"Magyarorszag"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"596fed7afc8c4632969b8923edfb297c","id":"3272"}, {"dataset":"MSV000093454","datasetNum":"93454","title":"Hepatic SerpinA1 Improves Energy and Glucose Metabolism through Regulation of Preadipocyte Proliferation and UCP1 Expression","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700620636000","created":"Nov. 21, 2023, 6:37 PM","description":"Fat tissue inducible specific IGF1R and IR (insulin receptor) KO mouse model to investigate the effect of insulin resistance on mature adipocytes. Mouse serum proteomics performed using TMT-10 analyses. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.","fileCount":"368","fileSizeKB":"41219762","spectra":"0","psms":"678205","peptides":"461680","variants":"507842","proteins":"82173","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"adipocyte;obesity;serum proteomics","pi":[{"name":"Wei-Jun Qian","email":"Weijun.Qian@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD047144","task":"8521ebfb946147cc8cda3b4763dc2aef","id":"3273"}, {"dataset":"MSV000093453","datasetNum":"93453","title":"O-GlcNAc Containing Proteins in Normal and Idiopathic Pulmonary Fibrosis Human Fibroblasts","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700610765000","created":"Nov. 21, 2023, 3:52 PM","description":"Isolated normal and IPF fibroblasts were homogenized in cold MilliQ water using a bullet blender. Samples were centrifuged and inhibitors were added: HALT (Thermo Fisher Scientific), Z-Pugnac (Tocris), Thiamet G (Cayman Chemicals), and benzonase (E1014, Millipore, Sigma). O-GlcNAc enzymatic labeling and protein capturing was performed as described using a Click-IT enrichment kit following the manufacturer's protocol (cat no: C33368, C33372, and C10416; Thermo Fisher Scientific). Following an alkyne agarose bead enrichment, proteins were reduced (5 mM DTT, 30 min at 37 C), alkylated (40 mM iodoacetamide, 1 h at 37C) and digested with trypsin (1:50 enzyme\/protein ratio). 0.5 ug of samples were analyzed by LC-MS\/MS on a Q-Exactive HF-X mass spectrometer. Data was searched using MSFragger in match between runs mode.","fileCount":"36","fileSizeKB":"14978296","spectra":"185582","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"fibroblasts;O-GlcNAc;fibrosis;glycan","pi":[{"name":"Jennifer E. Kyle","email":"jennifer.kyle@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"9d8c50b8eaf045be90aa7fde86122037","id":"3274"}, {"dataset":"MSV000093452","datasetNum":"93452","title":"Quantitative proteomics with Regen V standardization of optogenetics induced axon regeneration.","user":"sbhattacharya","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700600035000","created":"Nov. 21, 2023, 12:53 PM","description":"This labeled quantitative proteomics dataset was collected from a transgenic channel rhodopsin mouse model (Chr2) subjected to light stimulation after traumatic optic nerve crush (ONC) was performed. Mouse models expressing channel rhodopsin were subjected to therapeutic light stimulation promoting axon regeneration of retinal ganglion cell (RGC) axons post optic nerve crush. Experimental mice and wild type control mice were euthanized, and optic nerves were collected. A protein extraction was carried out by careful mincing of the tissue in extraction buffer (TEAB, NaCl and SDS). During extraction, three internal peptide standards, named as Regen III, were spiked to measure extraction efficiency. Protein amounts were estimated and normalized across experimental samples. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin. TMT (Tandem Mass Tag) labelling was carried out using 3 sets of 12 tags from a 16plex TMT kit for quantification. After combination and drying of all peptide samples, each TMT sample was spiked with two additional isobarically labelled human peptides to be used as an ionization control and cross-sample quantification standard (Regen II). Overall Regen V standards (refers to a combination of Regen III and Regen II, for extraction and ionization normalization) were used to compare and normalize against any future axon regeneration sample cohort. Untargeted liquid chromatography-mass spectrometry was performed on an Easy-nLC 1000 liquid chromatograph coupled to a QExactive mass spectrometer (LC-MS\/MS). Data analysis was performed using Proteome Discoverer 3.0 and Graph Pad Prism 10.\n\nAfter animals were euthanized, optic nerves were collected by dissection. There were 12 experimental conditions and three biological replicates for each condition for a total of 36 nerves. Protein extraction was carried out by mincing the optic nerve tissue in TEAB, NaCl and SDS. Three synthetic bacterial peptide standards (Regen III) were added to the samples during the extraction to measure extraction efficiency. Each standard was spiked into samples for a total concentration of 36uM per standard. After extraction was carried out, protein amounts were estimated using dot blot densitometry and ImageJ and normalized to 70ug\/ul. Samples were reduced using TCEP, alkylated with iodoacetamide and digested overnight with trypsin.\nPrior to labelling, three samples of mass spec grade pre-digested bovine serum albumin (BSA) were prepared at a concentration of 150pmol. These samples were included to account for differences in labelling efficiency between TMT batches. Three TMT batches were used to label the 36 experimental conditions, so three additional standards were prepared to be used for normalization. All samples, including the three BSA standards, were labelled using 3 sets of 13 tags from a 16plex TMT (Tandem Mass Tag) kit for quantification. Each BSA standard was labelled with a different tag. After combination and drying of all peptide samples, each combined TMT sample (including one BSA-labelled standard) was spiked with two additional human peptide standards containing isobaric labels (Regen II). The final concentration of Regen II was 54uM. These standards were spiked in directly before mass spectrometry analysis to be used as an ionization control. Additionally, all five standards, known as Regen V (Regen III + Regen II), serve as a normalization method that may be used to compare protein abundance data across multiple datasets.\n\nRaw mass spectrometry data files were analyzed using Proteome Discoverer 3.0. The mouse proteome was downloaded from UniProt and used as the target database for protein identification. Two additional local databases were created. One containing the Regen V internal standard peptide sequences, and the other containing BSA peptide sequences. The identification of the Regen V and BSA standards was run in a separate Proteome Discoverer workflow targeted to identify the internal standards separately from experimental proteins. Max missed cleavage site was set to 2 and minimum peptide length to 6. Precursor Mass Tolerance was set to 10ppm and Fragment Mass Tolerance to 0.02 Da. Post-translational modifications for experimental proteins included oxidation, acetylation, carbamidomethylation and TMTpro. Post translational modifications of the Regen II, (biotin, carbon-13 and nitrogen-15) were added during this step to ensure correct identification of the modified standards. The Normalization was set to total peptide amount and confidence to low.","fileCount":"14","fileSizeKB":"7610011","spectra":"0","psms":"43186","peptides":"29860","variants":"32605","proteins":"17160","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"Optogenetics, Axon Regeneration, Light Stimulation, Mouse, Optic Nerve, TMT Labeling, Quantitative Proteomics","pi":[{"name":"Sanjoy Bhattacharya","email":"sbhattacharya@med.miami.edu","institution":"University of Miami","country":"N\/A"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047136","task":"597a8c43a0634bc59c84a800d80adb6d","id":"3275"}, {"dataset":"MSV000093450","datasetNum":"93450","title":"TARGETING NEURONAL FTL1 RESCUES COGNTIVE IMPAIRMENTS IN AGING","user":"jmaynard","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700594288000","created":"Nov. 21, 2023, 11:18 AM","description":"Raw files of protein abundance from TMT-labeled mouse cortical and hippocampal synaptosomes analyzed on an Orbitrap Fusion Lumos","fileCount":"13","fileSizeKB":"13540436","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Aging, neurodegeneration, neuroprotection, cognition, iron metabolism, iron regulation","pi":[{"name":"Saul A. 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Reconstituted in water and 3uL","fileCount":"61","fileSizeKB":"5122733","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"reference materia;fecal;human","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"26f2c7d15b7b4b7cbcf2072202be4a54","id":"3278"}, {"dataset":"MSV000093440","datasetNum":"93440","title":"Impact of Charge State on Characterization of Large Middle-Down Sized Peptides by Tandem Mass Spectrometry","user":"jhellinger","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700519941000","created":"Nov. 20, 2023, 2:39 PM","description":"Fragmentation trends of large peptides were characterized by five activation methods, including HCD, ETD, EThcD, 213 nm UVPD and 193 nm UVPD. Sequence coverages and scores were assessed based on charge site, peptide sequence and peptide size. Results from four model peptides, neuromedin, glucagon, galanin and amyloid B, showed a charge state dependence on sequence coverage for collision and electron-based activation methods. The effect of charge state and peptide size on sequence coverage was also explored for a Glu-C digest of E. coli ribosomal proteins, resulting in a maximum sequence coverage between 2-6 kDa depending on the activation method. ","fileCount":"78","fileSizeKB":"9438668","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"middle-down;UVPD;ETD","pi":[{"name":"Jennifer Brodbelt","email":"jbrodbelt@cm.utexas.edu","institution":"University of Texas-Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e9ae58d5ca1d40649e0b334d82c40cd0","id":"3279"}, {"dataset":"MSV000093438","datasetNum":"93438","title":"Membrane Proteome Profiling of Erythroid Cell Lineages: A Valuable Resource for Advancing Plasmodium vivax Research","user":"jessicamolina","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700513791000","created":"Nov. 20, 2023, 12:56 PM","description":"Background: Erythropoiesis is an intricate maturation process culminating in the production of erythrocytes. As cells progress through erythropoiesis, they undergo surface loss, organelle expulsion, size reduction, and dynamic removal of membrane proteins, refining their structure for specialized physiological functions. This orchestrated process is essential for generating mature erythrocytes capable of efficient gas exchange in the circulatory system. The membrane composition of red blood cells, comprising lipid layers and embedded proteins that play a fundamental role in cellular stability, flexibility, and host interactions. Investigating the membrane proteome becomes particularly relevant in the context of infectious diseases, such as malaria caused by Plasmodium. These proteins critically interact with parasite ligands, allowing entry and progression through various life cycle stages within host cells. Among Plasmodium species, P. vivax exhibits a specific tropism for invading reticulocytes, posing challenges for in vitro continue cultures development due to their limited availability and rapid differentiation. To address this, we studied hematopoietic cell lines, JK-1 and BEL-A2, as potential alternatives to reticulocytes for studying P. vivax biology. Using a Data Independent Acquisition (DIA) LC-MS\/MS approach, we characterize and compare the membrane proteomes of reticulocytes, erythrocytes, and these cell lines. \nResults: Our results reveal distinct abundance patterns in transmembrane proteins, skeletal proteins, and membrane transporters during erythropoiesis. Additionally, we identified 6 potential receptor candidates for P. vivax merozoites ligands, shedding light on the intricate host-parasite interactions. Furthermore, we detected the loss of membrane proteins during erythroblast enucleation, providing insights into the cellular processes governing this transition.\nConclusions: This study significantly contributes to our understanding of erythropoiesis, offering valuable insights for P. vivax malaria research and in vitro culture system development. The comprehensive analysis of membrane proteomes in different cell stages establishes a foundation for future investigations into cellular homeostasis, disease mechanisms, and potential therapeutic targets.\n","fileCount":"25","fileSizeKB":"29224511","spectra":"1769579","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Malaria;Plasmodium vivax;red blood cells;erythroid cell lines;reticulocytes","pi":[{"name":"Manuel Alfonso Patarroyo","email":"mapatarr.fidic@gmail.com","institution":"Fundacion Instituto de Inmunologia de Colombia ","country":"Colombia"},{"name":"Markus Kalkum","email":"mkalkum@coh.org","institution":"City of Hope","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4ef2c2427fd349b2bc6f12f8da56e272","id":"3280"}, {"dataset":"MSV000093435","datasetNum":"93435","title":"Characterization of the molecular determinants of MLL3\/4 PHD2 and PHD3 (PHD2\/3) fingers binding to ASXL2","user":"LambertLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700501354000","created":"Nov. 20, 2023, 9:29 AM","description":"This submission contains the mass spectrometry files for the manuscript by Yi Zhang et al. that describes the functional characterization of the molecular determinants of MLL3\/4 PHD2 and PHD3 (PHD2\/3) fingers binding to ASXL2. AP-MS experiments were performed from K562 cells and MS files were acquired on an Orbitrap Fusion mass spectrometer. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca).","fileCount":"14","fileSizeKB":"3332073","spectra":"0","psms":"15226","peptides":"7897","variants":"9430","proteins":"9316","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:01160 - \\\"A protein modification that effectively results in the loss of an ammonia, usually by a process of vicinal dehydration, rearrangement, and rehydration with release of ammonia, resulting in a loss of nitrogen with no gain of oxygen.\\\"","keywords":"Chromatin","pi":[{"name":"Jean-Philippe Lambert","email":"jean-philippe.lambert@crchudequebec.ulaval.ca","institution":"Universite Laval","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047103","task":"90860ffeae904873917e01ab4c8b3530","id":"3281"}, {"dataset":"MSV000093434","datasetNum":"93434","title":"Single cell proteomics and epiproteomics of cancer cells treated with a histone deacetylate inhibitor","user":"ben_orsburn","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1700496330000","created":"Nov. 20, 2023, 8:05 AM","description":"NCI-H-358 cancer cells were treated with the histone deacetylase inhibitor mocetinostat or DMSO mock control. SIngle cells were isolated by FACs and were multiplexed using every other channel (c-Channels of the TMTPro reagent) a carrier channel of 75 control and 75 treated cells labeled with 135n were used for each experiment. Single cells were pseudo-randomized so that each following injection had an alternate mixture of control or treated cells as each label. Analysis was performed using an EvoSep system coupled to a TIMSTOF SCP. Cells were analyzed using 30SPD, 60SPD, 100SPD, 200SPD, 300SPD and 500SPD. After blank and carrier lanes, 7 cells were analyzed in each LCMS injection, allowing 210 cells, 420 cells, 700 cells, 1400 cells, 2100 cells and 3500 cells to be analyzed in a 24 hour day, respectively. Bruker .d files were converted to MGF and the reporter mass region was recalibrated to compensate for mass error. The resulting files were analyzed in Proteome Discoverer 2.4 and SCP-Viz. 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Clinical samples provided from 9 individuals before or after 45 minutes of intense exercise. Samples were SEC fractionated, TCEP reduced, and IAA alkylated. Proteins were precipitated with acetone and digested with either LysC and trypsin or using an S-trap microtube, then analyzed by LC-MS\/MS. Data was searched with FragPipe.","fileCount":"175","fileSizeKB":"125575518","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus;Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"extracellular vesicles enrichment;human plasma;size exclusion chromatography;SEC","pi":[{"name":"Ernesto S. 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Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. 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As such, interventions that restore proteostasis should slow down the aging process and improve healthspan. Two of the most broadly used anti-aging interventions that are effective in organisms from yeast to mammals are calorie restriction (CR) and rapamycin (RM) treatment. To identify the regulatory mechanisms by which these interventions improve the protein homeostasis in the muscle, we carried out ribosome footprinting in the muscle from mice aged under standard conditions, or under long-term treatment with CR or RM. We found that RM primarily remodels the translation of upstream, and CR the translation of downstream, open reading frames (ORFs). Mass spectrometry analysis reveals the expression of numerous non-canonical ORFs at the protein level. 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In adipose tissue, we here show expression of OLFM2 to be adipocyte-specific and opposed to obesity. OLFM2 levels are increased during adipogenesis, and impaired when differentiated fat cells are challenged with conditions emulating inflammation in the context of obesity. On the molecular level, examination of OLFM2 deficiency in human adipocytes indicated down-regulation of genes related to cell cycle. At the cellular level, the loss of OLFM2 compromised adipogenesis, while its over-production enhanced the adipogenic transformation of 3T3-L1 cells. Complementary loss and gain of function assays coupled to untargeted proteomics revealed the modulation of key protein pathways, including regulation of citrate cycle, fatty acid degradation, axon guidance and focal adhesion in mature adipocytes and precursor cells. Transferring these findings into animal models using a whole-body knockout and transcriptionally depleted adipose Olfm2 highlighted, respectively, a cluster of molecular changes connected with defective cell cycle (in both), fat mass accretion and impaired metabolism (in the latter). Our data underscores a key role for OLFM2 in fat cells, and suggests that the association between adipose OLFM2 and obesity is not only correlative but also causative.","fileCount":"129","fileSizeKB":"451285896","spectra":"3971080","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:366 - \\\"Deamidation in presence of O18.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Olfactomedin-2, adipocytes, adipose tissue, metabolism, obesity;label-free, Orbitrap Eclipse, DIA","pi":[{"name":"Francisco J. 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Causation was confirmed in mice with targeted deletion of 4 of 6 MIDN protein isoforms. MIDN augmented proteasome activity in lymphocytes but few other cell types. By cryo-electron microscopy we showed that MIDN binds directly to the 26S proteasome. MIDN-deficient B cells displayed aberrant activation of the IRE-1\/XBP-1 pathway of the unfolded protein response. Partial or complete MIDN deficiency suppressed B lymphoproliferation in three models of B cell malignancies. Thus, MIDN is required for proteasome activity in support of lymphopoiesis and malignant B cell proliferation over a broad range of differentiation states. Targeting MIDN in B cell malignancies may avoid off-tumor toxicities caused by proteasome inhibition throughout the body.","fileCount":"26","fileSizeKB":"5114962","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Midnolin, proteasome, lymphopoiesis, B cell cancer ","pi":[{"name":"Bruce Beutler","email":"Bruce.Beutler@utsouthwestern.edu","institution":"UT Southwestern Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046953","task":"cd804a1b8fc4420185efe986c36d6b2f","id":"3295"}, {"dataset":"MSV000093396","datasetNum":"93396","title":"Cross-talks between Metabolic and Translational Controls during Beige Adipocyte Differentiation","user":"DaehwaYoun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699942186000","created":"Nov. 13, 2023, 10:09 PM","description":"Measurement of protein levels upon beige adipocyte differentiation. Adipocyte precursor cells were isolated from inguinal white adipose tissue, and induction of beige adipocyte differentiation was performed. Non-induced and differentiated samples for 4 or 8 days were used for sample preparation. For each condition, triplicates were constructed. Peptide fragmentation was performed for 9 samples, and then an equal volume of each sample was pooled to generate Ref 1 and 2. Next, a total of 11 samples were labeled with 11 different TMT reagents. Labeled samples were pooled into one. 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Furthermore, the GRN-\/- condition induces significant alterations across the proteome, lipidome, and metabolome of induced pluripotent stem cells (iPSC) and iPSC-derived neurons, unveiling unique metabolic pathways. Although this study was conducted at a whole cell level, this comprehensive perspective contributes to our understanding of the intricate interplay among proteins, lipids, and metabolites in neurodevelopment and neurodegenerative diseases. 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Rickettsia spp. are obligate intracellular bacteria that can cause life-threatening disease, but their absolute dependence on the host cell environment has impeded discovery of rickettsial effectors and their host targets. We implemented bioorthogonal non-canonical amino acid tagging (BONCAT) during R. parkeri infection to selectively label, isolate, and identify secreted effectors. As the first use of BONCAT in an obligate intracellular bacterium, our screen more than doubles the number of experimentally validated effectors for R. parkeri. The novel secreted rickettsial factors (Srfs) we identified include Rickettsia-specific proteins of unknown function that localize to the host cytoplasm, mitochondria, and ER. We further show that one such effector, SrfD, interacts with the host Sec61 translocon. Altogether, our work uncovers a diverse set of previously uncharacterized rickettsial effectors and lays the foundation for a deeper exploration of the host-pathogen interface.","fileCount":"6","fileSizeKB":"2983069","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rickettsia parkeri str. Portsmouth (NCBITaxon:1105108)","instrument":"Orbitrap Exploris 480","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\";MOD:00046 - \\\"A protein modification that effectively converts an L-serine residue to O-phospho-L-serine.\\\";MOD:00047 - \\\"A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine.\\\";MOD:00048 - \\\"A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";[M] [551.31] Met replacement with biotin-azidonorleucine;[M] [23.05] Met replacement with azidonorleucine","keywords":"BONCAT;Rickettsia","pi":[{"name":"Rebecca Lamason","email":"rlamason@mit.edu","institution":"Massachusetts Institute of Technology","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2455caa9aad448ee983784811c6981b2","id":"3302"}, {"dataset":"MSV000093378","datasetNum":"93378","title":"The endogenous protein-protein interaction network of the NPC Cholesterol Transporter 1 in the cerebral cortex ","user":"RJavanshad","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699850218000","created":"Nov. 12, 2023, 8:36 PM","description":"The endogenous protein-protein interaction network of the NPC Cholesterol Transporter 1 in the cerebral cortex","fileCount":"19","fileSizeKB":"29589567","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090);Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"NPC1;Niemann-Pick disease, type C","pi":[{"name":"Stephanie Cologna","email":"cologna@uic.edu","institution":"University of Illinois at Chicago","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6a566052e0ea4488a8e357cf9f1f3014","id":"3303"}, {"dataset":"MSV000093375","datasetNum":"93375","title":"Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity","user":"syjung","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699742962000","created":"Nov. 11, 2023, 2:49 PM","description":"Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome-enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.","fileCount":"143","fileSizeKB":"154410908","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"C. elegans lysosome","pi":[{"name":"Meng Wang","email":"wmeng@bcm.edu","institution":"Baylor College of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046869","task":"cc4a1599a9a341ec84a900aeb783a0dd","id":"3304"}, {"dataset":"MSV000093372","datasetNum":"93372","title":"Wheat-based glues in conservation and cultural heritage: (dis)solving the proteome of flour and starch pastes and their adhering properties ","user":"solazzoc","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699718903000","created":"Nov. 11, 2023, 8:08 AM","description":"Plant-based adhesives, such as the ones made from wheat, have been prominently used for books and paper-based objects and are also used as conservation adhesives. Starch paste originates from starch granules, whereas flour paste encompasses the entire wheat endosperm proteome, offering strong adhesive properties due to gluten proteins. From the conservation perspective, understanding the precise nature of the adhesive is vital, as the longevity, resilience, and reaction to environmental changes can differ substantially between starch and flour-based pastes. We devised a proteomics method to discern the protein content of these pastes. Protocols involved extracting soluble proteins using 0.5 M NaCl and 30 mM Tris-HCl solutions, then targeting insoluble proteins, such as gliadins and glutenins, with a buffer containing 7M urea, 2M thiourea, 4% CHAPS, 40 mM Tris, and 75 mM DTT. Flour paste's proteome is diverse (1942 proteins across 759 groups), contrasting with starch paste's predominant starch-associated protein makeup (218 proteins in 58 groups). Transformation into pastes reduces proteomes' complexity. Testing on historical bookbindings confirmed the use of flour-based glue, rich in gluten and serpins. High levels of deamidation were detected, particularly for glutamine residues, which can impact the solubility and stability of the glue over time. ","fileCount":"106","fileSizeKB":"19274443","spectra":"0","psms":"75283","peptides":"7492","variants":"17693","proteins":"5412","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Triticum aestivum (NCBITaxon:4565);Ovis aries (NCBITaxon:9940);Capra hircus (NCBITaxon:9925);Bos taurus (NCBITaxon:9913);Gallus gallus (NCBITaxon:9031)","instrument":"Orbitrap Fusion","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"wheat;starch;flour;collagen;leather","pi":[{"name":"Caroline Solazzo","email":"solazzoc@si.edu","institution":"Smithsonian Institution","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046866","task":"cf01324861fb46bd983a02d19f368024","id":"3305"}, {"dataset":"MSV000093361","datasetNum":"93361","title":"GNPS - Co-Culture Penicillium spp BuOH-1","user":"ynurulita","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699657676000","created":"Nov. 10, 2023, 3:07 PM","description":"Co-culture liquid fermentation of Riau peat swamp soil isolates, penicillium spp. in BuOH extract-1","fileCount":"7","fileSizeKB":"557651","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Penicillium citrinum (NCBITaxon:5077);Penicillium verrucosum (NCBITaxon:60171)","instrument":"Q Exactive GC Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Penicillium spp BuOH","pi":[{"name":"Yuana Nurulita","email":"ynurulita@lecturer.unri.ac.id","institution":"Universitas Riau","country":"Indonesia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ea6dca93e6024487aa104efd163cf5c6","id":"3306"}, {"dataset":"MSV000093357","datasetNum":"93357","title":"BAD BioID in 2D MCF10A cell culture","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699640974000","created":"Nov. 10, 2023, 10:29 AM","description":"BioID proximity labeling experiment on Bcl2-associated agonist of cell death (BAD) using BAD-miniTurbo stable cell line in MCF10A, 2D cell culture. Sample: BAD-turbo-biotin; controls: BAD-biotin, turbo-biotin, BAD-turbo (n=3).","fileCount":"13","fileSizeKB":"15746466","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"BioID;miniTurbo;BAD","pi":[{"name":"Ing Swie Goping","email":"igoping@ualberta.ca","institution":"University of Alberta","country":"Canada"},{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b2e222b144dd467dbd5a7c2172ac07ea","id":"3307"}, {"dataset":"MSV000093355","datasetNum":"93355","title":"SERBP1 interactome defines its novel regulatory roles in the cytoplasm and nucleus in conjunction with PARP1-, G-quadruplex- and PAR-binders - DIA-MS data","user":"stweintraub","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699633291000","created":"Nov. 10, 2023, 8:21 AM","description":"Background\nRNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics allow liquid-liquid phase separation (LLPS) and formation of membraneless organelles or molecular condensates such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system, regulating brain function, neurogenesis and synapse plasticity. Their dysfunction is associated with neurodegenerative diseases and brain tumor development. SERBP1 is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We have previously defined SERBP1 as an oncogenic factor in glioblastoma. Here, we investigated the SERBP1 interactome using a proteomics approach.