{ "datasets" : [ {"dataset":"MSV000095855","datasetNum":"95855","title":"Cardiolipin from bovine heart authentic standard analysed in negative mode","user":"JarmoK","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"0"}, {"dataset":"MSV000095853","datasetNum":"95853","title":"RiPP Low pH metal Competition_09122024 ","user":"aronlabshared","site":"MassIVE","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":"6","fileSizeKB":"187557","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"1"}, {"dataset":"MSV000095847","datasetNum":"95847","title":"Fasting is required for many benefits of calorie restriction ","user":"babygirija","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1726149627000","created":"Sep. 12, 2024, 7:00 AM","description":"Targeted metabolomics of brain after feeding regimens","fileCount":"62","fileSizeKB":"21438389","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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","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":"2"}, {"dataset":"MSV000095844","datasetNum":"95844","title":" Specialized metabolome seed coat\/endosperm and seed embryo of Arabidopsis thaliana","user":"macorso","site":"MassIVE","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","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":"3"}, {"dataset":"MSV000095843","datasetNum":"95843","title":"Untargeted metabolomic analysis in Brassica napus seed coat\/endosperm and embryo - GNPS","user":"macorso","site":"MassIVE","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":"MS:1002666","modification":"MS:1002864","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":"4"}, {"dataset":"MSV000095842","datasetNum":"95842","title":"Specific redox and iron homeostasis responses in the root tip of Arabidopsis upon zinc excess","user":"stephINRAE","site":"MassIVE","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. \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). \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. \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":"MS:1002666","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":"5"}, {"dataset":"MSV000095826","datasetNum":"95826","title":"IQ-1687 10\/SEPT\/2024 Aspergillus spp","user":"albertopardo97","site":"MassIVE","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","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":"6"}, {"dataset":"MSV000095819","datasetNum":"95819","title":"20240909_piperamides_standards","user":"Tito_Damiani","site":"MassIVE","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":"MS:1003112","modification":"MS:1002864","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":"7"}, {"dataset":"MSV000095811","datasetNum":"95811","title":"Chesneau_et_al_MetaFlowTrain_Exometabolites","user":"sperin","site":"MassIVE","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). \nThere are four folders:\n - \"221208_Guillaume_Chambers_AA\"\n - \"221208_Guillaume_Chambers_TCA&Gly\"\n - \"230530_Guillaume_Chambers_AA\"\n - \"230530_Guillaume_Chambers_TCA&Gly\".\nData in the folders from 221208 were used to build Figure 2, while data from 230530 were used for Figures 3 and 4. \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":"8"}, {"dataset":"MSV000095808","datasetNum":"95808","title":"hoihhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh","user":"KecskemetiGabor2","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1725859108000","created":"Sep. 8, 2024, 10:18 PM","description":"jkdbcsfal baulsgfsdagfzcakv chsjadvfhsadvbchjdkashzjgsykzbsalvubsak","fileCount":"31","fileSizeKB":"11806899","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003094","modification":"MS:1002864","keywords":"izfzurbdbjtzdbjz","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":"6947a81f0a5e4303b4b948c9d4e6d056","id":"9"}, {"dataset":"MSV000095805","datasetNum":"95805","title":"DOM samples from experimental Kelp cultures as well as symbiont culture extracts","user":"JarmoK","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1725749887000","created":"Sep. 7, 2024, 3:58 PM","description":"Nontargeted ESI-MS data from DOM extracts of laboratory cultures of kelp specimens, as well as kelp microbial symbiont extracts","fileCount":"297","fileSizeKB":"38762679","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003028","modification":"MS:1002864","keywords":"Kelp;DOM;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":"d4277d1a25d945ce88dba73a1cd2596b","id":"10"}, {"dataset":"MSV000095803","datasetNum":"95803","title":"Plant extracts received from Malaga and run in August 2024","user":"JarmoK","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"11"}, {"dataset":"MSV000095802","datasetNum":"95802","title":"Using conserved protein to mRNA ratios across kingdoms to enhance microbial functional predictions","user":"Mengshi","site":"MassIVE","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. ","fileCount":"432","fileSizeKB":"107191432","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 ATCC 33277 (NCBITaxon:431947);Streptococcus gordonii str. Challis substr. 