\n\nResults\nWe defined novel roles for SERBP1 in splicing, cell division, DNA repair and ribosomal biogenesis based on the protein's interactome and functional analyses. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1\/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, SERBP1 and most of its associated proteins get PARylated and\/or bind to PAR, indicating that SERBP1 is present in regulatory complexes that are built on PAR binding. Finally, we determined that SERBP1 is potentially implicated in Alzheimer's where it is highly expressed and present in pathological stress granules and Tau aggregates.\n\nConclusion\nOur study established SERBP1 as a multi-functional protein that participates in distinct regulatory complexes assembled via G4- and PAR-binding.\n","fileCount":"29","fileSizeKB":"26363582","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"SERBP1;RNA binding protein;PARP1;G-quadruplex;interactome;proteomics;mass spectrometry","pi":[{"name":"Luiz O. Penalva, Ph.D.","email":"penalva@uthscsa.edu","institution":"University of Texas Health Science Center at San Antonio","country":"U.S.A."}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046851","task":"a775aabf74874af784b475db3a02c609","id":"3308"}, {"dataset":"MSV000093353","datasetNum":"93353","title":"GNPS - Plant SynCom single and co-culture extracts repetition ","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699629423000","created":"Nov. 10, 2023, 7:17 AM","description":"Non-targeted metabolomics of synthetic community created from the Arabidopsis phyllosphere microbiota. ","fileCount":"199","fileSizeKB":"36274323","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"SynCom;Plant Microbiota","pi":[{"name":"Danie Petras","email":"daniel.petras@uni-tuebingen.de","institution":"University of Tuebingen ","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2d2d8958b144497289cc0649c48d15d4","id":"3309"}, {"dataset":"MSV000093351","datasetNum":"93351","title":"GNPS - Development and application of mass spectrometric molecular networking for analyzing ingredients of areca nut","user":"18846429693","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699614712000","created":"Nov. 10, 2023, 3:11 AM","description":"Areca nut(Areca catechu L.) is commonly consumed as a chewing food in the Asian region. However, the investigations into the components of areca nut are limited. In this study, we have developed an approach that combines mass spectrometry with feature-based molecular network to explore the chemical characteristics of the areca nut. In comparison to the conventional method, this technique demonstrates a superior capability in annotating unknown compounds present in areca nut. We annotated a total of 52 compounds, including one potential previously unreported alkaloids, one carbohydrate, and one phenol and confirmed the presence of 6 of them by comparing with commercial standards. The validated method was used to evaluate chemical features of areca nut at different growth stages, annotating 25 compounds as potential biomarkers for distinguishing areca nut growth stages. Therefore, this approach offers a rapid and accurate method for the component analysis of areca nut. ","fileCount":"13","fileSizeKB":"24865","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Areca triandra (NCBITaxon:115441)","instrument":"LC-MS","modification":"0","keywords":"Areca nut;Chemical composition;LC-MS;GNPS;Feature-based molecular network","pi":[{"name":"Zhao Jialiang","email":"zjl989664@163.com","institution":"Jiangnan University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"117e0a79cc97404b8b574527fb1f3998","id":"3310"}, {"dataset":"MSV000093348","datasetNum":"93348","title":"Multiomics characterization of a less invasive microfluidic-based cell sorting technique","user":"janaz","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699566797000","created":"Nov. 9, 2023, 1:53 PM","description":"Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate\ncell subpopulations with a high level of recovery and accuracy. However, the cell sorting\nprocedure can impact the viability and metabolic state of cells. Here, we performed a comparative study and evaluated the impact of traditional high-pressure charged droplet-based and a microfluidic chip-based sorting approach on the metabolic and phosphoproteomic profile of different cell types. While microfluidic chip-based sorted cells more closely resembled the unsorted control group for most cell types tested, the droplet-based sorted cells showed significant metabolic and phosphoproteomic alterations. In particular, greater changes in redox and energy status were present in cells sorted with the droplet-based cell sorter along with higher transcriptional and spliceosomal regulation and mechanical stress signaling. These results\nindicate microfluidic chip-based sorting is less disruptive compared to droplet-based sorting.","fileCount":"123","fileSizeKB":"103918451","spectra":"12523425","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Ascend","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Sorter-induced cellular stress (SICS);Phosphoproteomics;Fluorescence-activated cell sorting (FACS);Sorting","pi":[{"name":"Sonja Hess","email":"sonja.hess@astrazeneca.com","institution":"AstraZeneca","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD046826","task":"5fd3925f1e8a4a128832e28ed6de83e5","id":"3311"}, {"dataset":"MSV000093347","datasetNum":"93347","title":"GNPS - Fecal metabolites identify liver transplant recipients at risk for peri-operative infection","user":"jess_cleary","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699565591000","created":"Nov. 9, 2023, 1:33 PM","description":"Targeted metabolomics performed by GC-MS (for SCFAs by PFBBr derivatization) and LC-MS (for bile acids) on fecal samples from liver transplant patients. ","fileCount":"873","fileSizeKB":"85159794","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Agilent 6546 Q-TOF;Agilent 8890\\\/7890B GC system, Agilent 5977B MSD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Liver Transplant;fecal;microbiome;metabolites","pi":[{"name":"Christopher Lehmann","email":"christopher.lehmann@bsd.uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"0663776423d34106838da5f66bfc1a2f","id":"3312"}, {"dataset":"MSV000093346","datasetNum":"93346","title":"Ttttttttttttttttttttttttttttttttttttttteszt9","user":"KecskemetiGabor2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699542387000","created":"Nov. 9, 2023, 7:06 AM","description":"dsakfhipoqewznfwezodfuiqgnewfuigawouiefgaweouifhnrewuiphfrew","fileCount":"2","fileSizeKB":"350788","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"lc-ms","pi":[{"name":"Kecskemeti Gabor","email":"kecskemeti.gabor8907@gmail.com","institution":"University of Szeged","country":"Magyarorszag"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c21378c927e841b981a83d56a5bf498d","id":"3313"}, {"dataset":"MSV000093344","datasetNum":"93344","title":"The dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons ","user":"tbockPCF","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699520216000","created":"Nov. 9, 2023, 12:56 AM","description":"Precise coordination of molecular programs and neuronal growth govern the formation, maintenance, and adaptation of neuronal circuits. RNA metabolism has emerged as a key regulatory node of neural development and nervous system pathologies. To uncover cell-type-specific RNA regulators, we systematically investigated expression of RNA recognition motif-containing proteins in the mouse neocortex. Surprisingly, we found RBM20, an alternative splicing regulator associated with dilated cardiomyopathy, to be expressed in cortical parvalbumin interneurons and mitral cells of the olfactory bulb. Genome-wide mapping of RBM20 target mRNAs revealed that neuronal RBM20 binds pre-mRNAs in distal intronic regions. Loss of neuronal RBM20 has only modest impact on alternative splice isoforms but results in a significant reduction in an array of mature mRNAs in the neuronal cytoplasm. This phenotype is particularly pronounced for genes with long introns that encode synaptic proteins. We hypothesize that RBM20 ensures fidelity of pre-mRNA splicing by suppressing non-productive splicing events in long neuronal genes. This work highlights a common requirement for RBM20-dependent transcriptome regulation in cardiomyocytes and neurons and demonstrates that a major genetic risk factor of heart disease impacts neuronal gene expression.\r\n","fileCount":"18","fileSizeKB":"3096387","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"MOD:01060 - \\\"A protein modification that effectively converts an L-cysteine residue to S-carboxamidomethyl-L-cysteine.\\\"","keywords":"Mouse, Heart, PRM","pi":[{"name":"Alexander Schmidt","email":"alex.schmidt@unibas.ch","institution":"Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD046806","task":"ed356ca6c5ff4f3883b0449bf4b3b5a5","id":"3314"}, {"dataset":"MSV000093343","datasetNum":"93343","title":"GNPS_Matlou Akanthomyces muscarius P02PL3_2","user":"SizweM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699516876000","created":"Nov. 9, 2023, 12:01 AM","description":"Untargeted metabolomics of Akanthomyces muscarius P02PL3, Matlou Semenya MSc 2023","fileCount":"9","fileSizeKB":"236483","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Akanthomyces muscarius (NCBITaxon:2231603)","instrument":"LCMS-9030","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Fungi;Untargeted metabolomics;Akanthomyces muscarius","pi":[{"name":"Sizwe Ndlovu","email":"msizwe@uj.ac.za","institution":"Fungal Functional Genomics, University of Johannesburg","country":"South Africa"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b8c74bfcc628460981a423672c4f0fbc","id":"3315"}, {"dataset":"MSV000093340","datasetNum":"93340","title":"LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function","user":"jdiedrich","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699494992000","created":"Nov. 8, 2023, 5:56 PM","description":"Mitochondria-associated RNA-binding proteins have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs. Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEM mRNAs, including LARP4, a La RBP family member. We show that LARP4s targets are particularly enriched in mRNAs that encode respiratory chain complex proteins and mitochondrial ribosome proteins across multiple human cell lines. Through quantitative proteomics, we demonstrate that depletion of LARP4 leads to a significant reduction in RCCP and MRP protein levels. Furthermore, we show that LARP4 depletion reduces mitochondrial function, and that LARP4 re-expression rescues this phenotype. Our findings shed light on a novel function for LARP4 as an RBP that binds to and positively regulates NEM mRNAs to promote mitochondrial respiratory function.","fileCount":"40","fileSizeKB":"39879731","spectra":"0","psms":"137498","peptides":"57193","variants":"72422","proteins":"5605","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mitochondrial mRNA targets, LARP4, OXPHOS function","pi":[{"name":"Tony Hunter","email":"hunter@salk.edu","institution":"Salk Institute for Biological Studies","country":"USA"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD046798","task":"20a8e106f7f5432297bf160df4404f3b","id":"3316"}, {"dataset":"MSV000093339","datasetNum":"93339","title":"Proteome analysis of the retina from RhoQ344X\/+ mouse","user":"ShimpeiTakita","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699484564000","created":"Nov. 8, 2023, 3:02 PM","description":"Retinal proteomes from wild-type and RhoQ344X mutant mice at postnatal day 35 were analyzed by label-free quantitative proteomics to understand proteomic change caused by the rhodopsin mutation.","fileCount":"18","fileSizeKB":"36550806","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Mouse, retina, LC-MS\/MS","pi":[{"name":"Yoshikazu Imanishi","email":"yimanish@iu.edu","institution":"Indiana University School of Medicine","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046795","task":"1f7f37590d1a4597bea6fd127c2bf426","id":"3317"}, {"dataset":"MSV000093337","datasetNum":"93337","title":"Dendrobates auratus PDMS in vivo temporal sampling","user":"mabel_gonzalez","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699470943000","created":"Nov. 8, 2023, 11:15 AM","description":"In vivo analysis of skin secretions from D. auratus","fileCount":"938","fileSizeKB":"69069954","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Dendrobates auratus (NCBITaxon:43471)","instrument":"GC-Q-TOF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Poison frogs;Dendrobatidae;Alkaloids;VOCs","pi":[{"name":"Mabel Gonzalez","email":"mabel.c.gonzalez@uniandes.edu.co","institution":"Uniandes","country":"Colombia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bffeb6b33154449394b58c392116d715","id":"3318"}, {"dataset":"MSV000093335","datasetNum":"93335","title":"Mitochondrial ribosomal protein L12 (MRPL12) post-translational modifications","user":"dittenhaferreed","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699468392000","created":"Nov. 8, 2023, 10:33 AM","description":"Analysis of post-translational modifications on mitochondrial protein L12 (MRPL12). MRPL12 was overexpressed in HeLa or HEK293 cells, immunoprecipitated, and subject to bottom-up proteomic analysis on an Agilent 6545 LC-qTOF.","fileCount":"1473","fileSizeKB":"3483691","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6545 Q-TOF LC\\\/MS","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"mitochondria;post-translational modification;mitochondrial ribosomal protein L12;phosphorylation;acetylation","pi":[{"name":"Kristin Dittenhafer-Reed","email":"dittenhaferreed@hope.edu","institution":"Hope College","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046790","task":"c60d533af23046aeaff241e5d5f2019a","id":"3319"}, {"dataset":"MSV000093332","datasetNum":"93332","title":"Amino acid- and protein-specificity of protein fatty acylation in C. elegans","user":"cornell_bz298","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699457241000","created":"Nov. 8, 2023, 7:27 AM","description":"Identification of fatty acylated proteins in Caenorhabditis elegans via alkyne fatty acid feeding and click chemistry workflows","fileCount":"49","fileSizeKB":"76192675","spectra":"1845359","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Caenorhabditis elegans (NCBITaxon:6239)","instrument":"Orbitrap Exploris 480","modification":"fatty acylation","keywords":"C. elegans;lipidation;palmitoylation;click chemistry","pi":[{"name":"Frank Schroeder","email":"schroeder@cornell.edu","institution":"Boyce Thompson Institute, Cornell University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d92e8fac06d24be793ffdccdc1ed7120","id":"3320"}, {"dataset":"MSV000093330","datasetNum":"93330","title":"Multimodal measurement of the transcriptome and proteome from dissociated human pancreatic islet cells using nanoSPLITS","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699406178000","created":"Nov. 7, 2023, 5:16 PM","description":"Human pancreatic islets from two human donors (Prodo Laboratories) were acquired and cultured for 24 hr in pancreatic islet media (PIMS, Prodo Laboratories). Single cells were dissociated with TrypLE for ~15-30 minutes, washed with PBS, stained with Calcein-AM\/propidium iodide, and sorted onto nanoSPLITS chips using a cellenONE cell sorter. For the proteomic sample prep all steps utilized the nanoPOTS sample handling robot. Lysates were reduced with DTT, alkylated with IAA, digested overnight with trypsin\/Lys-C at 37C, and vacuum dried \/ stored at -20C. LC-MS\/MS data was acquired using TIFF DDA methodology on a Thermo Tribrid mass spectrometer. Data was searched using FragPipe version 20.0 before downstream analysis in R.","fileCount":"304","fileSizeKB":"38049964","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\"","keywords":"nanoSPLITS;nanoPOTS;single-cell;multiomics;multimodal;scRNAseq;scProteomics;pancreas;islets","pi":[{"name":"James M. Fulcher","email":"james.fulcher@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"f332a0be454c4086a18a822647c38d4b","id":"3321"}, {"dataset":"MSV000093329","datasetNum":"93329","title":"GNPS - 83 actinomycetes cultured in 2 media","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699397362000","created":"Nov. 7, 2023, 2:49 PM","description":"Bacterial extracts from 83 actinomycetes cultured in two media conditions. Untargeted LC-MS\/MS acquisition performed in positive ion mode.","fileCount":"401","fileSizeKB":"37409541","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinomycetes - several strains","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Actinobacteria;Actinomycetes;Natural Products","pi":[{"name":"Hosein Mohimani","email":"hoseinm@andrew.cmu.edu","institution":"Carnegie Mellon University","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8c55b7917d3d43579e3d4b904edb6279","id":"3322"}, {"dataset":"MSV000093325","datasetNum":"93325","title":"Metabolic detection of early-stage breast cancer through absolute quantitative metabolomics and machine learning","user":"Songhuajie","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699343194000","created":"Nov. 6, 2023, 11:46 PM","description":"To achieve the best outcomes, breast cancer necessitates robust strategies for early detection. However, reliable blood-based tests for identifying early-stage disease remains elusive. Here we have employed plasma metabolomics and machine learning techniques to establish a non-invasive metabolic approach for early detection of breast cancer.","fileCount":"667","fileSizeKB":"59411776","spectra":"1971046","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Breast cancer; Plasma; Metabolomics;","pi":[{"name":"Songhuajie","email":"shj@pku.edu.cn","institution":"Peking university health science center","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"564b0eb6a835401cbab52fff597a1daa","id":"3323"}, {"dataset":"MSV000093323","datasetNum":"93323","title":"The ALPHA Phase 1 Study: Pulmonary ArteriaL Hypertension Treated with CardiosPHere-Derived Allogeneic Stem Cells","user":"NivedaS5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699331910000","created":"Nov. 6, 2023, 8:38 PM","description":"BACKGROUND: Pulmonary Arterial Hypertension (PAH) is a progressive condition with no cure. Even with pharmacologic advances, survival remains poor. Lung pathology on PAH therapies still shows impressive occlusive arteriolar remodeling and plexiform lesions. Cardiosphere derived cells (CDCs) are heart derived progenitor cells exhibiting anti inflammatory and immunomodulatory effects, are anti fibrotic, anti oxidative and anti apoptotic to potentially impact several aspects of PAH pathobiology. In preclinical trials CDCs reduced right ventricular (RV) systolic pressure, RV hypertrophy, pulmonary arteriolar wall thickness and inflammation. \nMETHODS: The ALPHA study was a Phase 1a\/b study in which CDCs were infused into patients with Idiopathic (I)PAH, Heritable (H) HPAH, PAH connective tissue disease (CTD ) and PAH human immunodeficiency virus (HIV). The study was IRB approved and DSMB monitored. Phase 1a, was an open label study (n=6). Phase 1b was a double blind placebo controlled study (n=20) in which half received 100 million CDCs (the maximum feasible dose from manufacturing perspective) and half placebo (PLAC) infusions. Right heart catheterization (RHC) and cardiac MR imaging (cMR) were performed at baseline and at 4 months post infusion. Patients were followed over a year. \nFINDINGS: No short term clinical safety adverse events (AE) were related to the IP, the primary outcome measure. There were no adverse hemodynamic, gas exchange, rhythm or other clinical events following infusion and in the 1st 23 hours monitored in hospital. There were no long term AEs over 12 months noted, including unrelated limited hospitalizations. No immunologic short or long term AEs were noted. We examined exploratory outcomes across multiple domains to determine encouraging signals to motivate future advanced phase testing. Phase 1a data showed encouraging observations for both 50 and 100 million CDC doses. Several encouraging findings favoring CDCs (n=16) compared to placebo (n=10) were noted. On cMR, the RV end diastolic volume (RVEDV) and index (RVEDVI) decreased with CDCs with a rise in the PLAC group. The 6 minute walk distance was increased 2 months post infusion in the CDC group compared with PLAC. With PLAC, diffusing capacity (DLCO) decreased at 4 months but was unchanged with CDCs. Serum creatinine decreased with CDCs at 4 months. Encouraging observations favoring CDCs were also noted for RV fractional area change on echo and RV ejection fraction (RVEF) on cMR at 4 months. No differences were observed for mean pulmonary artery pressures or pulmonary vascular resistance. Review of long term data to 12 months showed continued decline in DLCO for the PLAC cohort at 6 months with no change through 12 months. By contrast, CDC subjects showed an unchanged DLCO over 12 months. For parameters exhibiting early encouraging exploratory findings in CDC subjects, no further improvement was noted in long term follow up through 12 months. \nINTERPRETATION: Intravenous CDCs were safe in both the short and long term in PAH subjects and thus may be safe in larger cohorts, in line with our extensive track record of safety in clinical trials for other conditions. Further, CDCs exhibited encouraging exploratory findings across several domains. Repeat dosing (quarterly, over one year) of intravenous CDCs has been reported to yield highly significant sustained disease modifying bioactivity in subjects with advanced Duchenne muscular dystrophy. Because only single CDC doses were used here, the findings represent a lower limit estimate of CDCs potential in PAH. Upcoming phase 2 studies would logically use a repeat dosing paradigm.\n","fileCount":"38","fileSizeKB":"53028730","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Progenitor cell therapy;pulmonary arterial hypertension;short- and long-term safety;right ventricle;regenerative medicine","pi":[{"name":"Michael I Lewis","email":"Michael.Lewis@cshs.org","institution":"Cedars Sinai Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046721","task":"4e585e7fac6c4e8b9a7bff412eb0935c","id":"3324"}, {"dataset":"MSV000093320","datasetNum":"93320","title":"Essential role of STAT5 tyrosine phosphorylation in vivo","user":"ronholes7059","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699303659000","created":"Nov. 6, 2023, 12:47 PM","description":"STAT5 proteins are vital for lymphocyte development and function. Tyrosine phosphorylation of a C-terminal tyrosine is the key event in cytokine activation of STAT5A and STAT5B. However, the role of STAT5 tyrosine phosphorylation has not been assessed in vivo. Here we generated Stat5a and Stat5b tyrosine mutant knock-in (KI) mice and found that these animals had greatly reduced CD8+ T cell numbers. These cells exhibited profoundly diminished proliferation in response to IL-2, correlating with greatly reduced IL-2-induced pRB and a block in the G1-->S phase transition. The mutant cells also exhibited decreased IL-2-mediated activation of pERK and pAKT, which can in part be attributed to diminished IL-2-induced expression of IL-2R-beta and IL-2R-gamma. Our findings highlight that the tyrosine phosphorylation of both STAT5A and STAT5B is essential for maximal IL-2 signaling and elucidate the molecular basis for achieving an optimal mitogenic effect of IL-2 on CD8+ T cells.","fileCount":"13","fileSizeKB":"18813441","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Stat5, cytokine, IL-2, T cell, NK cell, tyrosine phosphorylation","pi":[{"name":"Warren Leonard","email":"leonardw@nhlbi.nih.gov","institution":"National Institute of Health, National Heart, Lung , and Blood Institute","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c3cffc32eb304a05ae975c44b9f3c630","id":"3325"}, {"dataset":"MSV000093319","datasetNum":"93319","title":"Exploring variability in methylxanthine content within Ilex guayusa: Impact of geographic location, age and sunlight exposure ","user":"NPLIKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699301613000","created":"Nov. 6, 2023, 12:13 PM","description":" DDA chromatograms, sample processing method, methylxanthines, sample in positive polarity, collision energy 40ev","fileCount":"91","fileSizeKB":"985110","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ilex guayusa","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"UPLC;DDA;Guayusa","pi":[{"name":"Mateo Andrei Fernandez Valverde","email":"mateo.fernandez@est.ikiam.edu.ec","institution":"Universidad Regional Amazonica Ikiam","country":"Ecuador"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bd415baa499b4a2c9136aa48e5ad7bdd","id":"3326"}, {"dataset":"MSV000093318","datasetNum":"93318","title":"Exploring variability in methylxanthine content within Ilex guayusa: Impact of geographic location, age and sunlight exposure ","user":"NPLIKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699301365000","created":"Nov. 6, 2023, 12:09 PM","description":"DDA chromatograms, sample processing method, methylxanthines, sample in positive polarity, collision energy 20ev","fileCount":"91","fileSizeKB":"864618","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ilex guayusa","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - 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No post-translational-modifications are included in the identified peptides of this dataset","keywords":"powdery mildew;TAG;lipid metabolism;lipidomics","pi":[{"name":"Mary Wildermuth","email":"mwildermuth@berkeley.edu","institution":" Department of Plant and Microbial Biology, University of California, Berkeley","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"76d96b267736471390f46a7b6ac84654","id":"3328"}, {"dataset":"MSV000093316","datasetNum":"93316","title":"Test PTFI GNPS Dataset 20231106.1","user":"lhenson","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699295258000","created":"Nov. 6, 2023, 10:27 AM","description":"Test dataset from PTFI data containing positive and negative injections from scallops, mascarpone cheese, and goat cheese","fileCount":"7","fileSizeKB":"397039","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pectinidae (NCBITaxon:6566);mascarpone cheese;goat cheese","instrument":"NA","modification":"NA","keywords":"scallops;mascarpone cheese;goat cheese","pi":[{"name":"Louie Henson","email":"lhenson@dayspringpartners.com","institution":"Dayspring Partners","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"36f996b9018347638e05c5f62a4eab29","id":"3329"}, {"dataset":"MSV000093315","datasetNum":"93315","title":"Exploring variability in methylxanthine content within Ilex guayusa: Impact of geographic location, age and sunlight exposure ","user":"NPLIKIAM","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699293583000","created":"Nov. 6, 2023, 9:59 AM","description":"DDA chromatograms, sample processing method, methylxanthines, sample in positive polarity, collision energy 10ev","fileCount":"91","fileSizeKB":"1066953","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ilex guayusa","instrument":"Xevo G2-XS QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"UPLC;DDA;Guayusa;Positive","pi":[{"name":"Mateo Andrei Fernandez Valverde","email":"mateo.fernandez@est.ikiam.edu.ec","institution":"Universidad Regional Amazonica Ikiam","country":"Ecuador"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5e3245faa3b644be888f65b748a19d4c","id":"3330"}, {"dataset":"MSV000093311","datasetNum":"93311","title":"GNPS - Fungal endophytes of the invasive grass Eragrostis lehmanniana shift metabolic expression in response to native and invasive grasses","user":"tayloraportman","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699288251000","created":"Nov. 6, 2023, 8:30 AM","description":"Characterization of the metabolome of three fungal isolates, Fusarium sp., Pseudothielavia sp., and Pseudophialophora sp. grown alone (axenically) and in the presence of seeds of the invasive grass Eragrostis lehmanniana and co-occuring native grasses Eragrostis intermedia, Bouteloua curtipendula, and Leptachloa dubia.","fileCount":"124","fileSizeKB":"58947150","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Fusarium sp. (NCBITaxon:29916);Pseudothielavia sp.;Pseudophialophora sp. (NCBITaxon:1707707)","instrument":"Orbitrap Exploris 480","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Endophyte;Germination;Fusarium sp.;Pseudothielavia sp.;Pseudophialophora sp.","pi":[{"name":"Malak M. Tfaily","email":"tfaily@arizona.edu","institution":"University of Arizona","country":"United States"},{"name":"Taylor A Portman","email":"tayloraportman@arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"797513e1c0504586b384afa7516c5f58","id":"3331"}, {"dataset":"MSV000093310","datasetNum":"93310","title":"Dissecting the properties of circulating IgG against Group A Streptococcus through a combined systems antigenomics-serology workflow ","user":"alejandro1018","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699285739000","created":"Nov. 6, 2023, 7:48 AM","description":"Most individuals maintain circulating antibodies against various pathogenic bacteria as a consequence of previous exposures. However, it remains unclear to what extent these antibodies contribute to host protection. This knowledge gap is linked to the need for better methods to characterize antimicrobial polyclonal antibodies, including their antigen and epitope repertoires, subclass distribution, glycosylation status, and effector functions. Here, we showcase a generic mass spectrometry-based strategy that couples systems antigenomics and systems serology to characterize human antibodies directly in clinical samples. The method is based on automated affinity purification workflows coupled to an integrated suite of high-resolution MS-based quantitative, structural- and glyco-proteomics readouts.\nWe focused on Streptococcus pyogenes (Group A Streptococcus; GAS), a major human pathogen still awaiting an approved vaccine. Our methodology reveals that both healthy and GAS infected individuals have circulating Immunoglobulin G (IgG) against a subset of genomically conserved streptococcal proteins, including numerous toxins and virulence factors. The antigen repertoire targeted by these antibodies was relatively constant across healthy individuals, but considerably changed in GAS bacteremia. Detailed analysis of the antigen-specific IgG indicates inter-individual variation regarding titers, subclass distributions, and Fc-signaling capacity, but not in epitope and Fc-glycosylation patterns. Importantly, we show that the IgG subclass has a major impact on the ability of GAS-antibodies to trigger immune signaling, in an antigen- and Fc receptor- specific fashion. Overall, these results uncover exceeding complexity in the properties of GAS-specific IgG, and showcase our methodology as high-throughput and flexible workflow to understand adaptive immune responses to bacterial pathogens.\n","fileCount":"2470","fileSizeKB":"77541753","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"human","instrument":"Q Exactive HF;timsTOF Pro","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Immunoglobulins;Streptococcus Pyogenes;Systems serology;antigenomics","pi":[{"name":"Johan Malmstrom","email":"johan.malmstrom@med.lu.se","institution":"Department of Clinical Sciences, Lund Division of Infection Medicine Sweden","country":"N\/A"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"8f373b9ad5704b0ab685caedd59fac3c","id":"3332"}, {"dataset":"MSV000093307","datasetNum":"93307","title":"GNPS - Celastraceae_plant_extracts_library_graphknowledge","user":"quirosgu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699276805000","created":"Nov. 6, 2023, 5:20 AM","description":"This set of mass spectrometry data contains de processed .mgf resulting form the MZmine datamining of a set of 76 species of the Celastraceae family. Additionally, it contains all the results from the application of the ENPKG workflow.","fileCount":"155","fileSizeKB":"697185","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"several species of the Celastraceae family","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Celastraceae;Graph Knowledge;Natural Products","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c7dfeddf5c364ca3aa583874c8366196","id":"3333"}, {"dataset":"MSV000093306","datasetNum":"93306","title":"Egg MVBs elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization ","user":"ylevinwis","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699266902000","created":"Nov. 6, 2023, 2:35 AM","description":"Abstract:\r\nMitochondria are maternally inherited, but the mechanisms underlying paternal mitochondrial elimination (PME) after fertilization are far less clear. In Drosophila, special egg-derived multivesicular bodies (MVBs) promote PME. To uncover the cellular degradative pathway mediated by the MVBs to degrade the sperm mitochondrial derivative, we isolated these vesicles from early fertilized eggs, using a subcellular fractionation procedure and subjected them to mass spectrometry (MS) analysis.\r\n\r\n","fileCount":"5","fileSizeKB":"2796124","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Drosophila melanogaster (NCBITaxon:7227)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Drosophila;MVB;multivesicular bodies","pi":[{"name":"Eli Arama","email":"eli.arama@weizmann.ac.il","institution":"Weizmann Institute of Science","country":"Israel"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046694","task":"a6ef3212194849cdb44b3b50f5d8488e","id":"3334"}, {"dataset":"MSV000093305","datasetNum":"93305","title":"GNPS - Dyrehaven Streptomyces P9-A2 monoculture and coculture data with Aspergillus tubingensis","user":"scottjarmusch11","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699266096000","created":"Nov. 6, 2023, 2:21 AM","description":"Extracts of Streptomyces sp. P9-A2 from Jaegersborg Dyrehaven, Denmark. Agar plug extracts from the inhibition zone of P9-A2 and Aspergillus tubingensis.\n","fileCount":"14","fileSizeKB":"2275826","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces sp.;Aspergillus tubingensis (NCBITaxon:5068)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces;monoculture;coculture","pi":[{"name":"Scott A. Jarmusch","email":"salja@dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e2c7f64638b74269a273b32be007fa0c","id":"3335"}, {"dataset":"MSV000093304","datasetNum":"93304","title":"Ttttttttttttttttttttttttttttttttttttttteszt9","user":"KecskemetiGabor2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699257726000","created":"Nov. 6, 2023, 12:02 AM","description":"dfsauhsoqenfgosagfzusagfzdsaidzsaibncgdsaufgdomsafh","fileCount":"15","fileSizeKB":"5110031","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"dsahnfuioagfunsadgonsiifuldas","pi":[{"name":"Kecskemeti Gabor","email":"kecskemeti.gabor8907@gmail.com","institution":"University of Szeged","country":"Magyarorszag"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f2865a2200184be6bb59df775ce18d80","id":"3336"}, {"dataset":"MSV000093302","datasetNum":"93302","title":"GNPS - Methanolic extracts of Amycolatopsis spp. on ISP2 - 8cae4ec6622e4cc0959042f087315336","user":"ka26lul","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699117650000","created":"Nov. 4, 2023, 10:07 AM","description":"Comparative metabolomics analysis of three Amycolatopsis strains isolated from distant geographical locations.","fileCount":"17","fileSizeKB":"665584","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Amycolatopsis saalfeldensis (NCBITaxon:394193);Amycolatopsis sp. M39 (NCBITaxon:1825094);Amycolatopsis sp. PS_44_ISF1","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Amycolatopsis;Comparative metabolomics;Antimicrobial compounds;ecology-guided natural product isolation","pi":[{"name":"Christine Beemelmanns","email":"christine.beemelmanns@helmholtz-hips.de","institution":"Helmholtz Institute for Pharmaceutical Research Saarland","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7c1ba2e849ed42f88592c69f6a599d83","id":"3337"}, {"dataset":"MSV000093301","datasetNum":"93301","title":"A mammalian-specific Alex3\/Galphaq protein complex regulating mitochondrial dynamics, dendritic complexity, and neuronal survival","user":"CBeninca","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699117031000","created":"Nov. 4, 2023, 9:57 AM","description":"Immunoprecipitation of GNAQ protein by immunoprecipitation with two different antibodies from Santa Cruz Biotechnology (C-19 and E-17) in isolated mitochondria from different cell lines. The cell lines used include: Mouse embryonic fibroblasts (MEF) wild-type (WT), GNAQ knockout (KO) and knockout expressing GNAQ WT (KO_Gq). NIH3T3 cells were also used. \n","fileCount":"34","fileSizeKB":"14882489","spectra":"0","psms":"269183","peptides":"33182","variants":"47055","proteins":"5389","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive HF","modification":"NA","keywords":"GNAQ ALEX3 mitochondria immunoprecipitation","pi":[{"name":"Anna Aragay Combas","email":"aarbmc@ibmb.csic.es","institution":"IBMB","country":"Spain"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046668","task":"85ee9056209c4fd0ad3b74b0bcde7fc0","id":"3338"}, {"dataset":"MSV000093299","datasetNum":"93299","title":"mitochondrial and dengue virus_2023","user":"marjollycb","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699091757000","created":"Nov. 4, 2023, 2:55 AM","description":"Dengue virus non-structural protein 3 inhibits mitochondrial respiration by impairing complex I function \n\n","fileCount":"139","fileSizeKB":"60119758","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Dengue virus 2 Thailand\\\/16681\\\/84 (NCBITaxon:31634)","instrument":"Synapt HDMS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"mitochondria ;dengue virus;DENV NS3","pi":[{"name":"Andrea T. Da Poian","email":"dapoian@bioqmed.ufrj.br","institution":"Universidade Federal do Rio de Janeiro, Rio de Janeiro","country":"Brazil"},{"name":"Julianna D Zeidler","email":"julianna.zeidler@biof.ufrj.br","institution":"Universidade Federal do Rio de Janeiro, Rio de Janeiro","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"7d70d4ca24cb400297f272d4e9fa9ef4","id":"3339"}, {"dataset":"MSV000093298","datasetNum":"93298","title":"GNPS - Bacterial crude extracts from Bacillus sp. strain 16060 (a member of the Bacillus subtilis group) and Serratia marcescens strains SE1 and SE2","user":"loi032","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699084502000","created":"Nov. 4, 2023, 12:55 AM","description":"This dataset includes MS-DIAL processed data from ethyl acetate extracts of bacterial supernatants obtained from Bacillus sp. strain 16060, Serratia marcescens strain SE1, and Serratia marcescens strain SE2.","fileCount":"10","fileSizeKB":"89305","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus subtilis group (NCBITaxon:653685);Serratia marcescens (NCBITaxon:615)","instrument":"6545 series Q-TOF","modification":"MS:1001460 - This term should be given if the modification was unknown.","keywords":"untargeted analysis","pi":[{"name":"Hoai Huong Nguyen","email":"nh.huong@hutech.edu.vn","institution":"Hutech Institute of Applied Sciences, HUTECH University","country":"Vietnam"},{"name":"Lai Loi Trinh","email":"trinhlailoi@gmail.com","institution":"Hutech Institute of Applied Sciences, HUTECH University","country":"Vietnam"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD046665","task":"cbb9f17a3c004657b3316562b252c574","id":"3340"}, {"dataset":"MSV000093297","datasetNum":"93297","title":"20231103 DDA analysis of various rubber products with Agilent q-TOF","user":"zhaohaoq","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699051334000","created":"Nov. 3, 2023, 3:42 PM","description":"DDA analysis of 19 catories of rubber or elastomer consumer products. ","fileCount":"79","fileSizeKB":"14469983","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"na","instrument":"6530B Q-TOF LC\\\/MS","modification":"na","keywords":"rubber products","pi":[{"name":"Edward Kolodziej","email":"koloj@uw.edu","institution":"University of Washington","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4f0643080d6b42e98ef8a8b6440df584","id":"3341"}, {"dataset":"MSV000093296","datasetNum":"93296","title":"GNPS - Characterization of molecular factors involved in plant metabolic and morphological reprogramming during gall formation","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699049933000","created":"Nov. 3, 2023, 3:18 PM","description":"Understanding how plant tissue and organs may be transformed into novel structures by other organisms provides a unique opportunity to study the molecular processes that dictate facets of plant anatomy and morphology. Certain groups of wasps have evolved the ability to transform plant tissues into ornate structures called galls, which provide shelter and nutrition for their larvae. However, the exact mechanism for how gall wasps remodel the plant\u2019s physical structure and metabolism is still largely unknown. At their core, galls alter the morphology and repurpose the function of plant tissue. One common trait that unites all galls is the distinct cellular reprogramming and tumor-like growth that is necessary to produce a gall. There are over 1,400 gall wasps from the family Cynipidae, resulting in a wide diversity of gall structures, shapes, and colors that have been described. Thus, discovering the core molecular determinants that dictate the radical transformation of plant cells will help reveal principles of how plant morphology and function can be rewired by external factors. Little molecular work has been done to elucidate the factors (i.e., genes, proteins, or small molecules) that may be involved in this dramatic repurposing and dedifferentiation of plant tissue. We plan to utilize modern -omics approaches to investigate and identify the molecular factors that underlie the initiation and development of plant galls.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000461) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"850","fileSizeKB":"57501462","spectra":"342938","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Quercus","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"oak gall;gall induction;cynipid gall wasp","pi":[{"name":"Patrick Shih","email":"pmshih@lbl.gov","institution":"Lawrence Berkeley National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dcf46fd379d04e77bb3e1edde9b247b4","id":"3342"}, {"dataset":"MSV000093294","datasetNum":"93294","title":"Genetic, community, and ecosystem consequences of co-introduction of mycorrhizal fungiwith exotic pines","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699042669000","created":"Nov. 3, 2023, 1:17 PM","description":"Suillus luteus mycorrhizae will be experimentally synthesized on the roots of pine seedlings, grown in aseptic conditions from seeds representing either native wild-type European genotypes of Pinus pinaster (a native host of S. luteus) or typical forestry production genotypes of P. radiata.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001406) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"2342","fileSizeKB":"158166220","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"ectomycorrhizal fungi;soil;Pinus;Suillus","pi":[{"name":"Hui-Ling (Sunny) Liao","email":"sunny.liao@ufl.edu","institution":"University of Florida","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a56788e97424409391c3a6153d388800","id":"3343"}, {"dataset":"MSV000093293","datasetNum":"93293","title":"MSX Spleen DIA and DDA Proteomics","user":"seeramlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699040741000","created":"Nov. 3, 2023, 12:45 PM","description":"This project evaluates the immune regulating properties of maple syrup extract in spleen samples utilizing an LPS induced peritonitis mouse model.","fileCount":"82","fileSizeKB":"165871503","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus (NCBITaxon:10088)","instrument":"TripleTOF 5600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"LPS, peritonitis, inflammation, extract, maple syrup","pi":[{"name":"Navindra Seeram","email":"bbrluri@gmail.com","institution":"University of Rhode Island","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"8f2843e7238841988b257a21af12c618","id":"3344"}, {"dataset":"MSV000093291","datasetNum":"93291","title":"GNPS - Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration","user":"jess_cleary","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699040277000","created":"Nov. 3, 2023, 12:37 PM","description":"Targeted GC-MS detection of host and dietary metabolites and modifications by gut bacteria.","fileCount":"356","fileSizeKB":"8860170","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Holdemania filiformis (NCBITaxon:61171);Eggerthella lenta (NCBITaxon:84112);Sutterella wadsworthensis (NCBITaxon:40545)","instrument":"Agilent 7890A GC system, Agilent 5975C MS detector","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"microbiome;metabolomics;anaerobic respiration","pi":[{"name":"Sam Light","email":"samlight@uchicago.edu","institution":"University of Chicago","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"365b6b62ef34444c821aff7d6ff9e499","id":"3345"}, {"dataset":"MSV000093287","datasetNum":"93287","title":"Detection of a Mitochondrial Stress Phenotype using the Cell Painting Assay","user":"janning","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699008589000","created":"Nov. 3, 2023, 3:49 AM","description":"Proteome profiling of different small molecules influencing mitochaondrial homeostasis.","fileCount":"53","fileSizeKB":"210258030","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"proteome profiling, mitochondrial stress, cell painting, TMT labeling","pi":[{"name":"Petra Janning","email":"petra.janning@mpi-dortmund.mpg.de","institution":"MPI of Molecular Physiology","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046639","task":"268dae38aad841879f927fa2714e48ad","id":"3346"}, {"dataset":"MSV000093286","datasetNum":"93286","title":"GNPS - Pseudoalteromonas and Phaeobacter coexistence study","user":"PeterSvend","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1699000868000","created":"Nov. 3, 2023, 1:41 AM","description":"Study involving two marine bacteria, Pseudoalteromonas piscicida and a Phaeobacter sp., both isolated from Jyllinge Harbor, Zealand, Denmark. Processed files from MZmine for FBMN are included as well as the metadata.","fileCount":"42","fileSizeKB":"1241272","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudoalteromonas piscicida (NCBITaxon:43662);Phaeobacter sp. (NCBITaxon:1902409)","instrument":"6545 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cocultivation;Marine;Untargeted","pi":[{"name":"Lone Gram","email":"gram@bio.dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"d235b8638a384309961af78d85b33d91","id":"3347"}, {"dataset":"MSV000093282","datasetNum":"93282","title":"A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling","user":"Natalie_1234","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698975350000","created":"Nov. 2, 2023, 6:35 PM","description":"In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal (PP) and pericentral (PC) axis. How these mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combined intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We found that PP and PC mitochondria are morphologically and functionally distinct; beta-oxidation was elevated in PP regions, while lipid synthesis was predominant in the PC mitochondria. In addition, comparative phosphoproteomics revealed spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifted mitochondrial phenotypes in the PP and PC regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease. ","fileCount":"121","fileSizeKB":"142311255","spectra":"15640268","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Mitochondria, Liver zonation, nutrient sensing","pi":[{"name":"Natalie Porat-Shliom","email":"natalie.porat-shliom@nih.gov","institution":"Center for Cancer Research, National Cancer Institute, NIH","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"35c70fffa1ad4c29bd8c0dd02d19ae06","id":"3348"}, {"dataset":"MSV000093280","datasetNum":"93280","title":"Yang_NuA4_TIP60_structural_features","user":"LambertLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698968061000","created":"Nov. 2, 2023, 4:34 PM","description":"This submission contains the mass spectrometry files for the manuscript by Zhenlin Yang et al. that describes the unique structural features of the NuA4\/TIP60 acetyltransferase and chromatin remodeling complex. MS experiments were performed from TAP purified complexes from K562 cells and MS files were acquired on Orbitrap Fusion mass spectrometers. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca).","fileCount":"17","fileSizeKB":"12631914","spectra":"313593","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";MOD:01160 - \\\"A protein modification that effectively results in the loss of an ammonia, usually by a process of vicinal dehydration, rearrangement, and rehydration with release of ammonia, resulting in a loss of nitrogen with no gain of oxygen.\\\"","keywords":"chromatin","pi":[{"name":"Jean-Philippe Lambert","email":"jean-philippe.lambert@crchudequebec.ulaval.ca","institution":"Universite Laval","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e6d83a814ee441bdbe3168eea1c29b3f","id":"3349"}, {"dataset":"MSV000093279","datasetNum":"93279","title":"Multiplex substrate profiling by mass spectrometry Nf20S marizomib","user":"elanybs","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698966508000","created":"Nov. 2, 2023, 4:08 PM","description":"Multiplex substrate profiling by mass spectrometry obtained from the cleavage of Nf20S under presence of marizomib after time zero (T0, 4 replicates) and time 240minutes (T240, 4 replicates).","fileCount":"21","fileSizeKB":"14494768","spectra":"0","psms":"6422","peptides":"840","variants":"1161","proteins":"221","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Naegleria fowleri (NCBITaxon:5763)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Nf20S, marizomib","pi":[{"name":"Anthony O'Donoghue","email":"ajodonoghue@ucsd.edu","institution":"UCSD","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046621","task":"104d14d0cd7d4d7cbaf0e3fea29ff60f","id":"3350"}, {"dataset":"MSV000093278","datasetNum":"93278","title":"20231102_RAD_KRAS4B_TD_Assay_Submission","user":"dippolitora","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698955831000","created":"Nov. 2, 2023, 1:10 PM","description":"Raw files for bottom-up, top-down, and intact mass analyses, BioPharma Finder reports, Proteome Discoverer search result files, ProSight Lite result files, and converted peak list.","fileCount":"3596","fileSizeKB":"418224765","spectra":"0","psms":"57192","peptides":"528","variants":"3722","proteins":"115","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos;Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:27 - \\\"Pyro-glu from E.\\\";UNIMOD:28 - \\\"Pyro-glu from Q.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:765 - \\\"Removal of initiator methionine from protein N-terminus.\\\";UNIMOD:766 - \\\"Removal of initiator methionine from protein N-terminus, then acetylation of the new N-terminus.\\\";UNIMOD:522 - \\\"Maleimide-Biotin.\\\";UNIMOD:1039 - \\\"Maleimide-Biotin + Water.\\\"","keywords":"Top-Down;Compound Engagement;Relative Quantitation;RAS;Mass Spectrometry;Bottom-Up;Proteomics;Intact Mass","pi":[{"name":"Caroline DeHart","email":"caroline.dehart@nih.gov","institution":"Frederick National Laboratory for Cancer Research","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046618","task":"5a1e87f971134b478e14cb438b2eef0d","id":"3351"}, {"dataset":"MSV000093277","datasetNum":"93277","title":"GNPS - Comparative and Population Genomics of Xylariaceae","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954372000","created":"Nov. 2, 2023, 12:46 PM","description":"We are examining the metabolites produced during co-culture of Xylariaceae fungi.