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","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":"12"}, {"dataset":"MSV000095801","datasetNum":"95801","title":"2024 09 04 Alexandre TRONEL PAPER 1","user":"alegouellec","site":"MassIVE","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. ","fileCount":"132","fileSizeKB":"3339828","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":"Intestinal liquid","pi":[{"name":"LE GOUELLEC AUDREY","email":"alegouellec@chu-grenoble.fr","institution":"UGA","country":"FRANCE"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"eda38a6dc78c4e54a1719dd94420d65f","id":"13"}, {"dataset":"MSV000095799","datasetNum":"95799","title":"Data_Cempasuchil_Tagetes_erecta_Extract_Mexico","user":"Lucho","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1725686790000","created":"Sep. 6, 2024, 10:26 PM","description":" ESI-QTOF data from Cempasuchil Tagetes erecta Root Extract Mexico","fileCount":"7","fileSizeKB":"291406","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002786","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":"995453f84d194d9b8d195398374b3e6e","id":"14"}, {"dataset":"MSV000095791","datasetNum":"95791","title":"Cempasuchil_(Tagetes_erecta)_Root_Extract_Mexico","user":"Lucho","site":"MassIVE","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":"MS:1002786","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":"15"}, {"dataset":"MSV000095790","datasetNum":"95790","title":"MS MS MS for Liu group jingjie","user":"huzhijuan","site":"MassIVE","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","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":"16"}, {"dataset":"MSV000095789","datasetNum":"95789","title":"GNPS - Pooled Chemical Standard (DDA & Full-scan)","user":"spxing","site":"MassIVE","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":"17","fileSizeKB":"1994616","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"17"}, {"dataset":"MSV000095787","datasetNum":"95787","title":"GNPS - NIST Reference Human Feces","user":"spxing","site":"MassIVE","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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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":"37"}, {"dataset":"MSV000095719","datasetNum":"95719","title":"Japan waterproof products and sludge samples for PFAS analysis","user":"Bing","site":"MassIVE","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":"45","fileSizeKB":"20009193","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"38"}, {"dataset":"MSV000095718","datasetNum":"95718","title":"GNPS - Refractory DOM Characterization","user":"ikoester","site":"MassIVE","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","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":"39"}, {"dataset":"MSV000095716","datasetNum":"95716","title":"Hepatic stellate cells isolated from PBS- or thioacetamide (TAA)-treated wild-type and Cyp1b1 knockout ","user":"haihaba","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"40"}, {"dataset":"MSV000095712","datasetNum":"95712","title":"GNPS - Terrestrial DOM Indonesia peatland 2024","user":"ikoester","site":"MassIVE","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":"295","fileSizeKB":"33481592","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"41"}, {"dataset":"MSV000095708","datasetNum":"95708","title":"GNPS - Bolnick Alaska Experimental Evolution (2023) - PRJ1","user":"marwa38","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"42"}, {"dataset":"MSV000095706","datasetNum":"95706","title":"GNPS - Temperature induced lipidomic alterations","user":"VdL_VdL","site":"MassIVE","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":"MS:1002582","modification":"MS:1002864","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":"43"}, {"dataset":"MSV000095704","datasetNum":"95704","title":"GNPS - Long Island Sound PFAS Effects on Fish - PRJ2","user":"marwa38","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"44"}, {"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","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":"MS:1003094","modification":"MS:1002864","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":"45"}, {"dataset":"MSV000095702","datasetNum":"95702","title":"TO_DELETE GNPS - Long Island Sound PFAS Effects on Fish - PRJ2","user":"marwa38","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1724737764000","created":"Aug. 26, 2024, 10:49 PM","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":"228","fileSizeKB":"18012586","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003094","modification":"MS:1002864","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":"a5582fe487044f1c8af7bb634c238525","id":"46"}, {"dataset":"MSV000095695","datasetNum":"95695","title":"Internalization of therapeutic antibodies into Dendritic cells as a risk factor for