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001144) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"682","fileSizeKB":"45809510","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Xylaria cubensis; Daldinia sp.","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"endophytic fungi","pi":[{"name":"Jana U'Ren","email":"juren@email.arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"744a760b81294f7583a48f44f70d82a7","id":"3352"}, {"dataset":"MSV000093276","datasetNum":"93276","title":"GNPS - Metabolite profiles of two Pantoea species with divergent traits for onion virulence.","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954371000","created":"Nov. 2, 2023, 12:46 PM","description":"Bacteria in the genus Pantoea (family Enterobacteriales) are metabolically diverse, cosmopolitan, and form a wide range of interactions with eukaryotic hosts including plants, fungi, insects and humans. Several Pantoea species have pathogenic interactions with plants. Strains of at least four Pantoea species (P. ananatis, P. allii, P. stewartii subsp. indologenes and P. agglomerans) are known to cause onion center rot disease. P. ananatis is very unusual among characterized bacterial plant pathogens. Virulence factors that distinguish onion-virulent and non-virulent P. ananatis have only recently been described. Most bacterial plant pathogens are dependent on specialized virulence protein secretion systems for pathogenicity. However, to cause plant cell death, P. ananatis instead requires the HiVir (High Virulence) proposed secondary metabolite synthetic cluster for an as of yet undescribed phosphonate compound. P. allii is also pathogenic on onion but, surprisingly, lacks the HiVir gene cluster associated with onion-virulent P. ananatis. P. allii carries a completely distinct predicted phosphonate compound synthetic cluster which has, interestingly, also been identified in P. stewartiii subsp indologenes that have expanded their host range from millet onto onions. We obtained the cell pellet metabolite profiles of P. ananatis PNA 97-1, the P. allii type strain LMG 24248, and the two corresponding biosynthetic mutant strains lacking a key gene (pepM) for the synthesis of phosphonate compounds. Understanding the unique chemistry of onion-virulent Pantoea will yield important insights into novel frameworks for plant- pathogen interactions.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001193) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"386","fileSizeKB":"30243269","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pantoea","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"virulence factors;onion center rot disease;plant-pathogen interaction","pi":[{"name":"William (Barny) Whitman","email":"whitman@uga.edu","institution":"University of Georgia","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bb0eb06ff46244d29397541cfe23a63b","id":"3353"}, {"dataset":"MSV000093275","datasetNum":"93275","title":"GNPS - A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954280000","created":"Nov. 2, 2023, 12:44 PM","description":"Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir. Exometabolites, including small molecules, extracellular enzymes, and antibiotics, are assayed from the reservoir using sensitive mass spectrometry. Community member outcomes, such as growth, productivity, and gene regulation, can be determined using flow cytometry, biomass measurements, and transcript analyses, respectively. The synthetic community design allows for determination of the consequences of microbiome diversity for emergent community properties and for functional changes over time or after perturbation. Because it is versatile, scalable, and accessible, this synthetic community system has the potential to practically advance knowledge of microbial interactions that occur within both natural and artificial communities. See publications: https:\/\/journals.asm.org\/doi\/10.1128\/mSystems.00129-17 and https:\/\/journals.asm.org\/doi\/10.1128\/mSystems.00493-20 and https:\/\/www.biorxiv.org\/content\/10.1101\/2021.09.05.459016v2.full.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000724) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"614","fileSizeKB":"23787262","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"synthetic microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"synthetic community;microbial interactions;bioactive exometabolites","pi":[{"name":"Ashley Shade","email":"shadeash@msu.edu","institution":"Michigan State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"1de98b8ce06c4765bf253113b05478f2","id":"3354"}, {"dataset":"MSV000093274","datasetNum":"93274","title":"GNPS - Global metabolic profile comparison between 2 ecotypes upon inoculation with Azoarcus olearius","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954278000","created":"Nov. 2, 2023, 12:44 PM","description":"Arabidopsis thaliana associated with Plant Growth Promoting Bacteria (PGPB) Azoarcus olearius (DQS4) innoculated with WS (Wassilewskija) and Col0 (Columbia) ecotypes.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000448) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"317","fileSizeKB":"10937947","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis thaliana","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis thaliana;Plant Growth Promoting Bacteria;Azoarcus olearius","pi":[{"name":"Gary Stacey","email":"staceyg@missouri.edu","institution":"University of Missouri","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4c5acccb3ae5421bb999f359d386c9c0","id":"3355"}, {"dataset":"MSV000093273","datasetNum":"93273","title":"GNPS - Elucidate metabolism of bioenergy-relevant Clostridial and Streptomyces species","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954278000","created":"Nov. 2, 2023, 12:44 PM","description":"The goal of this study is to use both \"targeted\" and \"untargeted\" metabolomics to elucidate metabolism of Clostrial and Streptomyces species for biofuel production and plant growth promotion, respectively. For these species, we aim to improve the curation of genome-scale metabolic networks and elucidate their novel secondary metabolism to make secondary metabolites whose identities are waiting to be discovered. These metabolic networks will be used to study cell physiology, metabolism, regulation, and metabolic engineering.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000463) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"99","fileSizeKB":"6408526","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Clostridia; Streptomyces","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"biofuel production, metabolic networks","pi":[{"name":"Cong Trinh","email":"ctrinh@utk.edu","institution":"University of Tennessee Knoxville","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"aae8cb1ca5d145bf82a1aad11a0bf419","id":"3356"}, {"dataset":"MSV000093272","datasetNum":"93272","title":"GNPS - Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954249000","created":"Nov. 2, 2023, 12:44 PM","description":"Aquatic microbial communities contain a vast amount of genetic diversity and we have much to learn about how this manifests to functional diversity. Existing long-term time series data includes 16S tags, metagenomes, single amplified genomes (SAGs), and genomes from metagenomes (GFMs). Information about functional diversity and metabolic capabilities is often unavailable. The study sites include three lakes that are the subject of intense study through the North Temperate Lakes Long Term Ecological Research site: Sparkling Lake (oligotrophic), Lake Mendota (eutrophic), and Trout Bog Lake (dystrophic).\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000947) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"789","fileSizeKB":"85479449","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"freshwater lake microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Sparkling Lake;Trout Bog;Lake Mendota;freshwater lake","pi":[{"name":"Katherine McMahon","email":"tmcmahon@engr.wisc.edu","institution":"University of Wisconsin Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a66fd2bf4d9e451d961d1e17c03c98a1","id":"3357"}, {"dataset":"MSV000093271","datasetNum":"93271","title":"GNPS - Unearthing the active microbes, viruses, and metabolites in dynamic-redox tropical soils with quantitative SIP and metagenomics","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954247000","created":"Nov. 2, 2023, 12:44 PM","description":"This research focuses on changes in the microbial communities of tropical soils during aerobic to anaerobic transitions following wetting. Of particular interest is the natural cycling of the soil microbiome through aerobic and anaerobic metabolism over relative short time periods.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000880) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"440","fileSizeKB":"21731394","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"soil microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"tropical soil;redox;carbon cycling;mineral-organic matter interactions","pi":[{"name":"Jennifer Pett-Ridge","email":"pettridge2@llnl.gov","institution":"LLNL","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9cacec4101f84fa7972d2a5b349c1db0","id":"3358"}, {"dataset":"MSV000093270","datasetNum":"93270","title":"GNPS - Exploring Genetics by Environment - 'omic analysis of engineered biomass crops in the lab and field","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954247000","created":"Nov. 2, 2023, 12:44 PM","description":"Clonal QSuB switchgrass plants (3 independent transformation events), and their corresponding wild type (var Alamo), grown in a growth chamber and the field, were harvested at two time points (five replicates) during the growing season across two years (2018, 2019), to compare the effects of environment on genetically identical engineered plants. To complement this, we used QsuB plus wild type for Arabidopsis grown in a walk in growth chamber. Three replicates of tissue will be harvested at a single time point. Plants will be well-watered or drought stressed.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000997) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"1589","fileSizeKB":"96389754","spectra":"2065600","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Arabidopsis or switchgrass??","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Arabidopsis;drought stress","pi":[{"name":"Jenny Mortimer","email":"jcmortimer@lbl.gov","institution":"JBEI","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"db3a2a68cd054a43bac6841387d4d963","id":"3359"}, {"dataset":"MSV000093269","datasetNum":"93269","title":"GNPS - Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours Postinoculation","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954246000","created":"Nov. 2, 2023, 12:44 PM","description":"Sphaerulina musiva is an economically and ecologically important fungal pathogen that causes Septoria stem canker and leaf spot disease of Populus species. To bridge the gap between genetic markers and structural barriers previously found to be linked to Septoria canker disease resistance in poplar, we used hydrophilic interaction liquid chromatography and tandem mass spectrometry to identify and quantify metabolites involved with signaling and cell wall remodeling. Fluctuations in signaling molecules, organic acids, amino acids, sterols, phenolics, and saccharides in resistant and susceptible P. trichocarpa inoculated with S. musiva were observed. The patterns of 222 metabolites in the resistant host implicate systemic acquired resistance (SAR), cell wall apposition, and lignin deposition as modes of resistance to this hemibiotrophic pathogen. This pattern is consistent with the expected response to the biotrophic phase of S. musiva colonization during the first 24 h postinoculation. The fungal pathogen metabolized key regulatory signals of SAR, other phenolics, and precursors of lignin biosynthesis that were depleted in the susceptible host. This is the first study to characterize metabolites associated with the response to initial colonization by S. musiva between resistant and susceptible hosts.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000891) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"2597","fileSizeKB":"223574636","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Sphaerulina musiva; Populus trichocarpa","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Septoria canker;plant pathogens;disease resistance","pi":[{"name":"Jared LeBoldus","email":"lebolduj@oregonstate.edu","institution":"Oregon State University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"73ccc3fa95db4b0c835b48ea750709fe","id":"3360"}, {"dataset":"MSV000093268","datasetNum":"93268","title":"GNPS - Leveraging pan genomes to investigate diel transcriptomic and metabolomic responses to abiotic stress in Brassica. rapa and B. napus diversity panels.","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954185000","created":"Nov. 2, 2023, 12:43 PM","description":"Metabolomic analysis of the abiotic stress experiments on tissue from Brassicaceae genotypes.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001202) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"2182","fileSizeKB":"118107162","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Brassica","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Root exudates;Rhizosphere;Root microbiome;glucosinolates","pi":[{"name":"Katie Greenham","email":"katie.greenham@gmail.com","institution":"University of Minnesota","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"97c82494287f43c3bde5756ae75771ab","id":"3361"}, {"dataset":"MSV000093267","datasetNum":"93267","title":"GNPS - Botryococcus braunii circadian time course","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698954094000","created":"Nov. 2, 2023, 12:41 PM","description":"Botryococcus braunii is a colony forming green microalga of the order Chlorophyta. During the growth cycle of this organism, the algae synthesizes long chain liquid hydrocarbon isoprenoid compounds and sequesters them in the extracellular matrix of the colony. Metabolomics was done on samples from a circadian time series.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000723) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"318","fileSizeKB":"22952148","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Botrycoccus braunii","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"circadian cycle;isoprenoids","pi":[{"name":"Andy Koppisch","email":"Andy.Koppisch@nau.edu","institution":"Northern Arizona University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f762186d48624010a841180c877d51b8","id":"3362"}, {"dataset":"MSV000093266","datasetNum":"93266","title":"29 million years of diverse mammalian proteomes recovered from the East African Rift System 2","user":"tpcleland","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698953161000","created":"Nov. 2, 2023, 12:26 PM","description":"DDA files of the 1.5 Ma Palaeoloxodon recki from the Turkana Basin of Kenya.","fileCount":"532","fileSizeKB":"5133057","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Palaeoloxodon recki","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Paleoproteomics;enamel","pi":[{"name":"Timothy Cleland","email":"clelandtp@si.edu","institution":"Smithsonian Institution","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046617","task":"7740cb265e6a4fa9ab0b3f313ec9dcbd","id":"3363"}, {"dataset":"MSV000093265","datasetNum":"93265","title":"GNPS - LC-MS2 and BGC paired data from actinomycetes","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698950586000","created":"Nov. 2, 2023, 11:43 AM","description":"Paired genomics (.fasta) and metabolomics (.mzML) from 320 actinomycetes strains for NPOmix workflow","fileCount":"2278","fileSizeKB":"80187164","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Actinomyces (NCBITaxon:1654)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"BGCs;Metabolomics;Natural Products;Actinomyces","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e9ca47d1971b4b77b000ef61f95aed27","id":"3364"}, {"dataset":"MSV000093263","datasetNum":"93263","title":"GNPS - MS2 data of zwitterionic metabolites from phyto- and bacterioplankton using ZIC-HILIC column","user":"Muhaiminatul","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698949024000","created":"Nov. 2, 2023, 11:17 AM","description":"MS\/MS data of zwitterionic metabolites from phytoplankton: Amphidinium carterae CCMP1314, Alexandrium tamarense CCMP1771, Karenia brevis CCMP2229, Lingulodinium polyedra CCMP1738, Prymnesium parvum CCAP946\/6, Tetraselmis striata RCC131, Dunaliella salina RCC3579, Prorocentrum minimum CCMP2233. \r\nMS\/MS data of zwitterionic metabolites from bacterioplankton: Pelagibaca bermudensis HTCC2601.\r\nMS\/MS data of compound at m\/z 157.0970 from algal extract (Dunaliella salina RCC3579)","fileCount":"11","fileSizeKB":"416891","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Amphidinium carterae CCMP1314;Alexandrium tamarense CCMP1771;Karenia brevis CCMP2229;Lingulodinium polyedra CCMP1738;Prymnesium parvum CCAP946\\\/6;Dunaliella salina RCC3579;Prorocentrum minimum CCMP33;Tetraselmis striata RCC131;Pelagibaca bermudensis HTCC2601 (NCBITaxon:314265)","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Phytoplankton;Bacterioplankton;Zwitterions","pi":[{"name":"Georg Pohnert","email":"georg.pohnert@uni-jena.de","institution":"Friedrich Schiller University Jena","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3e195c9cdf174534b7eff5428fbd28c8","id":"3365"}, {"dataset":"MSV000093262","datasetNum":"93262","title":"GNPS - Bile Acid Standards for MSV000093200","user":"spthomasGNPS","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698945637000","created":"Nov. 2, 2023, 10:20 AM","description":"Bile acid standards run alongside MSV000093200 (Gates Foundation SEPSIS project).","fileCount":"133","fileSizeKB":"7807767","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:34 - \\\"Methylation.\\\"","keywords":"bile acid","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b08571a92f98458d9b844ae79f198168","id":"3366"}, {"dataset":"MSV000093257","datasetNum":"93257","title":"The effect of abiotic stress on rhizosphere microbiota","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698945543000","created":"Nov. 2, 2023, 10:19 AM","description":"The ultimate aim is see if rhizosphere microbiota are influenced by changes in root exudate composition resulting from abiotic stress. The abiotic variables we are focusing on at this stage are salinity, temperature and pH. This can be divided into two questions: (a) how do plant exudates change in response to abiotic stress, and (b) how do these changes influence bacteria. In order to test this we will produce plant exudates under controlled stressed conditions, measure their composition and measure bacterial growth in these exudates. Data has also been produced from synthetic community experiments comparing the community composition under a variety of controlled stress conditions (temperature, salinity, pH, and phosphate).\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000944) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"193","fileSizeKB":"15514174","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"rhizosphere;stress conditions;pH;temperature;salinity;root exudates;synthetic community","pi":[{"name":"Jeff Dangl","email":"dangl@email.unc.edu","institution":"University of North Carolina Chapel Hill","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ae0314cf389245ecbdbc06a05979e62f","id":"3367"}, {"dataset":"MSV000093248","datasetNum":"93248","title":"The effect of abiotic stress on rhizosphere microbiota","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698945229000","created":"Nov. 2, 2023, 10:13 AM","description":"The ultimate aim is see if rhizosphere microbiota are influenced by changes in root exudate composition resulting from abiotic stress. The abiotic variables we are focusing on at this stage are salinity, temperature and pH. This can be divided into two questions: (a) how do plant exudates change in response to abiotic stress, and (b) how do these changes influence bacteria. In order to test this we will produce plant exudates under controlled stressed conditions, measure their composition and measure bacterial growth in these exudates. Data has also been produced from synthetic community experiments comparing the community composition under a variety of controlled stress conditions (temperature, salinity, pH, and phosphate).\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60000944) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"193","fileSizeKB":"15514174","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"microbiome","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"rhizosphere;stress conditions;pH;temperature;salinity;root exudates;synthetic community","pi":[{"name":"Jeff Dangl","email":"dangl@email.unc.edu","institution":"University of North Carolina Chapel Hill","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3bb96188ba5548858643dce7ec7287d5","id":"3368"}, {"dataset":"MSV000093247","datasetNum":"93247","title":"GNPS - Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698945198000","created":"Nov. 2, 2023, 10:13 AM","description":"The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus Streptomyces. We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence\/absence within Streptomyces, even in strains identical by 16S. Furthermore, we identified key differences in shared ecologically important characters, such as antibiotic resistance, carbohydrate metabolism, biosynthetic gene clusters (BGCs), and other metabolic hallmarks, within 16S identities commonly treated as the same operational taxonomic units (OTUs). Differences between common phylogenetic measures and metabolite-gene annotations confirmed this incongruence. Our results highlight the metabolic diversity and variability within OTUs and add to the growing body of work suggesting 16S-based studies of Streptomyces fail to resolve important ecological and metabolic characteristics. See publication: https:\/\/doi.org\/10.3389\/fmicb.2019.02170.\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001100) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"482","fileSizeKB":"42366867","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces;diversity","pi":[{"name":"Cameron Currie","email":"currie@bact.wisc.edu","institution":"University of Wisconsin Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4ea19a5620ce4cbdab67a7860a9c2c6c","id":"3369"}, {"dataset":"MSV000093246","datasetNum":"93246","title":"Exploring the role of drought-induced plant-associated microbes in promoting plant fitness in Sorghum bicolor and Oryza sativa","user":"bpbowen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698944639000","created":"Nov. 2, 2023, 10:03 AM","description":"We investigate the role of root-associated Actinobacteria in promoting host fitness under drought stress in two plants important to the DOE mission of sustainable biofuels: Sorghum bicolor and Oryza sativa.\n\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001083) conducted by the U.S. Department of Energy Joint Genome Institute (https:\/\/ror.org\/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.","fileCount":"2121","fileSizeKB":"142236834","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Actinobacteria;drought stress;Sorghum bicolor;Oryza sativa;root endosphere","pi":[{"name":"Devin Coleman-Derr","email":"Devin.Coleman-derr@ARS.USDA.GOV","institution":"USDA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"0862ba3d232e485b896e574d9ee8d88c","id":"3370"}, {"dataset":"MSV000093243","datasetNum":"93243","title":"Cytoskeleton-associated protein 4 (CKAP4) affects podocyte cytoskeleton dynamics in diabetic kidney disease","user":"haiyanzheng","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698939983000","created":"Nov. 2, 2023, 8:46 AM","description":"Cytoskeleton-associated protein 4 (CKAP4) stabilizes the endoplasmic reticulum, by regulating its folding and anchoring to the microtubular cytoskeleton. Since podocytes are highly dependent on an intact cytoskeleton to exert their function, the role of CKAP4 was explored during normal conditions and in diabetic kidney disease (DKD). Methods. The differences in CKAP4 gene expression between patients with chronic kidney disease (CKD) and controls were explored in publicly available databases. Expression of CKAP4 in patients with DKD was investigated with in situ hybridization. Localization in human kidney tissue was determined using immunofluorescence, qPCR, and western blot. The CKAP4 homolog was knocked down (KD) in zebrafish. Proteinuria and glomerular morphology were investigated. CKAP4 KD and overexpression in podocytes were investigated using proteomics, immunofluorescence, and western blot. Results. Glomerular CKAP4 gene expression was reduced in DKD patients compared to healthy individuals, but not in other CKDs. The glomerular expression of CKAP4 was most pronounced in podocytes. CKAP4 KD zebrafish became proteinuric and podocyte FPE (foot process effacement) was observed. CKAP4 KD in podocytes in vitro led to disruption of actin stress fibers, microtubular rearrangement and loss of integrin expression. Conclusion. CKAP4 reduction causes podocyte FPE and proteinuria in vivo. Loss of CKAP4 disrupts the podocyte actin cytoskeleton, its microtubular orientation, and integrin-based glomerular basement membrane attachment. This indicates that CKAP4 is a crucial connector between cell body and structural elements in podocytes. The reduction of CKAP4 observed in glomeruli from DKD patients may thus be coupled to impaired podocyte function and proteinuria.","fileCount":"10","fileSizeKB":"14037272","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Danio rerio (NCBITaxon:7955)","instrument":"Orbitrap Eclipse","modification":"no","keywords":"CKAP4; podocytes;cytoskeleton;diabetic kidney disease;microtubules;integrins","pi":[{"name":"Roberto Boi","email":"roberto.boi@neuro.gu.se","institution":"Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Box 432, 40530, Gothenburg,","country":"Sweden"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"592c1358230847978519aeb556e69e40","id":"3371"}, {"dataset":"MSV000093241","datasetNum":"93241","title":"Development of a Global Metabo-Lipid-Prote-omics Method to Compare Healthy Distal and Proximal Colon Biopsies of Mice","user":"kkleigrewe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698935483000","created":"Nov. 2, 2023, 7:31 AM","description":"This research focuses on understanding the molecular and protein structures of mouse proximal and distal colons (PC\/DC) by developing of an integrated multi-omics approach. ","fileCount":"487","fileSizeKB":"17408933","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"TripleTOF 6600;QTRAP 5500","modification":"metabolomics","keywords":"Metabo-lipid-proteomics ;Methyl tert-butyl ether extraction ;proximal and distal colon ","pi":[{"name":"Karin Kleigrewe","email":"Karin.Kleigrewe@tum.de","institution":"Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f3aa9c9e0f4041b0a9013da92bcd9c6b","id":"3372"}, {"dataset":"MSV000093232","datasetNum":"93232","title":"Itaconate modulates immune responses via inhibition of peroxiredoxin 5","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698882740000","created":"Nov. 1, 2023, 4:52 PM","description":"Wild type and Irg1 knockout mouse bone marrow derived macrophages (BMDMs) were processed with a redox proteomics workflow and analyzed by LC-MS\/MS with TMT based quantification.","fileCount":"186","fileSizeKB":"19696922","spectra":"251998","psms":"258392","peptides":"175967","variants":"197056","proteins":"29973","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"itaconate;peroxiredoxin;redox","pi":[{"name":"Wei-Jun Qian","email":"Weijun.Qian@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD046597","task":"7b4c0e1a118647b79c0f08158d09abb3","id":"3373"}, {"dataset":"MSV000093230","datasetNum":"93230","title":"GNPS - 3XTG AGMP QiitaID 14748","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698874831000","created":"Nov. 1, 2023, 2:40 PM","description":"Mouse fecal samples from animal model 3XTG Aim 1-Alzheimers Gut Microbiome Project - ID 14748. Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1096","fileSizeKB":"42013575","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus sp. (NCBITaxon:10095)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Alzheimer;3XTG;Fecal;Mouse","pi":[{"name":"Sarkis Mazmanian","email":"sarkis@caltech.edu","institution":"California Institute of Technology","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fbf55f75f495413abc9cec3499e5eca7","id":"3374"}, {"dataset":"MSV000093229","datasetNum":"93229","title":"intracellular MMP-2 proteolysis in cardiac tissue","user":"julienlab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698870762000","created":"Nov. 1, 2023, 1:32 PM","description":"Induced proteolysis of rat heart extracts with recombinant MMP-2 followed by subtiligase-N-terminomics","fileCount":"9","fileSizeKB":"18604107","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus (NCBITaxon:10114)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"N-terminomics;Matrix metalloproteinase","pi":[{"name":"Olivier Julien","email":"ojulien@ualberta.ca","institution":"University of Alberta","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"abd0b924a3d1416a88aa9129b7e06292","id":"3375"}, {"dataset":"MSV000093227","datasetNum":"93227","title":"Human Keratinocyte Responses to Woodsmoke","user":"brettsp1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698862015000","created":"Nov. 1, 2023, 11:06 AM","description":"Air pollution consists of complex mixtures of chemicals with serious deleterious health effects from acute and chronic exposure. To help understand mechanisms by which adverse effects occur, present work examines responses of cultured human epidermal keratinocytes to specific chemicals commonly found in woodsmoke. Our earlier findings with liquid smoke flavoring (aqueous extract of charred wood) revealed that such extracts stimulated expression of genes associated with oxidative stress and proinflammatory response, activated the aryl hydrocarbon receptor, thereby inducing cytochrome P4501A1 activity, and induced cross-linked envelope formation, a lethal event ordinarily occurring during terminal differentiation. Present results showed that furfural produced transcriptional responses resembling those of liquid smoke, cyclohexanedione activated the aryl hydrocarbon receptor, and several chemicals induced envelope formation. Of these, syringol permeabilized the cells to egress of lactate dehydrogenase at a concentration close to that yielding envelope formation, while furfural induced envelope formation without permeabilization detectable in this way. Furfural (but not syringol) stimulated incorporation of amines into cell protein in extracts in the absence of transglutaminase activity. Nevertheless, both chemicals substantially increased the amount of cellular protein incorporated into envelopes and greatly altered the envelope protein profile. Moreover, the proportion of keratins in envelopes was dramatically increased. These findings are consistent with chemically induced protein cross-linking in the cells. Elucidating mechanisms by which this phenomenon occurs may help interpret bioassays of complex pollutant mixtures and suggest additional sensitive ways to monitor exposures.","fileCount":"20","fileSizeKB":"19987867","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"woodsmoke;Keratinocyte","pi":[{"name":"Robert H. Rice","email":"rhrice@ucdavis.edu","institution":"University of California Davis","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046590","task":"ed21315ddc5b41719d7e6f3323c2278c","id":"3376"}, {"dataset":"MSV000093224","datasetNum":"93224","title":"GNPS - ","user":"klongnecker","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698855194000","created":"Nov. 1, 2023, 9:13 AM","description":"Surface seawater samples collected from the Atlantic Ocean. Three types of samples were collected: seawater inside a patch of Sargassum ('in'), seawater in the downstream slick of Sargassum ('slick'), and seawater outside the patch ('out'). Samples were collected by hand from a small boat, and DOM was extracted using solid phase extraction with Bond Elut PPL cartridges. Both positive and negative ion mode data are available.","fileCount":"40","fileSizeKB":"20741648","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"not applicable","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"seawater, Sargassum","pi":[{"name":"Elizabeth Kujawinski","email":"ekujawinski@whoi.edu","institution":"Woods Hole Oceanographic Institution","country":"United States of America"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"b9a2e08f933d445d86f2de1dc745dc70","id":"3377"}, {"dataset":"MSV000093223","datasetNum":"93223","title":"Stable-isotope analysis of nitrate using ESI-Orbitrap IRMS","user":"isoorbi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698851876000","created":"Nov. 1, 2023, 8:17 AM","description":"Data analyzed within Procedure 2 in Kantnerova et al. 2024 in Nature Protocols (https:\/\/doi.org\/10.1038\/s41596-024-00981-5). Procedure 2 describes the stable isotope analysis of the model analyte nitrate (NO3-) by applying the flow injection using an HPLC system with an autosampler. The nitrate data were collected using a Thermo Scientific Orbitrap Exploris 240 Isotope Solutions. Sample = USGS32, Reference = USGS35 (nitrate isotopic reference materials from the United States Geological Survey), 50 uM nitrate in methanol. Isotopocule data collected \"with M0\" base peak. RAW files were processed using the IsoX software (version 2022) using the isotopologs.tsv files as input. There are three datasets with the following prefixes: \"01_\" - USGS32 vs USGS35, optimal ion source conditions, 13 alternating injections of USGS35 and USGS32 + 2 blank methanol measurements \"02_\" - USGS32 vs USGS35, non-optimal ion-source conditions, 13 alternating injections of USGS35 and USGS32 + 2 blank methanol measurements \"03_\" - USGS32 vs USGS35, alternating injections of USGS35 and USGS32 extended to a total of 315 injections. Before rerunning the IsoX data analysis, remove the prefixes \"01_\", \"02_\" and \"03_\" from the respective .tsv files.","fileCount":"1195","fileSizeKB":"6864275","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"ESI-Orbitrap Exploris 240 Isotope Solutions ","modification":"not applicable","keywords":"isotope analysis;nitrate;stable isotopes;isotopocule;IRMS","pi":[{"name":"Cajetan Neubauer","email":"123caj@gmail.com","institution":"University of Colorado Boulder","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a93f04f4d70c4975994f59fbc1458071","id":"3378"}, {"dataset":"MSV000093222","datasetNum":"93222","title":"Stable-isotope analysis of TFA and MRFA using ESI-Orbitrap IRMS","user":"isoorbi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698851255000","created":"Nov. 1, 2023, 8:07 AM","description":"Data analyzed within Procedure 1 in Kantnerova et al. 2024 in Nature Protocols (https:\/\/doi.org\/10.1038\/s41596-024-00981-5). Procedure 1 describes a direct infusion analysis using an easily accessible Orbitrap MS calibration solution FlexMix, analyzing its two compounds: a) trifluoroacetate (TFA) in the negative ESI mode, and b) the peptide MRFA (Met-Arg-Phe-Ala) and its amino acid fragments (MS\/MS analysis) in the positive ESI mode. The TFA data were collected using a Thermo Scientific Orbitrap Exploris 240 Isotope Solutions. The MRFA data were collected using a Thermo Scientific Orbitrap Exploris 480 Isotope Solutions. RAW files were processed using the IsoX software (version 2022) using the isotopologs.tsv files as input. Before rerunning the IsoX data analysis, remove the suffixes \"_TFA\", \"_MRFA\" and \"_MRFA_2\" from the respective .tsv files.","fileCount":"33","fileSizeKB":"202901","spectra":"1382","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"no species","instrument":"ESI-Orbitrap Exploris 240 Isotope Solutions;ESI-Orbitrap Exploris 480 Isotope Solutions","modification":"not applicable","keywords":"isotope analysis;MRFA;trifluoroacetic acid;stable isotopes;isotopocule;IRMS","pi":[{"name":"Cajetan Neubauer","email":"123caj@gmail.com","institution":"University of Colorado Boulder","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"154ebe2d38334cb5969b780ccb8fbb22","id":"3379"}, {"dataset":"MSV000093221","datasetNum":"93221","title":"SPHINGOSINE 1-PHOSPHATE INITIATED E-SYT1 DEPENDENT ER-PM CONTACTS SUPPORT THE RAPID TRANSPORT OF HDL-DERIVED CHOLESTEROL","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698850913000","created":"Nov. 1, 2023, 8:01 AM","description":"Data deposited contain results from proximity-dependent biotinylation LC-MS (BioID) experiments in which T-REx Flp-In HEK293 cells express SCARB1 protein fused to biotin carboxylase BirA.\n","fileCount":"19","fileSizeKB":"2359237","spectra":"0","psms":"73192","peptides":"7906","variants":"9008","proteins":"7826","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap Velos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"SCARB1, SR-BI, BioID, biotin, streptavidin, BirA, LC-MS, T-REx Flp-In HEK293","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046581","task":"0dc0fee0614445148f92066d0035cafa","id":"3380"}, {"dataset":"MSV000093220","datasetNum":"93220","title":"NAK-associated protein 1\/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis.","user":"aordureau","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698846910000","created":"Nov. 1, 2023, 6:55 AM","description":"Supporting raw MS data for paper (DOI:10.1083\/jcb.202303082) by Paul S. et al., titled \"NAK-associated protein 1\/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis\". Index of MS supporting files uploaded: - Related to Figure 6A;S4A (AO3556-AO3579: whole proteome (Unimod: 35; 2016; 4)). - Related to Figure 6A-D;S4B-D (AO3580-AO3603: phospho proteome (Unimod: 35; 21; 2016; 4)). TMTpro channel: WT-UT (126, 127n, 127c, 128n), WT-MRT (128c, 129n, 129c, 130n), TBK1_KO-UT (130c, 131n, 131c, 132n), TBK1_KO-MRT (132c, 133n, 133c, 134n).","fileCount":"49","fileSizeKB":"21347203","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Mitosis;TBK1;Mitotic;Phosphorylation;Cell division;TMTpro","pi":[{"name":"Alban Ordureau","email":"OrdureaA@mskcc.org","institution":"Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c8bd806ceff04b198a0476221f4ea7a7","id":"3381"}, {"dataset":"MSV000093219","datasetNum":"93219","title":"ROS transfer at peroxisome-mitochondria contact sites maintains mitochondrial redox homeostasis","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698846568000","created":"Nov. 1, 2023, 6:49 AM","description":"Data deposited contain results from proximity-dependent biotinylation LC-MS (BioID) experiments in which T-REx Flp-In HEK293 cells express ACBD5 or PTPIP51 proteins fused to biotin carboxylase BirA.\n","fileCount":"35","fileSizeKB":"11447782","spectra":"0","psms":"382611","peptides":"43141","variants":"69885","proteins":"21686","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"BioID, LC-MS, BirA, streptavidin, biotin, T-REx Flp-In HEK293, PTPIP51, ACBD5","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046577","task":"6d92c87a5e3e4bf8aa8be9357e612445","id":"3382"}, {"dataset":"MSV000093217","datasetNum":"93217","title":"GNPS - Streptomyces leeuwenhoekii C34 mutasynthesis","user":"scottjarmusch11","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698845108000","created":"Nov. 1, 2023, 6:25 AM","description":"Dataset of S. leeuwenhoekii C34 extracts for a mutasynthesis study on their production of antimicrobial polyketides with halogenated precursors.","fileCount":"53","fileSizeKB":"27494937","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Streptomyces leeuwenhoekii (NCBITaxon:1437453)","instrument":"maXis","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Streptomyces;mutasynthesis;MSMS","pi":[{"name":"Marcel Jaspars","email":"m.jaspars@abdn.ac.uk","institution":"University of Aberdeen","country":"Scotland"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c02593eb859f4929a6f084abe0855057","id":"3383"}, {"dataset":"MSV000093216","datasetNum":"93216","title":"GNPS - honey quechers data submission","user":"Wang_1999","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698836286000","created":"Nov. 1, 2023, 3:58 AM","description":"Use CEN quechers method to extract 2.5g honey and use PSA to clean up matrix. Using ACN-water-0.01%HCOOH for compound separation and HRMS analysis with Thermo Orbitrap Exploris 120. Data was acquired in Full scan-ddms2 mode. This included a full scan over the m\/z range 100- 1000 at full width at half maximum (FWHM) resolution of 60,000, and a data-dependent-MS2 scan at FWHM resolution of 15,000 on the top 4 ions. The ionization was performed in positive ESI with an inlusion list collated from OPPIN website, and to gain more information about fragment ions in the QC sample, we use an Automated Exclusion List Generation workflow, so one QC sample finally gave 3 injections.","fileCount":"3","fileSizeKB":"8296","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"honey","instrument":"Orbitrap Exploris 120","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"honey","pi":[{"name":"Jingsheng Wang","email":"pierce666@sjtu.edu.cn","institution":"Shanghai Jiao Tong University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cccf30dcfe524c2b90239cbc3221f0ce","id":"3384"}, {"dataset":"MSV000093215","datasetNum":"93215","title":"GNPS - Glutathione adduct_in vitro_human liver microsomes","user":"jyoungheun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698825366000","created":"Nov. 1, 2023, 12:56 AM","description":"GSH adduct formed via in vitro bioactivation in human liver microsomes","fileCount":"36","fileSizeKB":"1316215","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"glutathione;bioactivation;reactive metabolite","pi":[{"name":"Ju-Hyun Kim","email":"jhkim@yu.ac.kr","institution":"College of Pharmacy, Yeungnam University","country":"Republic of Korea"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c10d158c03d046e69c553184bf2e4bdd","id":"3385"}, {"dataset":"MSV000093214","datasetNum":"93214","title":"GNPS_LCMSMS_metabolomics approach ","user":"Nathareen","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698818327000","created":"Oct. 31, 2023, 10:58 PM","description":"Testing pooled samples and samples for metabolomics approach","fileCount":"197","fileSizeKB":"25051941","spectra":"680421","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"cannabis, cannabaceae, cannababis sativa L.","instrument":"6540 Q-TOF LC\\\/MS","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"nathareen","pi":[{"name":"Tongchai Saesong","email":"tongchai_saesong@hotmail.com","institution":"Naresuan University","country":"Thailand"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e978c1e860a846e38ca32078e29f4a67","id":"3386"}, {"dataset":"MSV000093213","datasetNum":"93213","title":"The modified RNA base acp3U is an attachment site for N-glycans in glycoRNA","user":"xie753951","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698809523000","created":"Oct. 31, 2023, 8:32 PM","description":"GlycoRNA consists of RNAs modified with secretory N-glycans that are presented on the cell surface. While previous work supported a covalent linkage between RNA and glycans, the direct chemical nature of the RNA-glycan connection was not described. Here we develop a sensitive and scalable protocol to detect and characterize native glycoRNAs. Leveraging periodate oxidation and aldehyde ligation (rPAL) and Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS), we identified the modified RNA base 3-(3-amino-3-carboxypropyl)uridine (acp3U) as a site of attachment of N-glycans in glycoRNA. rPAL offers sensitivity and robustness as an approach for characterizing direct glycan-RNA linkages occurring in cells, and its flexibility will enable further exploration of glycoRNA biology.\r\n","fileCount":"37","fileSizeKB":"11319583","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"ZenoTOF 7600","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"RNA;glycoRNA;glycosylation;epitranscriptomics","pi":[{"name":" Ryan A. Flynn","email":"ryan.flynn@childrens.harvard.edu","institution":" Boston Children's Hospital","country":"United States"},{"name":"Benjamin A. Garcia","email":"bagarcia@wustl.edu","institution":"Washington University School of Medicine in St. Louis","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"cbfe2163477d4565b0e7393419698382","id":"3387"}, {"dataset":"MSV000093211","datasetNum":"93211","title":"Proteomic analysis of ARF regulatory molecules co-immunoprecipitating with human SDC4 (huSDC4) ","user":"HoracioML","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698445644000","created":"Oct. 27, 2023, 3:27 PM","description":"Proteomic analysis of ARF regulatory molecules co-immunoprecipitating with human\nSDC4 (huSDC4) from Syn4WT, Syn4-\/-, Syn4Y180E and Syn4Y180L MEFs.\n \nPeptide analysis by LC-MS\/MS was performed using an UltiMate 3000 Rapid Separation LC (Dionex Corporation) coupled to an Orbitrap Elite mass spectrometer (Thermo Fisher). Peptides were selected for fragmentation automatically by data-dependent analysis. Data produced were searched using Mascot (Matrix Science UK), against the uniprot.2011-05-03 mammalia database, with fragment ion mass tolerance of 0.50 Da and parent ion tolerance of 10.0 PPM.\n \nScaffold 4 (Proteome Software) was used to validate MS\/MS-based peptide and protein identifications. Peptide identifications were accepted at >95.0% probability by the Peptide Prophet and protein identifications were accepted at >99.0%. Proteins that contained similar peptides and could not be differentiated based on MS\/MS analysis alone were grouped to satisfy principles of parsimony.\n\n\n","fileCount":"14","fileSizeKB":"2806519","spectra":"0","psms":"269338","peptides":"45986","variants":"57394","proteins":"32026","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Mus musculus (NCBITaxon:10090)","instrument":"LTQ Orbitrap Elite","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Syndecan-4;ARF6;CYTOHESIN2;IQSEC1","pi":[{"name":"Mark Morgan","email":"mmorgan@liverpool.ac.uk","institution":"Universtiy of Liverpool","country":"United Kingdom"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"d0f4749b77674b7197966e0c8dab7be5","id":"3388"}, {"dataset":"MSV000093210","datasetNum":"93210","title":"MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons","user":"fschulte","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698440087000","created":"Oct. 27, 2023, 1:54 PM","description":"This dataset comprises 15 raw AP-MS files, each with an associated peak list, captured using a Vanquish Neo nanoLC system in tandem with an Orbitrap Eclipse mass spectrometer. To generate MECP2 hESC-reporter lines for wild type (WT) and various mutations of MECP2, including R133C, R168X, and R270X, we first used CRISPR\/Cas9 to create MECP2 alleles carrying the green fluorescent protein (GFP) sequences in the endogenous gene. The R133C mutation was then introduced into the WT MECP2-GFP reporter line. Mutations R133C, R168X, and R270X are recognized as loss-of-function variants in MECP2 and are also identified as primary Rett syndrome-causing mutations. For efficient neuronal differentiation, a doxycycline (DOX)-responsive NGN2 construct was incorporated at their AAVS1 safe harbor locus. Upon the addition of DOX, homogenous populations of neurons were generated within three weeks from those four MECP2 hESC-reporter lines. Subsequently, GFP-pull down assay and AP-MS were performed using these WT MECP2-GFP neurons along with R133C-, R168X-, and R270X-mutant MECP2-GFP reporter neurons. Neurons expressing only the GFP tag served as a negative control. AP-MS analysis identified proteins interacting differently between WT and mutant MECP2 within human neurons. ","fileCount":"16","fileSizeKB":"5264842","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens","instrument":"Orbitrap Eclipse","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"MECP2;DIA","pi":[{"name":"Fabian Schulte","email":"fschulte@wi.mit.edu","institution":"Whitehead Institute","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"18b470315a3543fe8454b37466dea980","id":"3389"}, {"dataset":"MSV000093207","datasetNum":"93207","title":"GNPS - Rootstock vigor dictates the canopy light environment that regulates metabolite profile and internal fruit quality development in peach","user":"jprenni","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698361157000","created":"Oct. 26, 2023, 3:59 PM","description":"Five rootstock cultivars of differing vigor: vigorous (Atlas and Brights Hybrid 5), standard (Krymsk 86 and Lovell) and dwarfing (Krymsk 1) with Redhaven as scion were studied for their impact on internal fruit quality and maturity. Five years of data showed that average yield (kg per tree) and fruit count increased significantly with increasing vigor (trunk cross sectional area, TCSA), however, no difference was observed in fruit size across rootstocks. In 2019, a detailed peach fruit quality analysis on fruit of equal maturity (based on index of absorbance difference, IAD) coming from trees with equal crop load (no. of fruit cm-2 of TCSA) characterized the direct impact of rootstock vigor on peach internal quality. Twenty-five fruits from each rootstock were assessed for maturity [IAD and flesh firmness (FF)] and internal quality [dry matter content (DMC) and soluble solids concentration (SSC)]. Physiologically characterized peach fruit mesocarp was further analyzed by non-targeted metabolite profiling using gas chromatography mass spectrometry (GC-MS). To account for differences in light availability created by the varying levels of vigor, and its influence on the developing fruits internal quality, mid-canopy photosynthetic active radiation transmission (i.e., light availability) was collected across genotypes with a line quantum sensor. DMC and SSC increased significantly with decreasing vigor and increasing light availability, potentially due to reduced intra-tree shading and better light distribution within the canopy. Metabolite distribution was associated with rootstock vigor class, mid-canopy light availability and fruit quality characteristics. Fructose, glucose, sorbose, neochlorogenic and quinic acids, catechin and sorbitol were associated with high light environments and enhanced quality traits, while sucrose, butanoic and malic acids related to low light conditions and inferior fruit quality. These outcomes show that while rootstock genotype and vigor are influencing peach tree productivity and yield, their effect on manipulating the light environment within the canopy also plays a significant role in fruit quality development.","fileCount":"299","fileSizeKB":"552521","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Prunus persica (NCBITaxon:3760)","instrument":"Clarus SQ 8S Mass Spectrometer ","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Peach;rootstock;vigor","pi":[{"name":"Jessica Prenni","email":"jprenni@colostate.edu","institution":"Colorado State University","country":"United States"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"9b08e1a6a61d4033b4ea03c6acb77973","id":"3390"}, {"dataset":"MSV000093206","datasetNum":"93206","title":"Recruitment of FBXO22 for Targeted Degradation of NSD2","user":"jonstgermain","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698354957000","created":"Oct. 26, 2023, 2:15 PM","description":"Data deposited contain results from proximity-dependent biotinylation LC-MS (BioID) experiments in which T-REx Flp-In HEK293 cells express NSD2 protein fused to miniTurbo biotin carboxylase with or without treatment with the protac UNC8732.\n","fileCount":"336","fileSizeKB":"79963021","spectra":"1346460","psms":"824282","peptides":"72304","variants":"109930","proteins":"28225","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"BioID, biotin, streptavidin, T-REx Flpn-In HEK293, LC-MS, proximity labeling, FBXO22, UNC8732SAINT","pi":[{"name":"Brian Raught","email":"brian.raught@gmail.com","institution":"Princess Margaret Cancer Centre","country":"Canada"}],"complete":"true","quant_analysis":"Quantification Results","status":"Complete","private":"false","hash":"","px":"PXD046431","task":"196a833e99ad4dce8d7a36ea7fd33a8c","id":"3391"}, {"dataset":"MSV000093204","datasetNum":"93204","title":"Mitochondrial RNA Polymerase Post-translational Modifications","user":"dittenhaferreed","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698349310000","created":"Oct. 26, 2023, 12:41 PM","description":"Proteomics data set of mitochondrial RNA polymerase (POLRMT) immunopurified from HeLa cells. ","fileCount":"692","fileSizeKB":"771442","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"6545 Q-TOF LC\\\/MS","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"mitochondrial RNA polymerase;POLRMT","pi":[{"name":"Kristin Dittenhafer-Reed","email":"dittenhaferreed@hope.edu","institution":"Hope College","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046430","task":"d192383f0b6f4b059396df865b5b43ef","id":"3392"}, {"dataset":"MSV000093203","datasetNum":"93203","title":"An Improved Sample Preparation Method for Protein and Peptide Identification from Human Hair","user":"zhengzhang","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698342326000","created":"Oct. 26, 2023, 10:45 AM","description":"A fast and sensitive Direct Extraction (DE) method developed in our group can efficiently extract proteins in 30 min from a 5 cm-long hair strand. Previously we coupled DE to downstream analysis using gel electrophoresis followed by in-gel digestion, which can be time-consuming. In searching for a better alternative, we found that a combination of DE with a bead-based method (SP3) can lead to significant improvements in protein discovery from the human hair. Since SP3 is designed for general applications, we optimized it to process hair proteins following DE and compared it to several other in-solution-digestion methods. Of particular concern are genetically variant peptides (GVPs), which can be used for human identification in forensic analysis. Here we demonstrated improved GVP discovery with the DE and SP3 workflow which was three times faster than the previous in-gel digestion method and required significantly less instrument time depending on the number of gel slices processed. Additionally, it led to increased numbers of identified proteins and GVPs. Among the tested in-solution digestion methods, DE combined with SP3 showed the highest sequence coverage with higher abundances of the identified peptides. This provides a significantly enhanced means for identifying proteins and GVPs in human hair.","fileCount":"15","fileSizeKB":"17273084","spectra":"573551","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"hair","pi":[{"name":"Zheng Zhang","email":"zheng.zhang@nist.gov","institution":"NIST","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"03a27b42bb354aa4a85d4bd765378cd0","id":"3393"}, {"dataset":"MSV000093202","datasetNum":"93202","title":"Poirson_TPD_timsTOFPro2_VS13_14","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698337975000","created":"Oct. 26, 2023, 9:32 AM","description":"This dataset consists of 18 raw DDA MS files and associated peak lists and results files, acquired on timsTOF Pro2 mass spectrometer operated in Data Dependent Acquisition-PASEF (Parallel accumulation-serial fragmentation) mode. It also consists of 18 raw DIA MS files acquired in Data Independent-PASEF mode on timsTOF Pro2 mass spectrometer. \nSamples were generated by Juline Poirson. Sample processing and mass spectrometry acquisition was performed by Cassandra Wong. Analysis was performed by Cassandra Wong and Juline Poirson.