immunogenicity","user":"ducreta","site":"MassIVE","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":"77","fileSizeKB":"49061715","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002877","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":"47"}, {"dataset":"MSV000095687","datasetNum":"95687","title":" Multiomics Profiling of Extracellular Vesicles Supports Their Involvement in Endothelial Senescence-Associated Vascular Dysfunction","user":"gabrig","site":"MassIVE","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. ","fileCount":"3","fileSizeKB":"77657199","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003005","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\"","keywords":": Endothelial cells, miRNAseq, extracellular vesicles, proteomics, senescence","pi":[{"name":"Pamela J. 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":"48"}, {"dataset":"MSV000095680","datasetNum":"95680","title":"E. coli leverages growth arrest to remodel its proteome upon entry into starvation","user":"trendsetter","site":"MassIVE","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":"MS:1003028;MS:1003029","modification":"MS:1002864","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":"49"}, {"dataset":"MSV000095673","datasetNum":"95673","title":"mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation ","user":"RouhanifardLab","site":"MassIVE","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":"5","fileSizeKB":"5598109","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","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":"50"}, {"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","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. 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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":"MS:1003094","modification":"MS:1002864","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":"69"}, {"dataset":"MSV000095616","datasetNum":"95616","title":"GNPS Too Much Botrytis Co-culture","user":"smata","site":"MassIVE","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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Investigating the type of metal this binds is key","fileCount":"13","fileSizeKB":"428378","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 Spectrometer","modification":"MS:1002864","keywords":"RiPP, 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":"770020f80fbf434aa1a5ecf9176972d8","id":"74"}, {"dataset":"MSV000095597","datasetNum":"95597","title":"GNPS - Voacanga_africana bark alkaloid extract","user":"mbeniddir","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1723638739000","created":"Aug. 14, 2024, 5:32 AM","description":"LC-MS\/MS analysis of the bark alkaloid extract of Voacanga africana","fileCount":"2","fileSizeKB":"86223","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Voacanga africana (NCBITaxon:141630)","instrument":"MS:1002786","modification":"MS:1002864","keywords":"Alkaloids, Indoles, Apocynaceae, Voacanga africana","pi":[{"name":"Mehdi Beniddir","email":"mehdi.beniddir@universite-paris-saclay.fr","institution":"Universite Paris-Saclay","country":"France"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d4600a6e5fa94c928fcc419343e33cf3","id":"75"}, {"dataset":"MSV000095596","datasetNum":"95596","title":"GNPS - Pleiocarpa_mutica bark alkaloid extract","user":"mbeniddir","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1723630841000","created":"Aug. 14, 2024, 3:20 AM","description":"LC-MS\/MS analysis related to Pleiocarpa mutica bark alkaloid extract. 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This is a part of ICMR, New Delhi, India, sanctioned project titled Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits. 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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":"MS:1003029","modification":"MS:1002864","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":"79"}, {"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","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":"80"}, {"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","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":"MS:1002877","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":"81"}, {"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","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":"MS:1000122","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":"82"}, {"dataset":"MSV000095568","datasetNum":"95568","title":"Scnn1b transgenic mice: BALF exosome proteomics","user":"maomaobio_316","site":"MassIVE","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. 