\nThe files are associated with a manuscript submitted for publication by Juline Poirson et al. The main goal of this paper was to establish a synthetic proteome-scale platform to identify human proteins that promote degradation or stabilization of a target protein in a proximity-dependent manner. \nMikko Taipale is the corresponding author of the manuscript (mikko.taipale@utoronto.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca)\n\nThis submission is associated with 3 Supplementary Files (in addition to this README file)\nTable 1 describes the composition of this dataset\nTable 2 lists all the peptide identification evidence (as per iProphet)\nTable 3 lists the protein intensity values\n","fileCount":"991","fileSizeKB":"262785870","spectra":"0","psms":"1755645","peptides":"65825","variants":"88120","proteins":"6508","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro 2","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"Targeted protein degradation;Targeted protein stabilization;FBXL12;FBXL15;BCR-ABL1","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046426","task":"3a67419f4c64467c9fb72f378588e979","id":"3394"}, {"dataset":"MSV000093201","datasetNum":"93201","title":"COQ4 Affinity Enrichment Mass Spectrometry","user":"guerra","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698337572000","created":"Oct. 26, 2023, 9:26 AM","description":"Affinity enrichment mass spectrometry experiment to identify protein-protein interactions of hCOQ4-FLAG WT and hCOQ4-FLAG D164A.","fileCount":"10","fileSizeKB":"8694506","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"affinity enrichment mass spectrometry","pi":[{"name":"Leonardo Salviati","email":"leonardo.salviati@unipd.it","institution":"University of Padova","country":"Padova, Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3a6f22437e5a4c019609956e1d507d75","id":"3395"}, {"dataset":"MSV000093200","datasetNum":"93200","title":"GNPS_Sepsis_LP2_Trial_Untargeted_Metabolomics","user":"spthomasGNPS","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698337541000","created":"Oct. 26, 2023, 9:25 AM","description":"Samples from Gates Foundation Sepsis Project testing the effectiveness of probiotic LP2 on preventing infant sepsis in Dhaka, Bangladesh. Samples include infant fecal and serum and mother's milk. ","fileCount":"2734","fileSizeKB":"134967983","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive","modification":"UNIMOD:34 - \\\"Methylation.\\\"","keywords":"sepsis;maternal;pediatric;probiotic","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fdaa3935bb9f4ac9ac8884532801d9a8","id":"3396"}, {"dataset":"MSV000093199","datasetNum":"93199","title":"GNPS_Malpighiaceae_reprocess_ENPKG","user":"pmallard","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698336673000","created":"Oct. 26, 2023, 9:11 AM","description":"Processing (MzMine peak picking and generation of .mgf, quant files and Sirius ready .mgf) of the public MSV000085119 dataset. Check https:\/\/doi.org\/doi:10.25345\/C5S401 for further details on the original dataset.","fileCount":"397","fileSizeKB":"95523","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Malpighiaceae (NCBITaxon:4268)","instrument":"impact HD","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"enpkg","pi":[{"name":"Pierre-Marie Allard","email":"pierre-marie.allard@unifr.ch","institution":"COMMONS Lab - University of Fribourg","country":"Suisse"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b8cc234110e343c88801f66d37174bed","id":"3397"}, {"dataset":"MSV000093197","datasetNum":"93197","title":"SWATH data for human keratinocytes treated with erastin and reactive carbonyl species","user":"Huifang123","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698326495000","created":"Oct. 26, 2023, 6:21 AM","description":"SWATH-MS data for human keratinocytes (HaCaT cell line), sample 001-004 indicates HaCaT cells with no treatment, sample 005-008 indicates HaCaT cells induced by erastin, sample 009-012 indicates HaCaT cells induced by erastin plus MGO (methyglyoxal), and sample 013-016 indicates HaCaT cells induced by erastin plus GO (glyoxal). For more detailed information, please contact Dr.Chang Liu (hichang813@uri.edu)","fileCount":"55","fileSizeKB":"153247815","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"AB Sciex TripleTOF 5600 mass spectrometer","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"skin-aging; ferroptosis; reactive carbonyl species; proteomics; cell death; keratinocytes","pi":[{"name":"Navindra Seeram","email":"bbrluri@gmail.com","institution":"university of rhode island","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"74383dad792d404bb30de31528c7f215","id":"3398"}, {"dataset":"MSV000093196","datasetNum":"93196","title":"Antigen-specific Fab profiling achieves molecular resolution of human autoantibody repertoires in rheumatoid arthritis ","user":"DaniquevanRijswijck","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698326000000","created":"Oct. 26, 2023, 6:13 AM","description":"The presence of autoantibodies is a defining feature of many autoimmune diseases. The number of unique autoantibody clones is conceivably limited by immune tolerance mechanisms, but unknown due to limitations of the currently applied technologies. Here, we introduce an autoantigen-specific liquid chromatography-mass spectrometry-based IgG1 Fab profiling approach using the anti-citrullinated protein antibody (ACPA) repertoire in rheumatoid arthritis (RA) as an example. We show that each patient harbors a unique and diverse ACPA IgG1 repertoire dominated by only a few antibody clones. In contrast to the total plasma IgG1 antibody repertoire, the ACPA IgG1 sub-repertoire is characterized by an expansion of antibodies that harbor one, two or even more Fab glycans, and different glycovariants of the same clone can be detected. Together, our data indicate that the autoantibody response in a prominent human autoimmune disease is complex, unique to each patient and dominated by a relatively low number of clones.","fileCount":"51","fileSizeKB":"3495189","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480;Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"IgG1 clonal profiling, Rheumatoid arthritis, ACPA, Autoimmune disease, Antibodies, LC-MS","pi":[{"name":"Albert J.R. Heck","email":"a.j.r.heck@uu.nl","institution":"Biomolecular Mass Spectrometry and Proteomics groups, Utrecht University","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9f4a8745b11e44f885e8cdd086ea69d5","id":"3399"}, {"dataset":"MSV000093193","datasetNum":"93193","title":"Mapping the immunopeptidome of several SARS-CoV-2 antigens across common HLA haplotypes","user":"abraun","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698316495000","created":"Oct. 26, 2023, 3:34 AM","description":"Most COVID-19 vaccines have been designed to elicit immunity against the SARS-CoV-2 Spike protein. However, the repeated occurrence of new strains harbouring Spike protein mutations demonstrates ready immune evasion by the SARS-CoV-2 virus and the pressing need to develop more broadly targeting COVID-19 vaccines. To facilitate this, we used mass spectrometry to identify immunopeptides that are derived from seven structural and non-structural SARS-CoV-2 proteins that are relatively conserved across viral strains (N, E, Nsp1, Nsp4, Nsp5, Nsp8, Nsp9) and presented by prevalent Human Leukocyte Antigen (HLA) class I and class II molecules. Two different B-lymphoblastoid cell lines were chosen to map immunopeptidomes covering some of the major HLA types across the global human population. We used DNA plasmid transfection and direct antigen delivery approaches to sample different antigens. We found 248 unique HLA class I and HLA class II bound peptides with 12 derived from E, 71 from N, 28 from Nsp1, 19 from Nsp4, 73 from Nsp8 and 45 peptides derived from Nsp9. T cell responses were tested for 56 of the detected peptides and we show robust CD8+ and CD4+ T cell responses against several peptides from the N, E and Nsp9 proteins. Results from this study will aid the development of next-generation COVID vaccines targeting epitopes from across a number of SARS-CoV-2 proteins.","fileCount":"762","fileSizeKB":"1148588940","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Severe acute respiratory syndrome coronavirus 2 (NCBITaxon:2697049)","instrument":"timsTOF Pro","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"B lymphoblastoid cell line;SARS-CoV-2;COVID-19","pi":[{"name":"Anthony Wayne Purcell","email":"anthony.purcell@monash.edu","institution":"Deputy Head (Research), Department of Biochemistry and Molecular Biology Head Immunoproteomics Laboratory Infection and Immunity Program Monash Biomedicine Discovery Institute Monash University, Clayton Campus Clayton 3800 Victoria Australia","country":"N\/A"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046411","task":"bec484d9ddac4972a8d64e4a211e1088","id":"3400"}, {"dataset":"MSV000093192","datasetNum":"93192","title":"GNPS_Mouse_Maternal_Infant_Antibiotic_Administration","user":"spthomasGNPS","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698270409000","created":"Oct. 25, 2023, 2:46 PM","description":"Data from parent\/infant mice treated with antibiotics via three methods. Hypo1: IV ampicillin giving to the mother before birth. Hypo2: IV ampicillin given to the mother immediately after birth. Hypo3: IV ampicillin given directly to the pups. Also see MSV000092652 and MSV000089558. \r\nBile acid standards run alongside these samples are available in MSV000093262. Feature finding results and parameters are included in the supplementary files. ","fileCount":"410","fileSizeKB":"19914540","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Q Exactive","modification":"UNIMOD:34 - \\\"Methylation.\\\"","keywords":"antibiotic;maternal;pediatric","pi":[{"name":"Pieter C Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e774a757654c4c3aa740782cf192d1ee","id":"3401"}, {"dataset":"MSV000093190","datasetNum":"93190","title":"Analyzing the ER stress response in ALS patient derived motor neurons identifies druggable neuroprotective targets","user":"aordureau","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698248076000","created":"Oct. 25, 2023, 8:34 AM","description":"Supporting MS data files for paper (doi:10.3389\/fncel.2023.1327361) by Watts M.E. et al., titled \"Analyzing the ER stress response in ALS patient derived motor neurons identifies druggable neuroprotective targets\". See attached pdf for index of MS files uploaded.","fileCount":"38","fileSizeKB":"28735524","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"TMT;Phosphorylation;Motor Neurons;Proteome;ER stress;iPSC","pi":[{"name":"Alban Ordureau","email":"OrdureaA@mskcc.org","institution":"Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"890319d3da9e416ab566d95bd86b5923","id":"3402"}, {"dataset":"MSV000093188","datasetNum":"93188","title":"2022_Corsican_Bryophyta_collection_Neg","user":"anaisP2A","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698245750000","created":"Oct. 25, 2023, 7:55 AM","description":"Investigation of chemical composition of Corsican bryophytes collection (60 species) without fatty acid","fileCount":"144","fileSizeKB":"4608734","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bryophyta (NCBITaxon:3208)","instrument":"Q Exactive","modification":"PRIDE:0000398","keywords":"bryophyta","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "},{"name":"Muselli Alain ","email":"muselli_a@univ-corse.fr","institution":"Universita di Corsica","country":"France"},{"name":"Pannequin anais","email":"pannequin.anais@hotmail.fr","institution":"Universita di Corsica","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"774c814b36094d72a86a0db8b537cfc1","id":"3403"}, {"dataset":"MSV000093186","datasetNum":"93186","title":"2022_Corsican_Bryophyta_collection","user":"anaisP2A","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698228307000","created":"Oct. 25, 2023, 3:05 AM","description":"Investigation of chemical composition of Corsican bryophytes collection (60 species) without fatty acid","fileCount":"169","fileSizeKB":"8203045","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bryophyta (NCBITaxon:3208)","instrument":"Q Exactive","modification":"PRIDE:0000398","keywords":"bryophyta;metabolomics;molecular network;metabolite annotation;Mosses;Liverworts;Corsica bryoflora","pi":[{"name":"Jean-Luc Wolfender","email":"jean-luc.wolfender@unige.ch","institution":"University of Geneva","country":"Switzerland "},{"name":"Muselli Alain ","email":"muselli_a@univ-corse.fr","institution":"Universita di Corsica","country":"France"},{"name":"Pannequin anais","email":"pannequin.anais@hotmail.fr","institution":"Universita di Corsica","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"e07c6d399daf48019f465511973764f6","id":"3404"}, {"dataset":"MSV000093185","datasetNum":"93185","title":"Proteome wide analysis of SUMO interacting proteins from Huntingtons disease R6\/2 mouse striatum shows alterations in enrichment of functional synaptic proteins","user":"NivedaS5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698226536000","created":"Oct. 25, 2023, 2:35 AM","description":"Huntingtons disease (HD) is a neurodegenerative disorder caused by an expanded CAG repeat mutation in the Huntingtin (HTT) gene. The mutation impacts neuronal protein homeostasis and cortical\/striatal circuitry. SUMOylation, a post translational modification with broad cellular effects, directly modifies the Huntingtin protein (HTT), along with other key neuronal and synaptic proteins. Here we investigated proteome wide changes in striatal protein SUMOylation\/protein SUMO interactions in the context of HD using R6\/2 transgenic and non-transgenic (NT) control mice by performing SUMO protein enrichment from tissue followed by mass spectrometry. Significant changes in enrichment of known and previously unknown SUMOylated or SUMO interacting proteins were observed including those involved in presynaptic function and cytomatrix at the active zone scaffolding, cytoskeleton organization, and glutamatergic signaling. A network based approach identified altered pathways in HD tissue to include clathrin mediated endocytosis signaling, synaptogenesis signaling, synaptic long term potentiation, and SNARE signaling. Furthermore, the metabotropic glutamate receptor 7 (mGluR7), a key player in glutamatergic signaling, a core signaling pathway disrupted in HD was SUMO enriched and we show SUMO modification is enhanced by the E3 SUMO ligase Protein Inhibitor of Activated STAT1 (PIAS1). To evaluate functional measures of neuronal activity in HD cells in vitro we utilized primary neuronal cultures from R6\/2 and NT mice and evaluated how modulation of SUMOylation via reduction of PIAS1 may impact specific readouts. A receptor internalization assay showed decreased mGluR7 internalization in R6\/2 neurons compared to NT, and siRNA mediated knockdown of PIAS1 prevented this HD phenotype. In addition, microelectrode array analysis on primary neuron cultures indicated early timepoint hyperactivity in HD cells, while later timepoints demonstrated deficits in several measurements of neuronal activity within cortical neurons. HD phenotypes were rescued at select timepoints following knockdown of PIAS1. Taken together our results provide a mouse brain SUMO ome resource and show that significant alterations occur within the post-translational landscape and SUMO protein interactions for synaptic proteins in HD.","fileCount":"82","fileSizeKB":"29356334","spectra":"1115551","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:876 - \\\"SUMOylation by SUMO-1.\\\";UNIMOD:877 - \\\"SUMOylation by SUMO-2\\\/3.\\\"","keywords":"SUMOylation;Huntingtons disease","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046378","task":"3949ee44079b478ebbd99927b20f549b","id":"3405"}, {"dataset":"MSV000093184","datasetNum":"93184","title":"GNPS - Effects of Dapensutrile and Glycine on mice QiitaID 15108 and 14472","user":"amcaraballor","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1698188887000","created":"Oct. 24, 2023, 4:08 PM","description":"Ctns -\/- mice is a mouse model for cystinosis, a recessive genetic disorder in human, characterized by Fanconi syndrome and chronic kidney disease. We aim to characterize the microbiome and metabolomic phenotype from gut (fecal), urine and serum on Ctns -\/- mice versus wild type controls (c57BL\/6J). Dapansutrile (Qiita ID 15108) and Glycine supplementation were investigated (Qiita ID 14472). Untargeted LC-MS\/MS acquisition was performed on a Vanquish UHPLC system coupled to a Q-Exactive Hybrid Quadrupole-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 50 x 2.1 mm (Phenomenex, Torrance, CA).","fileCount":"1519","fileSizeKB":"45164442","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus sp. 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However, the signaling and nutritional potential of the stromal cell-secreted metabolites remains poorly understood. We identified a novel metabolic crosstalk between cancer associated fibroblasts (CAFs) and pancreatic cancer cells. We demonstrate that pancreatic CAFs regulate tumor cell metabolism through the secretion of acetate, which can be blocked by silencing ACLY in CAFs. Cancer cells present a unique dependence on CAF-derived acetate under acidosis. We further show that ACSS2 channels the exogenous acetate to regulate the dynamic cancer epigenome and transcriptome, thereby facilitating cancer cell survival in the acidic microenvironment. Comparative H3K27ac ChIP-Seq and RNA-Seq analyses revealed alterations in polyamine homeostasis through regulation of SAT1 gene expression and enrichment of the SP1-responsive signature. We observed novel acetate\/ACSS2-mediated acetylation of SP1 at lysine 19 residue that increased SP1 protein stability and transcriptional activity. Genetic or pharmacologic inhibition of the ACSS2-SP1-SAT1 axis diminished tumor burden in mouse models. Increased SAT1-mediated production of N1-acetylspermidine correlated with disease progression in the spontaneous tumor progression model and poor survival in cancer patients. 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The aim of the study was the LC MS\/MS proteomic analysis of exosomes released by FTC and 8305C thyroid cancer cell lines, and reference Nthy-ori 3-1 normal thyroid follicular cells. A total of 1769 unique proteins were identified in the exosome samples. For exosomes derived from Nthy ori 3 1 cell the highest number of 1504 proteins was identified, while exosomes from thyroid carcinomas FTC and 8305C cell lines had 730 and 1304 identified proteins, respectively. For the identified proteins, gene ontology analysis was performed in terms of their cellular location, molecular function and involvement in biological processes. For proteins that only appeared in tumor derived FTC- and 8305C-derived exosomes, enriched categories were related to cancer progression and included cell adhesion and positive regulation of cell migration. Also, proteins related to protein N linked glycosylation, drug resistance, and cell response to NK and T cell cytotoxicity were among those unique proteins. Finally label free quantification (LFQ) was performed for identified differentially expressed proteins between all possible group parings. For exosomes from thyroid cancer cells, the most differentiating proteins included collagen alpha 2(I) chain, tenascin, matrix metalloproteinase 1, Interstitial collagenase and C type lectin domain family 11 member A. The obtained results broadened the knowledge about the role of exosomal proteins in thyroid cancer and indicated potential biomarkers for further evaluation in clinical conditions. 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This well-defined method, profiling data, and functional characterization provide a solid and reliable framework for developing human in vitro neuronal models for disease modeling.","fileCount":"103","fileSizeKB":"53449318","spectra":"3321037","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"TMT;iPSC;NGN2;DDA","pi":[{"name":"Claire G. 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The gene deletion creates a hypersensitivity to salt when the bacteria are grown on carbon sources metabolized by the TCA cycle. This phenotype is due to the reduced translation of several genes of the TCA cycle and of genes involved in stress responses. In this work we have systematically compared three strains MG1655 WT, delta ettA and the delta ettA complemented with an exogenous chromosomal copy of ettA (CettA). Label-Free mass spectrometry studies performed on light (S15) and heavy (S150) fractions of proteins extracts from cultures grown in MMAA-NaCl medium, identified several protein expression changes in the delta ettA strain compared to the WT or the CettA strains.","fileCount":"144","fileSizeKB":"108429512","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli (NCBITaxon:562)","instrument":"Q Exactive Plus","modification":"MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"ABC-F protein family;quantification;label-free;mass spectrometry","pi":[{"name":"Gregory Boel","email":"Boel@ibpc.fr","institution":"UMR 8261, IBPC, CNRS","country":"France"}],"complete":"false","quant_analysis":"Quantification Results;Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"PXD046209","task":"a631512e05f54342be54c56666082154","id":"3424"}, {"dataset":"MSV000093140","datasetNum":"93140","title":"GNPS - Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life","user":"kkleigrewe","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697633363000","created":"Oct. 18, 2023, 5:49 AM","description":"Microbiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, infant formula and solid foods.","fileCount":"417","fileSizeKB":"48348008","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 6600","modification":"Metabolomics","keywords":"circadian rhythmicity","pi":[{"name":"Dirk Haller","email":"dirk.haller@tum.de","institution":"Technical University of Munich","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"ec88cf93dcc54a3db2105a5e7c269ae2","id":"3425"}, {"dataset":"MSV000093137","datasetNum":"93137","title":"Identification of non-conventional small molecule degraders and stabilizers of squalene synthase","user":"joseho","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697616299000","created":"Oct. 18, 2023, 1:04 AM","description":"The dataset was obtained by performing a TMTpro16plex expression proteomics experiment, where HeLa cells were treated with small molecule ligands of squalene synthase (FDFT1). The experiment was successful in re-producing previously obtained Western Blot results in regards to SQS (=FDFT1) levels and aimed at elucidating downstream effects on cholesterol biosynthesis and metabolism. The dataset comprises data for the following samples: DMSO (vehicle), KY02111, PROTAC 18, SQSI and a compound unrelated to this project (TMTpro16plex, processed by Maxquant, each collected in 30 fractions). The experiments were performed in three independent replicates for each compound (R1-R3). ","fileCount":"31","fileSizeKB":"9175085","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Eclipse","modification":"MOD:00394 - \\\"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";MOD:00935 - \\\"Oxidation of methionine to methionine sulfoxide with neutral loss of CH3SOH.\\\";MOD:00768 - \\\"Oxidation of methionine to methionine sulfone with neutral loss of CH3SO2H.\\\"","keywords":"expression proteomics;squalene synthase ;FDFT1","pi":[{"name":"Luca laraia","email":"luclar@kemi.dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"dafe99d4184348c8b243eff0d202b95a","id":"3426"}, {"dataset":"MSV000093136","datasetNum":"93136","title":"Signatures of Cysteine Oxidation on Structural and Contractile Proteins Are Associated with Physical Performance and Muscle Function in Older Adults","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697601227000","created":"Oct. 17, 2023, 8:53 PM","description":"Human muscle biopsies from older adults were processed with a redox proteomics workflow and analyzed by LC-MS\/MS with TMT based quantification.","fileCount":"212","fileSizeKB":"95264162","spectra":"0","psms":"2043985","peptides":"826988","variants":"1129896","proteins":"40263","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive HF-X","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:108 - \\\"N-ethylmaleimide on cysteines.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"muscle;power;fitness;thiol oxidation;post-translational modifications;redox","pi":[{"name":"Wei-Jun Qian","email":"Weijun.Qian@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046200","task":"df7827acfab9489980eeb4508e7da208","id":"3427"}, {"dataset":"MSV000093130","datasetNum":"93130","title":"GNPS - High-throughput profiling of Synechocystis sp. 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The goal was to validate findings of snRNA-seq and new informatics means to mine the data (UNAGI) and evaluate in silico drugs that could present efficiency against IPF. The samples were extracted using the MPLEx method, peptides were reduced, alkylated, and digested with trypsin and 5 ul of 0.1 ug\/ul were injected on LC-MS\/MS on a Lumos instrument. The analysis was performed in DDA label free mode.","fileCount":"88","fileSizeKB":"46709596","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Lung;IPF;Fibrosis","pi":[{"name":"Geremy Clair","email":"geremy.clair@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"8ec8e879e1e34e4494c806a0deecad82","id":"3429"}, {"dataset":"MSV000093127","datasetNum":"93127","title":"TMT isobaric profiling of PPIA heterozygous versus knockout haematopoietic stem cells","user":"acatic","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697501145000","created":"Oct. 16, 2023, 5:05 PM","description":"Mass spectrometry was performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) interfaced with an UltiMate 3000 Binary RSLCnano System (Dionex). Proteome Discoverer v.1.4 (Thermo Scientific) with SEQUEST HT search engines was used for the spectra-preprocessing and HCD MS2 spectra were used for peptide identification and quantitation based on TMT reporter ions. TMT isobaric comparison of Ppia heterozygous (het) versus knockout (KO) haematopoietic stem and progenitor cells. Het 1 is sample 126 and KO 1 is sample 131 of dataset UTH_2. Het 2 and KO 2 are samples 126 and 127 of UTH_4. Het 3 and KO 3 are samples 130 and 127 of dataset UTH_3.\n","fileCount":"19","fileSizeKB":"46855084","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cyclophilin A;PPIA;Aging","pi":[{"name":"Andre Catic","email":"Andre.Catic@bcm.edu","institution":"Baylor College of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046247","task":"48d33bf459154e1ab9ef27787dc2f338","id":"3430"}, {"dataset":"MSV000093126","datasetNum":"93126","title":"TMT isobaric profiling of young versus old haematopoietic stem cells","user":"acatic","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697500710000","created":"Oct. 16, 2023, 4:58 PM","description":"Mass spectrometry was performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) interfaced with an UltiMate 3000 Binary RSLCnano System (Dionex). Proteome Discoverer v.1.4 (Thermo Scientific) with SEQUEST HT search engines was used for the spectra-preprocessing and HCD MS2 spectra were used for peptide identification and quantitation based on TMT reporter ions. TMT isobaric comparison of old versus young haematopoietic stem and progenitor cells. Young 1 and Young 2 are samples 126 and 128 of dataset UTH_1. Old 1 and Old 2 are samples 129 and 130 of UTH_1. Young 3 is sample 131 and Old 3 is sample 130 of dataset UTH_4.\n","fileCount":"13","fileSizeKB":"27652752","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cyclophilin A;PPIA;Aging","pi":[{"name":"Andre Catic","email":"Andre.Catic@bcm.edu","institution":"Baylor College of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046246","task":"45c773bc89cf48e09b7a55b7d1ec4f84","id":"3431"}, {"dataset":"MSV000093125","datasetNum":"93125","title":"Pulsed SILAC study of cell lines following PPIA knockdown","user":"acatic","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697500184000","created":"Oct. 16, 2023, 4:49 PM","description":"Mass spectrometry was performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) interfaced with an UltiMate 3000 Binary RSLCnano System (Dionex). Proteome Discoverer v.1.4 (Thermo Scientific) with SEQUEST HT search engines was used for the spectra-preprocessing and HCD MS2 spectra were used for peptide identification and quantitation based on TMT reporter ions. Pulsed SILAC study of HEK293T cells and HeLa cells after knockdown (KD) of PPIA.","fileCount":"11","fileSizeKB":"28669042","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Cyclophilin A;PPIA;Aging","pi":[{"name":"Andre Catic","email":"catic@bcm.edu","institution":"Baylor College of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046245","task":"ec019510e1684ddeb9a0b669a6e0b316","id":"3432"}, {"dataset":"MSV000093124","datasetNum":"93124","title":"GNPS - klebsiella pneumoniae serum exposure","user":"lsanti","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697482819000","created":"Oct. 16, 2023, 12:00 PM","description":"A strain of Klebsiella pneumoniae exposed to native and heat-inactivated serum for different time points","fileCount":"18","fileSizeKB":"707922","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Klebsiella pneumoniae (NCBITaxon:573)","instrument":"LTQ Orbitrap","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"klebsiella, serum, resistance, siderophore","pi":[{"name":"Lucelia Santi","email":"lucelia.santi@ufrgs.br","institution":"UFRGS","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046166","task":"3dd243bb921d4c7fa7bd0c83dd9838b9","id":"3433"}, {"dataset":"MSV000093123","datasetNum":"93123","title":"GNPS - Secondary-Electrospray Ionization Mass Spectrometry-based Online Analyses of Mouse Volatilome Uncovers Gut Microbiome-Dictated Metabolic Changes in the Host","user":"choueiry_2","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697475520000","created":"Oct. 16, 2023, 9:58 AM","description":"In this study, mouse microbial populations were depleted using an antibiotic cocktail. The microbiome was reestablished using fecal matter transplant or single-strain bacteria species. Volatile organic compounds emitted from the mice were screened to determine if the diversity of the microbial populations can alter host volatilome. ","fileCount":"95","fileSizeKB":"16102890","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Escherichia coli;Bacteroides thetaiotaomicron;Akkermansia muciniphila","instrument":"Q Exactive","modification":"NA","keywords":"VOC;Volatile analysis;microbiome","pi":[{"name":"Jiangjiang Zhu","email":"zhu.2484@osu.edu","institution":"Ohio State University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c040fc934320486ab3fdbcc9132df705","id":"3434"}, {"dataset":"MSV000093121","datasetNum":"93121","title":"GNPS - Dataset Creation from GNPS Molcular Networking - e160b564fc7e48e6b82394991bfd79be","user":"bergeijkdavan","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697466136000","created":"Oct. 16, 2023, 7:22 AM","description":"Metabolic profiles of Actinobacteria isolated from a faecal sample that was taken from the intestinal tracts of a 28,000-year-old Siberian Mammoth. Strains have been grown on Nutrient Agar (Difco) for one week before metabolite extraction with ethyl acetate. \n720-722: medium blank\n723-725: Oerskovia sp. M15\n726-728: Streptomyces sp. M19\n729-731: Saccharopolyspora sp. M46\n732-734: Streptomyces sp. M10","fileCount":"16","fileSizeKB":"950026","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Micromonospora (NCBITaxon:1873);Streptomyces (NCBITaxon:1883);Oerskovia (NCBITaxon:162491);Saccharopolyspora (NCBITaxon:1835);Sanguibacter (NCBITaxon:60919)","instrument":"Shimadzu 9030 QTOF mass spectrometer","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Actinobacteria;Mammoth","pi":[{"name":"Gilles van Wezel","email":"g.wezel@biology.leidenuniv.nl","institution":"Institute of Biology, Leiden University","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9f44ae1b243f426ab0ec1f93272c5b7b","id":"3435"}, {"dataset":"MSV000093120","datasetNum":"93120","title":"GNPS - 20231016_RIA_ApF5_secondary-metabolites_2","user":"iaco","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697464443000","created":"Oct. 16, 2023, 6:54 AM","description":"Data for the manuscript: Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites. Authors: R. Iacovelli, T. He, J. L. Allen, T. Hackl, and K. Haslinger.","fileCount":"11","fileSizeKB":"11148301","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Anthostomella pinea (NCBITaxon:933095)","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Anthostomella pinea;secondary metabolites;sesquiterpenes;xanthoepocin","pi":[{"name":"Kristina Haslinger","email":"k.haslinger@rug.nl","institution":"Groningen Research Institute of Pharmacy, University of Groningen","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"157a391d84db484f832d15806fa65c02","id":"3436"}, {"dataset":"MSV000093118","datasetNum":"93118","title":"GNPS - Profiling of pancreatic adenocarcinoma using artificial intelligence-based integration of multi-omic and computational pathology features: lipid","user":"NivedaS5","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697436352000","created":"Oct. 15, 2023, 11:05 PM","description":"Contemporary analyses focused on a limited number of clinical and molecular features have been unable to accurately predict clinical outcomes in pancreatic ductal adenocarcinoma (PDAC). Here we describe a novel, conceptual approach and use it to analyze clinical, computational pathology, and molecular (DNA, RNA, protein, and lipid) analyte data from 74 patients with resectable PDAC. Multiple, independent, machine learning models were developed and tested on curated single and multi-omic feature\/analyte panels to determine their ability to predict clinical outcomes in patients. The multi-omic models predicted recurrence with an accuracy and positive predictive value (PPV) of 0.90, 0.91, and survival of 0.85, 0.87, respectively, outperforming every single-omic model. In predicting survival, we defined a parsimonious model with only 589 multi-omic analytes that had an accuracy and PPV of 0.85. Our approach enables discovery of parsimonious biomarker panels with similar predictive performance to that of larger and resource consuming panels and thereby has a significant potential to democratize precision cancer medicine worldwide.","fileCount":"471","fileSizeKB":"949700","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Shimadzu Nexera LC-30AD UHPLC system","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"multiomics;lipidomics","pi":[{"name":"Jennifer Van Eyk","email":"jennifer.vaneyk@cshs.org","institution":"Cedars Sinai Medical Center","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6ae04d67611f4635ad04d9b4b03b71ec","id":"3437"}, {"dataset":"MSV000093117","datasetNum":"93117","title":"Logan Smith Revised MSc Thesis","user":"logansmith851","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697418851000","created":"Oct. 15, 2023, 6:14 PM","description":"This data serves as an Appendix for the MSc thesis of Logan Jason Smith.","fileCount":"105","fileSizeKB":"26950235","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Rattus norvegicus (NCBITaxon:10116)","instrument":"Q Exactive","modification":"MOD:00565 - \\\"modification from UniMod N-linked glycosylation\\\";MOD:00046 - \\\"A protein modification that effectively converts an L-serine residue to O-phospho-L-serine.\\\";MOD:00047 - \\\"A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine.\\\";MOD:00048 - \\\"A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine.\\\"","keywords":"MSc Thesis Raw data;Logan Smith","pi":[{"name":"Prof Faadiel Essop","email":"mfessop@sun.ac.za","institution":"Stellenbosch University","country":"South Africa"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"dce20e0fcad440a6ad3178af253c474c","id":"3438"}, {"dataset":"MSV000093116","datasetNum":"93116","title":"Proteomic Analyses of Plasma from Patients with Fracture Related Infection Reveals Systemic Activation of the Complement and Coagulation Cascades","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697395210000","created":"Oct. 15, 2023, 11:40 AM","description":"Patients\/Participants: Twenty-seven patients meeting confirmatory FRI criteria were matched to 27 controls based on fracture region, age, and time after surgery\nIntervention: Tandem Mass Tag (TMT) LC-MS analysis of patient plasma samples\nMain Outcome Measurements: Abundances for over 1000 proteins were measured in the 54 plasma samples and the protein abundance ratios for FRI patients compared to matched controls were calculated.\nResults: Seventy-three proteins were found to be significantly increased or decreased in FRI patients compared to the matched controls (unadjusted t-test p<0.05). Thirty-two of these proteins were found in all 54 patient samples and underwent subsequent principal component analysis (PCA). A three component PCA accounted for 45.7% of the variation in the data set and was 88.9% specific for the diagnosis of FRI. STRING protein-protein interaction network analysis of these three PCs revealed activation of the complement and coagulation cascades via the Reactome pathway database.\nConclusions: Proteomic analyses of plasma from FRI patients demonstrates systemic activation of the complement and coagulation cascades in a highly specific manner. Further investigation along these lines may help to better understand the systemic response to FRI and improve diagnostic strategies using proteomics.\n","fileCount":"155","fileSizeKB":"251194554","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:738 - \\\"Duplex Tandem Mass Tag.\\\"","keywords":"fracture;infection;proteomics;bioinformatics","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046141","task":"d94eaa1cb96d476a84d7bc6387e72345","id":"3439"}, {"dataset":"MSV000093115","datasetNum":"93115","title":"Myrsine guianensis (syn. 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This dataset include inter-day, intra-day, analyst-to-analyst, and donor-to-donor variability as well as MAPPs data from different biotherapeutics.","fileCount":"130","fileSizeKB":"71159793","spectra":"0","psms":"493872","peptides":"273883","variants":"306211","proteins":"60082","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"MHC II;MAPPs;Biotherapeutic;Immunogenicity;PBMCs","pi":[{"name":"M. 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PCC 6803 (NCBITaxon:1148);Synechococcus sp. UTEX 2973 (NCBITaxon:1350461)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cyanobacteria;protein scaffold;PduA;nanofilament","pi":[{"name":"Julie A. Z. Zedler","email":"julie.zedler@uni-jena.de","institution":"Friedrich Schiller University Jena","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046137","task":"a83ff6dc0fea44f289cb59736da38731","id":"3442"}, {"dataset":"MSV000093110","datasetNum":"93110","title":"Can we boost N-glycopeptide identification confidence? Smart collision energy choice taking into account structure and search engine","user":"reveszagnes","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697283402000","created":"Oct. 14, 2023, 4:36 AM","description":"We investigated how the structural features of N-glycopeptides and the choice of the search engine influence the optimal collision energy, delivering highest identification confidence. We carried out LC-MS\/MS measurements using a series of collision energies on a large set of N-glycopeptides with both the glycan and peptide part varied, and studied the behavior of Byonic, pGlyco, and GlycoQuest scores.","fileCount":"385","fileSizeKB":"1513886","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Bos taurus (NCBITaxon:9913)","instrument":"maXis II","modification":"MOD:00506 - \\\"modification from UniMod N-linked glycosylation, Hex(5) HexNAc(2)\\\"","keywords":"tandem mass spectrometry;bottom-up proteomics;N-glycosylation;glyan structure;identification score;search engine;collision energy optimization;general linear model;lasso regression","pi":[{"name":"Agnes Revesz","email":"revesz.agnes@ttk.hu","institution":"HUN-REN Research Centre for Natural Sciences","country":"Hungary"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9d3b9e921ed746a69ea72c9804aef07b","id":"3443"}, {"dataset":"MSV000093109","datasetNum":"93109","title":"[SYPHU-SongLab] The Dataset of sesquiterpenes from the daphne genus","user":"SongLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697263789000","created":"Oct. 13, 2023, 11:09 PM","description":"The datasets for the sesquiterpenes from the daphne genus. 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Exploring the mechanisms of this transition could improve salt tolerance in C3 crops. We used transcriptomics, proteomics, and targeted metabolomics every 8 hours to track molecular shifts during this transition. Results confirmed changes in CAM photosynthesis, starch biosynthesis, degradation, and glycolysis\/gluconeogenesis. Transcripts displayed greater circadian regulation than proteins. Oxidative phosphorylation was crucial, with the inositol pathway, involving methylation and phosphorylation, potentially initiating the transition. V-type ATPases showed consistent transcription regulation, aiding in vacuolar osmotic pressure maintenance. ABI1, a major component in the ABA signaling pathway, could be the trigger for the salt-induced transition, as it inhibits ABA-dependent stomatal closure. Our work highlights the pivotal role of ABA pathways in the C3 to CAM shift.","fileCount":"74","fileSizeKB":"155804541","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mesembryanthemum crystallinum (NCBITaxon:3544)","instrument":"Q Exactive Plus","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Mesembryanthemum crystallinum;C3 to CAM transition;proteomics;ABA dependent stomatal movement;transcriptomics","pi":[{"name":"Sixue Chen","email":"schen8@olemiss.edu","institution":"University of Mississippi","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"002fd3ddf44a4d89b35fc6589161dda8","id":"3446"}, {"dataset":"MSV000093104","datasetNum":"93104","title":"GNPS melHKO Mm untargeted metabolomics","user":"Vitayo","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697217782000","created":"Oct. 13, 2023, 10:23 AM","description":"GNPS melHKO Mm \nuntargeted metabolomics\n(glycerol\/propionate\/cholesterol\/oleic acid\/pyruvate as sole carbon source)\nRP C18\/HILIC\/HIPLEX column \nPositive\/Negative phase","fileCount":"61","fileSizeKB":"930909","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mycobacterium marinum (NCBITaxon:1781)","instrument":"impact II","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"melH KO","pi":[{"name":"Nicole S Sampson","email":"nicole.sampson@stonybrook.edu","institution":"Stony Brook University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"94a339a2c4574441b17f3adafb58b08d","id":"3447"}, {"dataset":"MSV000093103","datasetNum":"93103","title":"Hesketh_GIGYF1_P116_Sciex6600_VS11","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697207671000","created":"Oct. 13, 2023, 7:34 AM","description":"The purpose of this dataset is to identify proximity-dependent interactions of GIGYF1 using BioID. 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To support the further studies of plants of daphne genus.","fileCount":"15","fileSizeKB":"531535","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"daphne","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sesquiterpenes, daphne","pi":[{"name":"Jingxian Ren","email":"1137310558@qq.com","institution":"Shenyang Pharmaceutical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3d54335a83944dc6a8b73e423205d17b","id":"3454"}, {"dataset":"MSV000093096","datasetNum":"93096","title":"[SYPHU-SongLab] The Dataset of 5,6,7-guaiacolane-type sesquiterpenes from the daphne genus","user":"SongLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697186482000","created":"Oct. 13, 2023, 1:41 AM","description":"The datasets for the 5,6,7-guaiacolane-type sesquiterpenes from the daphne genus. To support the further studies of plants of daphne genus.","fileCount":"15","fileSizeKB":"487150","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"daphne","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sesquiterpenes, daphne","pi":[{"name":"Jingxian Ren","email":"1137310558@qq.com","institution":"Shenyang Pharmaceutical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fb5b0c9cf9db4646817b06de680826e8","id":"3455"}, {"dataset":"MSV000093095","datasetNum":"93095","title":"[SYPHU-SongLab] The Dataset of 5,6,5-guaiacolane-type sesquiterpenes from the daphne genus","user":"SongLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697186267000","created":"Oct. 13, 2023, 1:37 AM","description":"The datasets for the 5,6,5-guaiacolane-type sesquiterpenes from the daphne genus. To support the further studies of plants of daphne genus.","fileCount":"61","fileSizeKB":"1352738","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"daphne","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sesquiterpenes, daphne","pi":[{"name":"Jingxian Ren","email":"1137310558@qq.com","institution":"Shenyang Pharmaceutical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e47948c44e32406da2c6267ccfce9803","id":"3456"}, {"dataset":"MSV000093094","datasetNum":"93094","title":"[SYPHU-SongLab] The Dataset of some other sesquiterpenes from the daphne genus","user":"SongLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697182611000","created":"Oct. 13, 2023, 12:36 AM","description":"The datasets for some other sesquiterpenes from the daphne genus. To support the further studies of plants of daphne genus.","fileCount":"5","fileSizeKB":"140243","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"daphne","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sesquiterpenes, daphne","pi":[{"name":"Jingxian Ren","email":"1137310558@qq.com","institution":"Shenyang Pharmaceutical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f0fbcbd017734f1c8978df7d713e3a50","id":"3457"}, {"dataset":"MSV000093093","datasetNum":"93093","title":"[SYPHU-SongLab] The Dataset of carotenoid-type sesquiterpenes from the daphne genus","user":"SongLab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697178681000","created":"Oct. 12, 2023, 11:31 PM","description":"The datasets for the carotenoid-type sesquiterpenes from the daphne genus. To support the further studies of plants of daphne genus.","fileCount":"15","fileSizeKB":"509274","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"daphne","instrument":"Q Exactive Plus","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"sesquiterpenes, daphne","pi":[{"name":"Jingxian Ren","email":"1137310558@qq.com","institution":"Shenyang Pharmaceutical University","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"16e4c629e3fb404384a8101e7b222142","id":"3458"}, {"dataset":"MSV000093092","datasetNum":"93092","title":"GNPS - Priestia endophytica fluorescent pigments","user":"alina_kharchuk","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697174485000","created":"Oct. 12, 2023, 10:21 PM","description":"The endophytic bacterium Priestia endophytica (Bacillus endophyticus) UCM B-5715 (= DSM 13796) has been found to produce a distinctive pink pigment exhibiting vibrant yellow fluorescence. Investigation of the pigment extract revealed the presence of 2 non-polar fluorescent-colored compounds, with molecular masses of 376 (14.12%) and 410 (82.02%) a.m.u. FTIR spectroscopy indicated the characteristic signatures of heliomycin and chlorxanthomycin IR spectra, respectively. The chlorxathomycin nature of the main compound was confirmed by H1 NMR spectroscopy. Light, luminescence, and transmission electron microscopy, as well as IR and H1 NMR spectroscopy, established a close association between the colored fluorescent compounds and poly-beta-hydroxybutyrate granules. Genome analysis utilizing the antiSMASH 6.0 tool unveiled key gene sequences encoding the type II polyketide synthase complex and halogenase, involved in the biosynthesis of heliomycin and chlorxanthomycin. Given the similarity of chlorxanthomycin to heliomycin, a well-known antimicrobial, and antitumor antibiotic, this pigment might share similar properties with the potential for medical application.","fileCount":"121","fileSizeKB":"33994","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Bacillus endophyticus (NCBITaxon:135735)","instrument":"1200 series LC\\\/MSD SL;Agilent 6890N\\\/5973inert","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"chlorxanthomycin;heliomycin;Priestia endophytica;3-hydroxy-butyric acid","pi":[{"name":"Alina Kharchuk","email":"alinapoliakova212@gmail.com","institution":"D. K. Zabolotny Institute of Microbiology and Virology","country":"Ukraine"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e143df90bfec48ceb2af3dbaf2343114","id":"3459"}, {"dataset":"MSV000093090","datasetNum":"93090","title":"Janer_et_al_ESYT1_mitochondria_ER_contacts_P129","user":"gingraslab","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697139442000","created":"Oct. 12, 2023, 12:37 PM","description":"This submission contains 24 raw mass spectrometry files and associated peak lists and result files for the manuscript by Alexandre Janer et al. that describes the proximity interactors of SMP-domain containing proteins, as well as an ER marker, an outer mitochondrial membrane marker and a tether between ER and mitochondria. BioID experiments were performed from Flp-In T-REx 293 cells and MS files were acquired on TripleTOF, Orbitrap Elite and Orbitrap Velos. MassIVE submissions corresponding to SAINT 6368 have been made. Samples were generated by Kathleen Daigneault, Mari Aaltonen and Hana Antonicka, affinity purification and mass spectrometric acquisition was performed by Zhen-Yuan Lin. Analysis was performed by Hana Antonicka under the supervision of Anne-Claude Gingras. Eric A. Shoubridge (eric.shoubridge@mcgill.ca) is the corresponding authors of the manuscript; Hana Antonicka (hana.antonicka@mcgill.ca) should be contacted for questions on this dataset.","fileCount":"113","fileSizeKB":"46339549","spectra":"0","psms":"551540","peptides":"95245","variants":"122198","proteins":"47048","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"TripleTOF 5600;LTQ Orbitrap Velos;LTQ Orbitrap Elite","modification":"MOD:00684 - \\\"A protein modification that effectively converts an L-asparagine residue to L-aspartic acid.\\\";MOD:00685 - \\\"A protein modification that effectively converts an L-glutamine residue to L-glutamic acid.\\\";MOD:00719 - \\\"A protein modification that oxygenates an L-methionine residue to one of the diastereomeric L-methionine sulfoxide residues.\\\"","keywords":"BioID;proximity-dependent biotinylation;mitochondria-ER contacts;tether;SYNJ2BP;ESYT1","pi":[{"name":"Anne-Claude Gingras","email":"gingras@lunenfeld.ca","institution":"LTRI","country":"Canada"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046094","task":"240a2b46ad6a4d5c97e4a31670bc4127","id":"3460"}, {"dataset":"MSV000093089","datasetNum":"93089","title":"A translational regulatory mechanism mediated by hypusinated eukaryotic initiation factor 5A facilitates beta cell identity and function","user":"edoud","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697135636000","created":"Oct. 12, 2023, 11:33 AM","description":"As professional secretory cells, beta cells require adaptable mRNA translation to facilitate a rapid synthesis of proteins, including insulin, in response to changing metabolic cues. Specialized mRNA translation programs are essential drivers of cellular development and differentiation. However, in the pancreatic beta cell, the majority of factors identified to promote growth and development function primarily at the level of transcription. Therefore, despite its importance, the regulatory role of mRNA translation in the formation and maintenance of functional beta cells is not well defined. In this study, we have identified a translational regulatory mechanism mediated by the specialized mRNA translation factor eukaryotic initiation factor 5A (eIF5a), which facilitates the maintenance of beta cell identity and function. The mRNA translation function of eIF5A is only active when it is post-translationally modified (hypusinated) by the enzyme deoxyhypusine synthase (DHPS). We have discovered that the absence of beta cell DHPS in mice reduces the synthesis of proteins critical to beta cell identity and function at the stage of beta cell maturation, leading to a rapid and reproducible onset of diabetes. Therefore, our work has revealed a gatekeeper of specialized mRNA translation that permits the beta cell, a metabolically responsive secretory cell, to maintain the integrity of protein synthesis necessary during times of induced or increased demand.","fileCount":"13","fileSizeKB":"17821063","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Fusion Lumos","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"beta cell maturation;mRNA translation;translational regulation;beta cell development;beta cell identity;beta cell function;diabetes","pi":[{"name":"Amber L. Mosley","email":"almosley@iu.edu","institution":"Indiana University School of Medicine","country":"USA"},{"name":"Teresa Mastracci","email":"tmastrac@iu.edu","institution":"Indiana University-Purdue University-Indianapolis","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046093","task":"d01f1b552c5e49019736aaed3d86468d","id":"3461"}, {"dataset":"MSV000093088","datasetNum":"93088","title":"SaLT&PepPr is an Interface-Predicting Language Model for Designing Peptide-Guided Protein Degraders","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697118247000","created":"Oct. 12, 2023, 6:44 AM","description":"Cell lysates were adjusted to 5% SDS, and 20 ugs was reduced with 10 mM DTT and alkylated with 25 mM iodoacetamide followed by digestion with 1:15 trypsin using an S-trap at 47 degC for 1 h. Lyophilized peptides were reconstituted at 0.5 ugs\/uL, and a study pool QC sample was made by mixing equal volumes of all samples. 