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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). [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","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":"84"}, {"dataset":"MSV000095564","datasetNum":"95564","title":"Endophytic fungi of Calea pinnatifida","user":"BiaBarna","site":"MassIVE","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","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":"85"}, {"dataset":"MSV000095560","datasetNum":"95560","title":"Lipid Supplements Protect Dilated Cardiomyopathy","user":"dwgree","site":"MassIVE","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":"68","fileSizeKB":"62567221","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002877","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":"86"}, {"dataset":"MSV000095559","datasetNum":"95559","title":"Label-free global proteome profiling of European American and African American bladder tumor patients.","user":"syjung","site":"MassIVE","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":"MS:1002634","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":"87"}, {"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","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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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":"29","fileSizeKB":"12716903","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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","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":"95"}, {"dataset":"MSV000095540","datasetNum":"95540","title":"GNPS - Bolnick Alaska Experimental Evolution (2024) - PRJ7","user":"marwa38","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"96"}, {"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","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","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":"97"}, {"dataset":"MSV000095536","datasetNum":"95536","title":"GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - LC-MS2 dataset ","user":"JRapp","site":"MassIVE","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). Therefore, we created a sorted CRISPRi library targeting all 1,515 metabolic genes in the most recent genome-scale metabolic model of E. coli (iML1515). 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. ","fileCount":"120","fileSizeKB":"171316004","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","keywords":"E. coli;CRISPRi;Targeted Metabolomics;LC-MS2 spectra","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":"03bd4b112d1e4bab9ff1b1d13bd42e8c","id":"98"}, {"dataset":"MSV000095535","datasetNum":"95535","title":"CoV 3'UTR cis-acting element interactome","user":"hwunchu","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1723015383000","created":"Aug. 7, 2024, 12:23 AM","description":"Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS\/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biological processes derived from analysis of interactome and the replication efficiency.","fileCount":"107","fileSizeKB":"5955565","spectra":"0","psms":"79160","peptides":"7377","variants":"7927","proteins":"1580","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Coronavirus BCoV\\\/PB675\\\/Art_lit\\\/PAN\\\/2011 (NCBITaxon:1269292)","instrument":"TripleTOF 6600","modification":"MS:1002864","keywords":"coronavirus","pi":[{"name":"Hung-Yi Wu","email":"hwu2@dragon.nchu.edu.tw","institution":"National Chung Hsing University","country":"Taiwan"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD054657","task":"b8317d2ed4cf448087038d21a1631f74","id":"99"}, {"dataset":"MSV000095534","datasetNum":"95534","title":"GNPS - A metabolism-wide CRISPRi library expands the measurable E. coli metabolome - FI-MS dataset","user":"JRapp","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1723014634000","created":"Aug. 7, 2024, 12:10 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 (iML151515). 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.","fileCount":"3061","fileSizeKB":"2091191940","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","keywords":"E. coli;CRISPRi;flow-injection mass spectrometry","pi":[{"name":"Prof. Hannes Link","email":"hannes.link@uni-tuebingen.de","institution":"University Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"8c638ee516e441d28a3f1a277ffc722b","id":"100"}, {"dataset":"MSV000095531","datasetNum":"95531","title":"PNACIC LC-IMS-MS\/MS Internal Standards","user":"smcolby","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1722993362000","created":"Aug. 6, 2024, 6:16 PM","description":"Samples containing stable isotope-labeled internal standards added to plasma and liver samples. Standards were obtained from a mix of NIH standards representing nine metabolite classes and the QreSS kit from Cambridge Isotope Laboratories (MA, USA). The samples were chromatographically separated using hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) chemistries in separate injections. The LC system was coupled to an Agilent 6560 ion mobility quadrupole time of flight mass spectrometer (Agilent Technologies, CA, USA), and the standards were analyzed in both positive and negative ionization mode. The MS\/MS data were acquired at collision energies of 10, 20, and 40eV using an all-ions fragmentation approach with frames alternating between high and low fragmentation using