1.75 uL of each sample was analyzed once, interspersed with 3 replicates of the SPQC pool, using a Waters M-Class in trap-elute configuration (75 uM x 25 cm HSS-T3 analytical column at 400 nl\/min, 5-30% MeCN over 90 min) interfaced to a Thermo Exploris 480 with staggered overlapping window DIA MS analysis. Raw files were deconvoluted with .HTRMS converter (Biognosys) followed by direct-DIA and peptide\/protein quantification with Spectronaut 16 (Biognosys).","fileCount":"13","fileSizeKB":"22636554","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"data-independent acquisition","pi":[{"name":"Pranam Chatterjee","email":"pranam.chatterjee@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD046088","task":"4346c949ac044f4389452dd6e4a803c0","id":"3462"}, {"dataset":"MSV000093086","datasetNum":"93086","title":"Selective inhibition of OSBP blocks retrograde trafficking by inducing partial Golgi degradation","user":"niahedtu","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697104062000","created":"Oct. 12, 2023, 2:47 AM","description":"The dataset contains mass spectrometric raw data from two series of TMT-based expression proteomics aimed at studying the selectivity profile of oxybipin-2 and proteins affected under the treatment of OSBP inhibitors. The dataset comprises the raw data for the ITDRF of oxybipin-2 at 4 different concentrations (TMTpro, processed by Proteome Discoverer), 4 OSBP inhibitors such as C3 and OSW-1 (TMTpro, processed by Proteome Discoverer) measured on both tested-compounds and DMSO (vehicle), each collected in 30 fractions. The experiments were performed in three independent replicates for each compound (R1-R3).","fileCount":"63","fileSizeKB":"20995596","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q-Exactive HF-X (Thermo Fisher)","modification":"UNIMOD:2016 - \\\"TMTpro 16plex Tandem Mass Tag\\\"","keywords":"expression proteomics;Thermal proteome profiling;OSBP","pi":[{"name":"Luca laraia","email":"luclar@kemi.dtu.dk","institution":"Technical University of Denmark","country":"Denmark"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e21cfb07826d4819a9331dd14a1ee815","id":"3463"}, {"dataset":"MSV000093084","datasetNum":"93084","title":"Binding partners of Annexin A2 in MDA-MB-231 cells","user":"amira_mahdi","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697042243000","created":"Oct. 11, 2023, 9:37 AM","description":"A mass-spec of proteins found bound to Annexin A2 following a immunoprecipitation of Annexin A2 from cell lysate of MDAMB231 cells plated 1) on plastic or 2) on collagen-1","fileCount":"11","fileSizeKB":"100161","spectra":"0","psms":"10053","peptides":"2957","variants":"3255","proteins":"1993","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"QSTAR XL","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"breast cancer, Annexin A2, collagen","pi":[{"name":"Amira Mahdi","email":"amira.mahdi@ul.ie","institution":"Univerisity of Limerick","country":"Ireland"},{"name":"Patrick Kiely","email":"patrick.kiely@ul.ie","institution":"Univeristy of Limerick,","country":"Ireland"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"9aabbec2073143debbea46e86581ae40","id":"3464"}, {"dataset":"MSV000093083","datasetNum":"93083","title":"PHF6 cooperates with SWI\/SNF complexes to facilitate transcriptional progression","user":"mittal","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697033697000","created":"Oct. 11, 2023, 7:14 AM","description":"Genes encoding subunits of SWI\/SNF (BAF) chromatin remodeling complexes are mutated in nearly 25% of cancers. To gain insight into the mechanisms by which SWI\/SNF mutations drive cancer, we contributed ten rhabdoid tumor (RT) cell lines mutant for SWI\/SNF subunit SMARCB1 to a genome-scale CRISPR Cas9 depletion screen performed across 896 cell lines. We identify PHF6 as specifically essential for RT cell survival and demonstrate that dependency on Phf6 extends to Smarcb1-deficient cancers in vivo. As mutations in either SWI\/SNF or PHF6 can cause the neurodevelopmental disorder Coffin-Siris syndrome, our findings of a dependency suggest a previously unrecognized functional link. We demonstrate that PHF6 co-localizes with SWI\/SNF complexes at promoters, where it is essential for maintenance of an active chromatin state. We show that in the absence of SMARCB1, PHF6 loss disrupts the recruitment and stability of residual SWI\/SNF complex members, collectively resulting in the loss of active chromatin at promoters and stalling of RNA Polymerase II progression. Our work establishes a mechanistic basis for the shared syndromic features of SWI\/SNF and PHF6 mutations in CSS and the basis for selective dependency on PHF6 in SMARCB1-mutant cancers.","fileCount":"8","fileSizeKB":"7117","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Fusion","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\"","keywords":"PHF6;chromatin;SWI\/SNF;pediatric cancer;dependency","pi":[{"name":"Charles W M Roberts","email":"charles.roberts@stjude.org","institution":"St Jude Childrens Hospital","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046064","task":"3a84614d02f546a39b0bd451732478e6","id":"3465"}, {"dataset":"MSV000093082","datasetNum":"93082","title":"GNPS - Alterations in lipidome profiles distinguish early-onset hyperuricemia, gout, and the effect of urate-lowering treatment","user":"AlesKvasnicka","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1697032925000","created":"Oct. 11, 2023, 7:02 AM","description":"Background Currently, it is not possible to predict whether patients with hyperuricemia (HUA) will develop gout and how this progression may be affected by urate-lowering treatment (ULT). Our study aimed to evaluate differences in plasma lipidome between patients with asymptomatic HUA detected < 40 years (HUA<40) and > 40 years, gout patients with disease onset < 40 years (Gout<40) and > 40 years, and normouricemic healthy controls (HC).\r\n\r\nMethods Plasma samples were collected from 94 asymptomatic HUA (77% HUA<40) subjects, 196 gout patients (59% Gout<40), and 53 HC. A comprehensive targeted lipidomic analysis was performed to semi-quantify 608 lipids in plasma. Univariate and multivariate statistics and advanced visualizations were applied.\r\n\r\nResults Both HUA and gout patients showed alterations in lipid profiles with the most significant upregulation of phosphatidylethanolamines and downregulation of lysophosphatidylcholine plasmalogens\/plasmanyls. More profound changes were observed in HUA<40 and Gout<40 without ULT. Multivariate statistics differentiated HUA<40 and Gout<40 groups from HC with an overall accuracy of > 95%.\r\n\r\nConclusion Alterations in the lipidome of HUA and Gout patients show a significant impact on lipid metabolism. The most significant glycerophospholipid dysregulation was found in HUA<40 and Gout<40 patients, together with a correction of this imbalance with ULT.\r\nKeywords LC-MS, Lipidomics, Glycerophospholipids, Hyperuricemia, Gout, Urate-lowering treatment\r\n\r\nStudy was published and is accessible under this DOI: https:\/\/doi.org\/10.1186\/s13075-023-03204-6\r\n\r\nPlease cite as follows: Kvasni?ka, A., Friedecký, D., Brumarová, R. et al. Alterations in lipidome profiles distinguish early-onset hyperuricemia, gout, and the effect of urate-lowering treatment. 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We set out to find specific metabolomic biomarkers of oxidative stress and we developed a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionisation technique for mass spectrometry, laser-desorption rapid evaporative ionisation mass spectrometry (LD-REIMS). We demonstrate the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100 % accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrate that HOCl stress impacted the Pseudomonas Quinolone Signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were significantly reduced in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors. ","fileCount":"4153","fileSizeKB":"10648689","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Pseudomonas aeruginosa UCBPP-PA14 (NCBITaxon:208963)","instrument":"Xevo G2-S QTof","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"Pseudomonas aeruginosa;LD-REIMS;quorum sensing;oxidative stress","pi":[{"name":"Huw Williams","email":"h.d.williams@imperial.ac.uk","institution":"Imperial College London","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3d7cadeff0e34a1aa4df10ce705e0162","id":"3484"}, {"dataset":"MSV000093054","datasetNum":"93054","title":"Proteomics of human peripheral blood mononuclear cells under normal circadian cycle and under a simulated night shift","user":"alchemistmatt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696564902000","created":"Oct. 5, 2023, 9:01 PM","description":"Proteomic data from human peripheral blood mononuclear cells (PBMCs). Samples taken over a 24 hour constant light and diet following 3 days of normal day shift cycle or a night shift - circadian misaligned schedule where sleep and wake cycles were reversed. Time points (in clock time) 1, 7, 14, 21 hours; 6 volunteers for each condition. Samples were digested with trypsin, then analyzed by LC-MS\/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline.","fileCount":"249","fileSizeKB":"60467349","spectra":"0","psms":"2091314","peptides":"689678","variants":"795947","proteins":"39408","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Q Exactive Plus","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"circadian misalignment;shift work","pi":[{"name":"Jason E. McDermott","email":"Jason.McDermott@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD045923","task":"c56797047aed470180fa0306d0eaa7d3","id":"3485"}, {"dataset":"MSV000093052","datasetNum":"93052","title":"H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in paediatric high-grade glioma cells","user":"majewski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696536727000","created":"Oct. 5, 2023, 1:12 PM","description":"Diffuse intrinsic pontine gliomas (DIPG) are a deadly paediatric brain tumours, non-resectable due to brainstem localisation and diffusive growth. Patients with DIPG have a dismal prognosis of 9-12 months of survival with no effective therapy. Over 80% of DIPGs harbour a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine to methionine substitution (H3K27M). H3K27M causes global epigenetic alterations (a loss of H3K27 trimethylation and an increase in H3K27 acetylation) resulting in aberrant gene expression. To date, no therapeutic strategy exists to suppress the levels of oncogenic H3K27M.\nWe show that pan-HDAC inhibitors (HDACi) lead to the temporary but significant reduction in the H3.33K27M protein (up to 80%) in multiple glioma cell lines expressing the H3.3K27M histone variant, without changes in the H3F3A mRNA expression. The H3.3K27M occupancy at the chromatin is greatly reduced upon HDACi (SB939) treatment, as shown by ChIPseq analysis. H3.3K27M loss is most striking at SB939-upregulated genes suggesting the role in repression of these genes. In addition, genes previously reported as H3K27M-dependent become downregulated in response to SB939 treatment. We discover that the SB939-mediated loss of H3.3K27M is partially blocked by a lysosomal inhibitor, chloroquine. Moreover, the loss of H3.3K27M is facilitated by co-occurrence of H2A.Z, as evidenced by the knock-down of H2A.Z histone isoforms. ChIPseq analysis confirms the occupancy of H3.3K27M and H2A.Z at the same SB939-inducible genes.\nAltogether, we provide new insight into disease-specific mechanism of HDAC inhibition and demonstrate pharmacological modulation of the oncogenic H3.3K27M protein levels. These findings open a new possibility to directly target the H3.3K27M oncohistone, which may be exploited in future therapies.\n\n","fileCount":"39","fileSizeKB":"24895595","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"H3.3K27M;H2A.Z;HDAC inhibitors;DIPG;paediatric high-grade gliomas ","pi":[{"name":"Jacek Majewski","email":"jacek.majewski@mcgill.ca","institution":"McGill University Genome Centre","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD045917","task":"3782c2c1dcf74f4685e1d6ec59f97142","id":"3486"}, {"dataset":"MSV000093051","datasetNum":"93051","title":"A carboxy-terminal ubiquitylation site regulates androgen receptor activity","user":"mnouri","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696533231000","created":"Oct. 5, 2023, 12:13 PM","description":"Immunoprecipitated androgen receptor from vehicle and dihydrotestosterone treated VCaP cells was run on SDS-PAGE and bands corresponding to unmodified AR ~110kD (\"DN\") and an area above ~125 kD (UP) were excised. Gel fragments were treated with trypsin and eluted proteins were analyzed by microcapillary reversed-phase (C18) liquid chromatography-tandem mass spectrometry (LC-MS\/MS).","fileCount":"18","fileSizeKB":"955877","spectra":"0","psms":"284","peptides":"51","variants":"136","proteins":"1","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"LTQ Orbitrap XL","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:121 - \\\"Ubiquitinylation residue.\\\"","keywords":"prostate cancer;androgen receptor;VCaP cells","pi":[{"name":"Steven P. Balk","email":"sbalk@bidmc.harvard.edu","institution":"Beth Israel Deaconess Medical Center\/Harvard Medical School","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"eee182d7b705438390f1301f6c91275e","id":"3487"}, {"dataset":"MSV000093049","datasetNum":"93049","title":"Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation","user":"majewski","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696523499000","created":"Oct. 5, 2023, 9:31 AM","description":"Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its demonstrated importance in development, disease, and cancer, the molecular agents responsible for the deposition of H3K36me are not yet well understood. Here, we use a mouse mesenchymal stem cell model to comprehensively perturb the components of the H3K36me deposition machinery and infer the activities of the five most prominent players: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and that it is predominantly deposited at intergenic regions by NSD1, and in part by NSD2. In contrast, H3K36me1\/3 are most abundant within exons and have a positive correlation with gene expression. We further demonstrate that while SETD2 is responsible for depositing most H3K36me3, it also deposits a modest amount of H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting that other H3K36 methyltransferases may prime gene bodies with lower methylation states ahead of transcription. Through a reductive approach, we uncover the genome-wide distribution patterns of NSD3- and ASH1L-catalyzed H3K36me2. While NSD1\/2 establish broad intergenic H3K36me2 domains, NSD3 deposits broad H3K36me2 peaks centered on active promoter and enhancer regions. Meanwhile, the activity of ASH1L is focused primarily on the promoters of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor for ASH1L to these regions. Overall, our study provides new insights into the regulation of H3K36me by the H3K36 methyltransferase family and helps to consolidate the wealth of previous observations in the context of a structured analysis.","fileCount":"35","fileSizeKB":"34424093","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus musculus (NCBITaxon:10090)","instrument":"Orbitrap Exploris 240","modification":"UNIMOD:37 - \\\"Tri-Methylation.\\\";UNIMOD:36 - \\\"Di-Methylation.\\\";UNIMOD:34 - \\\"Methylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"H3K36me;Epigenetic;methylation","pi":[{"name":"Jacek Majewski","email":"jacek.majewski@mcgill.ca","institution":"Department of Human Genetics, McGill University","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD045915","task":"1dc5f6891e9c426480a5c31ac2fc6702","id":"3488"}, {"dataset":"MSV000093047","datasetNum":"93047","title":"Chlorpyrifos induces autophagy in murine GnRH neurons by repressing the mTOR pathway and affecting androgen and estrogen alpha\/beta receptor expression","user":"Marialuisa_PX","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696506389000","created":"Oct. 5, 2023, 4:46 AM","description":"Chlorpyrifos (CPF) is a widely used pesticide inducing neurodevelopmental and reproductive adverse effects. Little is known about the underlying mechanisms, especially in hypothalamus. We investigated CPF mode of action at human relevant concentrations (1 nM_100 nM) in immortalized murine hypothalamic GnRH neurons (GT1_7), an elective model to study central derangement of the hypothalamus_pituitary_gonads (HPG) axis. Treated cells were examined for cell vitality, proliferation, spheroid morphology, apoptosis, neuron functionality, gene expression, Transmission Electron Microscopy, immunoreactivity and proteomics profiles. CPF dose_dependently decreased cell vitality. At 100 nM, CPF induced autophagy and mitochondria damage, and inhibited GnRH gene expression and secretion. Spheroid morphology was impaired and immunoreactivity of MAP2 neuron marker decreased with the dose. Estrogen Receptor alpha and beta (ERalpha, ERbeta), Androgen Receptor (AR), aromatase and oxytocin receptor gene expression was non_monotonically induced by CPF but with different patterns. The differentially expressed proteins enriched the Autophagy, mTOR signaling and Neutrophil extracellular trap (NET) formation pathways, supported by the dose_dependent decrease of mTOR immunoreactivity. A core module of interacting proteins featuring ERalpha_AR_mTOR and proteins of the NET pathway was identified. Overall, our results support CPF as inhibitor of the mTOR pathway, possibly involving ERalpha_AR signaling, leading to autophagy of GnRH neurons, thus raising concern on possible adverse effects on HPG axis. 30ug of proteins were subjected to a bottom_up proteomics workflow: in the fist step they were treated with TCEP and IAM, for the reduction and alkylation of the cysteines, respectively. Then, proteins were precipitated using a solution of methanol, acetone and ethanol (25, 25 and 50 v_v) at minus 20C over_night and after a centrifugation at maximum speed for 15 min at 4C the resulting pellet was resuspended in urea and ammonium bicarbonate and the proteins were digested adding trypsin, at a substrate to enzyme (S_E) ratio of 50 (w_w) for 16 h at 37 C on Thermo Mixer heat block. The day after, formic acid was added to block digestion and 20uL of the resulting peptide mixture was injected in an Ultimate 3000 UHPLC coupled with an Orbitrap Fusion Tribrid mass spectrometer. Peptides were desalted on a trap column and then separated on a 45cm long silica capillary, packed in house with a C18, 1,9um, 100 A resin. The analytical column was encased by a column oven (Sonation, 40C during data acquisition) and attached to a nanospray flex ion source. Peptides were separated on the analytical column by running a 180 min gradient of buffer A (95water, 5acetonitrile, and 0,1 formic acid) and buffer B (95acetonitrile, 5 water, and 0,1 formic acid), at a flow rate of 250 nl min. The mass spectrometer was operated in positive ion mode and precursor ion scanning was performed in the Orbitrap analyzer (FTMS; Fourier Transform Mass Spectrometry) in the scan range of m_z 350 1550 with 120K resolution. Data_dependent acquisition was performed in top_speed mode (3 s long maximum total cycle): the most intense precursors were selected through a monoisotopic precursor selection (MIPS) filter and with charge greater than1, quadrupole isolated and fragmented by higher energy collision dissociation (HCD) (30 collision energy). Product ion spectra were recorded in the ion trap (ITMS) with a rapid scan rate. Peptide spectra were searched in Proteome Discoverer 2,4 (Thermo Fisher Scientific) using Sequest HT as search engine against Mus Musculus database from UniProtKB_Swiss_Prot (Release 2022; 17090 sequences). Spectral matches were filtered using Percolator node, based on q values, with 0.01 false discovery rate (FDR), based on a target_decoy approach. Only master proteins were taken into account and only specific trypsin cleavages with two miscleavages were admitted. Cysteine carbamydomethylation was set as static modification, while methionine oxidation and N_acetylation on protein terminus were set as variable modifications. Precursor mass tolerance was set to 15 ppm while the MS_MS match tolerance was set 0.6 Da. Quantification was based on precursor intensity of unique and razor peptides using match between runs option.","fileCount":"14","fileSizeKB":"97948605","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Mus Musculus","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"GT1_7 cell line;LC_MS_MS;Chlorpyrifos (CPF);hypothalamus pituitary gonads (HPG) axis; proteomics","pi":[{"name":"Marialuisa Casella","email":"marialuisa.casella@iss.it","institution":"Istituto Superiore Sanita","country":"Italy"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD045909","task":"c3874552fde84f828df47fe39ff089ef","id":"3489"}, {"dataset":"MSV000093046","datasetNum":"93046","title":"CSF shotgun proteomics in human sCAA patients","user":"marcvervuurt","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696495727000","created":"Oct. 5, 2023, 1:48 AM","description":"This project utilized a timsTOF Pro instrument (Bruker) and applied a data independent acquisition (DIA) method, followed by spectral analysis in PaSER (Bruker) to study proteomic changes in the cerebrospinal fluid of sporadic cerebral amyloid angiopathy patients. Results revealed distinct differentially expressed proteins in sCAA patients.","fileCount":"1475","fileSizeKB":"48553292","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"timsTOF Pro","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"cerebral amyloid angiopathy","pi":[{"name":"Marcel Verbeek","email":"marcel.verbeek@radboudumc.nl","institution":"Radboud University Medical Center","country":"the Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f66744f3ef374a87b003ef9ad039eac2","id":"3490"}, {"dataset":"MSV000093045","datasetNum":"93045","title":"GNPS - Eva and Anil first test - polymer contaminations","user":"oloap1","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696488291000","created":"Oct. 4, 2023, 11:44 PM","description":"Non-target metabolomics of environmental samples using Methanol extraction. ","fileCount":"21","fileSizeKB":"2589246","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"environmental samples (NCBITaxon:33858)","instrument":"Q Exactive HF","modification":"MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"quinones;ferrihydrite-organic carbon","pi":[{"name":"Daniel Petras","email":"daniel.petras@uni-tuebingen.de","institution":"UNiversity of Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4c84337dc3e9447a9d349b07bfb52e1b","id":"3491"}, {"dataset":"MSV000093044","datasetNum":"93044","title":"Proteome analysis of epithelial-mesenchymal transition extracellular vesicles: exosomes, microparticles and shed midbody remnants","user":"dwgree","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696477472000","created":"Oct. 4, 2023, 8:44 PM","description":"Cell-derived extracellular vesicles (EVs) are evolutionary-conserved secretory organelles that, based on their molecular composition, are important intercellular signaling regulators. At least three classes of circulating EVs are known based on mechanism of biogenesis: exosomes (sEVs\/Exos), microparticles (lEVs\/MPs) and shed midbody remnants (lEVs\/sMB-Rs). Here we conducted large-scale purification of exosomes, MPs and sMBRs isolated from MDCK and 21D1 cells, and performed comprehensive proteomics analysis to differentiate these EV subtypes. Findings from this study suggests that sMBRs may hold crucial clues to the regulation of EMT and the involvement of different subtypes of EVs based on their dynamic proteome landscape in this process.","fileCount":"21","fileSizeKB":"19059256","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Canis lupus familiaris (NCBITaxon:9615)","instrument":"Q Exactive HF-X","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"extracellular vesicles;proteomics;subtypes;shed midbody remnants; epithelial-mesenchymal transition","pi":[{"name":"David Greening","email":"david.greening@baker.edu.au","institution":"Baker Heart & Diabetes Institute","country":"Australia"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3ad3b9f115244953bbf0725cfa6bee03","id":"3492"}, {"dataset":"MSV000093043","datasetNum":"93043","title":"Cerebrospinal fluid proteome of patients with persistent pain and\/or postpartum depression after elective caesarean delivery: An exploratory prospective cohort study","user":"mwfoster","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696472708000","created":"Oct. 4, 2023, 7:25 PM","description":"CSF was pooled to make a study-specific QC (SPQC) sample. 500 uL of each sample was lyophilized and reconstituted in 8M urea followed by reduction\/alkylation, trypsin digestion and solid phase extraction. After lyophilization, reconstituted peptides were separated by direct injection, microflowLC (1 mm ACQUITY Premier column, 100 uL\/min, 60 min gradient) with post-column DMSO (3%) and interfaced to an Exploris 480 using a HESI source. MS\/MS analysis used a staggered\/overlapping DIA method. Additional SPQC sample was fractionated by HPRP, and 12 fractions were analyzed by microflow-DDA. A hybrid spectral library was built, and data analyzed using Spectronaut.","fileCount":"88","fileSizeKB":"120960414","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Orbitrap Exploris 480","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"CSF;Data-independent acquisition;microflow","pi":[{"name":"Mary Yurashevich","email":"mary.yurashevich@duke.edu","institution":"Duke University","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD045906","task":"9b91a8267b274f078c75b476803bface","id":"3493"}, {"dataset":"MSV000093041","datasetNum":"93041","title":"CPTAC CCRCC Discovery Study - DIA Proteome","user":"cptac","site":"massive.ucsd.edu","flowname":"MASSIVE-COMPLETE","createdMillis":"1696460449000","created":"Oct. 4, 2023, 4:00 PM","description":"This is a supplementary study to the CPTAC CCRCC Discovery Study - Proteome. Unlabeled, digested peptide material from individual tissue samples (ccRCC and NAT) was spiked with index Retention Time (iRT) peptides (Biognosys) and subjected to data-independent acquisition (DIA) analysis.\n\nKidney cancer is among the 10 most common cancers in both men and women and each year there are approximately 60,000 new cases with over 14,000 deaths (NCI, Surveillance, Epidemiology and End Results (SEER) Program<\/a>). Several histological and molecular subtypes have been identified and clear cell renal cell carcinoma (CCRCC) is the most prevalent (Hsieh el al., 2017 Nat Rev Dis Primers<\/a>). To advance the proteogenomic understanding of CCRCC, the CPTAC program has investigated 110 tumors (CPTAC discovery cohort) and subjected these samples to global proteome and phosphoproteome analysis. An optimized workflow for mass spectrometry of tissues using isobaric tags (TMT (tandem mass tags)-10) was used (Mertins et al., Nature Protocols 2018<\/a>). Proteome and phosphoproteome data from the CCRCC tumors is available below along with peptide spectrum analyses (PSMs) and protein summary reports from the CPTAC common data analysis pipeline (CDAP).\n\nClinical data is provided. Additional attributes along with genotypes will be available as cohort characterization proceeds.\n\nGenomic data will be available from the NCI Genomic Data Commons.\n\nNote: Sample-wise assessment of genomic profiles in this cohort identified seven tumor samples with molecular aberrations atypical for ccRCC. While these seven non-ccRCC samples (C3L-00359-01, C3N-00313-03, C3N-00435-05, C3N-00492-04, C3N-00832-01, C3N-01175-01, C3N-01180-01) and their corresponding NATs (C3N-00435-06, C3N-00492-05, C3N-01175-05) were excluded from the ccRCC cohort in all downstream analyses, the non-ccRCC samples served as useful controls to highlight ccRCC-specific features. These seven samples were therefore annotated as non-ccRCC samples.<\/em>\n\n