a mass range of 50-1500 m\/z.","fileCount":"26","fileSizeKB":"39927469","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002792","modification":"MS:1002864","keywords":"internal standards;isotope labeled;liquid chromatography;ion mobility spectrometry;tandem mass spectrometry","pi":[{"name":"Thomas O. Metz","email":"thomas.metz@pnnl.gov","institution":"Pacific Northwest National Laboratory","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f40fb2d5e375497fb3b0103b95d84602","id":"101"}, {"dataset":"MSV000095529","datasetNum":"95529","title":"GNPS - Cardiomyocyte-specific NAMPT Knockout Mice: Untargeted Metabolomics from Heart Ventricle Tissues (dataset1)","user":"Khanh_UPenn_Baur","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1722973717000","created":"Aug. 6, 2024, 12:48 PM","description":"Untargeted metabolomics from heart ventricular tissues of wild-type (WT) and cardiomyocyte-specific conditional NAMPT knockout (KO) mice, 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":"19","fileSizeKB":"679017","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002634","modification":"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":"5588f23f1f92486693f62c6d3b4493ef","id":"102"}, {"dataset":"MSV000095525","datasetNum":"95525","title":"Si11 - standards mixture to test annotation of ISF features","user":"raimofranke","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1722953684000","created":"Aug. 6, 2024, 7:14 AM","description":"A mixture of 11 compounds (2-methoxybenzoic acid, biochanin A, trans-ferulic acid, 3-indoleacetonitrile, indole-3-carboxaldehyd, kaempferol, kinetin, p-coumaric acid, L-(+)-alpha-phenylglycine, phloridzin dihydrate, rutin trihydrate) each at a concentration of 20 µM was prepared in a 1:1 mixture of acetonitrile and water.\r\n\r\n1 µl of the Si11-mixture was analyzed by reversed phase ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry multiple times. 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. The sample was analyzed by positive mode electrospray ionization quadrupole time-of-flight mass spectrometry on a maXis HD QTOF (Bruker, Bremen, Germany) using data-dependent MS\/MS by collision-induced dissociation of the three most abundant ions in each scan, making use of Bruker\u2019s \u201CSmart Exclusion\u201D functionality to minimize multiple fragmentation of the same ion. Accurate masses were obtained by internal calibration using an ion cluster of sodium formate and lock mass calibration. \r\n\r\n","fileCount":"8","fileSizeKB":"175132","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"pure standards mixture","instrument":"MS:1003004","modification":"MS:1002864","keywords":"standards","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":"9d66d007facc4a7ca081d9b6346cde4e","id":"103"}, {"dataset":"MSV000095524","datasetNum":"95524","title":"LC-MS\/MS analysis of the purified Ceres protein","user":"Anton_Stepnov","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1722941629000","created":"Aug. 6, 2024, 3:53 AM","description":"LC-MS\/MS analysis of the purified recombinantly produced Ceres protein: raw spectrum file","fileCount":"2","fileSizeKB":"595858","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Galleria mellonella (NCBITaxon:7137)","instrument":"RSLCnano UHPLC\\\/Q-Exactive ","modification":"carbamidomethyl cysteine ","keywords":"Ceres hexamerin","pi":[{"name":"Anton Stepnov","email":"anton.stepnov@nmbu.no","institution":"NMBU","country":"Norway"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"517336e6127a466592dba48ce4d93290","id":"104"}, {"dataset":"MSV000095522","datasetNum":"95522","title":"CoV 3'UTR cis-acting element interactome","user":"hwunchu","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1722931215000","created":"Aug. 6, 2024, 1:00 AM","description":"Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS\/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biological processes derived from analysis of interactome and the replication efficiency.","fileCount":"43","fileSizeKB":"5444904","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Coronavirus BCoV\\\/PB675\\\/Art_lit\\\/PAN\\\/2011 (NCBITaxon:1269292)","instrument":"TripleTOF 6600","modification":"MS:1002864","keywords":"coronavirus","pi":[{"name":"Hung-Yi Wu","email":"hwu2@dragon.nchu.edu.tw","institution":"National Chung Hsing University","country":"Taiwan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"12f14678105b4e3286a236d2d2c73502","id":"105"}, {"dataset":"MSV000095515","datasetNum":"95515","title":"NAR-00644-Z-2024 RNA analysis by direct infusion","user":"yufeixiang","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"106"}, {"dataset":"MSV000095508","datasetNum":"95508","title":"Northern elephant seal juvenile plasma proteome response to repeated ACTH administration ","user":"mirounga","site":"MassIVE","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. Solvent B (ACN) was used as follows: 2 percent at 5 min, 2-22 percent at 75 min, 22-38 percent at 100 min, 38-95 percent at 105 min, 95 percent returning to 2 percent at 115 min, and lastly maintained at 2 percent at 140 min.\n\nMass spectrometry analysis was performed using Orbitrap Fusion Tribrid mass spectrometer equipped with an EASY-SprayTM ion source and operated by Xcalibur 4.0 software. MS1 spectra were resolved by the orbitrap with a resolution of 120,000, scan range of 200-1400 m\/z, RF lens of 60 percent, AGC target of 1.0e6, and max injection time of 50 ms. Precursor ions were isolated by quadrupole and fragmented using HCD with a collision energy of 28 percent. MS2 product ions were resolved by the orbitrap (resolution: 30,000, AGC target: 5.0e5, first mass: 100 m\/z, and max injection time: 150 ms). ","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":"107"}, {"dataset":"MSV000095503","datasetNum":"95503","title":"The Glycolytic Metabolite Methylglyoxal Covalently Inactivates the NLRP3 Inflammasome.","user":"carrose73","site":"MassIVE","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":"108"}, {"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","flowname":"MASSIVE-COMPLETE","createdMillis":"1722458809000","created":"Jul. 31, 2024, 1:46 PM","description":"Sample data for MassLite and result file. First data pretreatment platform specifically compatible with improvised SCMS data acquisition. ","fileCount":"3","fileSizeKB":"120466","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","keywords":"Single cell;data pretreatment;Alignment;Auto Background removal","pi":[{"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":"f44976908ef347aa97b71e2ef2e0f879","id":"109"}, {"dataset":"MSV000095497","datasetNum":"95497","title":"Exploring Protein Post-Translational Modifications of Breast Cancer Cells Using a Novel Combinatorial Search Algorithm","user":"metodi","site":"MassIVE","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":"110"}, {"dataset":"MSV000095492","datasetNum":"95492","title":"The C. elegans PTPN22 ortholog functions in diverse developmental processes","user":"sbyrum","site":"MassIVE","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":"MS:1003028","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":"111"}, {"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","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. 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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","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":"113"}, {"dataset":"MSV000095486","datasetNum":"95486","title":"GNPS - LC-MS compound 4BL laboratorio 147 USP","user":"Gomes","site":"MassIVE","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. 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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":"118"}, {"dataset":"MSV000095466","datasetNum":"95466","title":"GNPS - Metabolomics of human urine and stool samples from the PRIMA study","user":"nicolaproch","site":"MassIVE","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":"13","fileSizeKB":"14393376","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002728","modification":"MS:1002864","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":"119"}, {"dataset":"MSV000095463","datasetNum":"95463","title":"GNPS - Livia Soman research group - fungi metabolites","user":"liviasoman","site":"MassIVE","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. 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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). 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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":"124"}, {"dataset":"MSV000095455","datasetNum":"95455","title":"Lusk_2024_aTRAQ_AA_quant_OvC_Secondary_Metastasis","user":"hlusk0529","site":"MassIVE","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":"MS:1003124","modification":"MS:1002864","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":"125"}, {"dataset":"MSV000095454","datasetNum":"95454","title":"P. fluorescens in Succinate Minimal Media, Iron Infusion","user":"aronlabshared","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"126"}, {"dataset":"MSV000095452","datasetNum":"95452","title":"E. meliloti Strains USDA 1021 and USDA 1157, Succinate Minimal Media with\/without Iron","user":"aronlabshared","site":"MassIVE","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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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":"144"}, {"dataset":"MSV000095406","datasetNum":"95406","title":"GNPS - wild elk tissue extracts","user":"zhaohaoq","site":"MassIVE","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. 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":"f60af135aab84f068abcb12d8e8d58df","id":"145"}, {"dataset":"MSV000095404","datasetNum":"95404","title":"Proteomic profile regarding antihypertensive therapy in preeclampsia pregnant","user":"lucilene","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721655494000","created":"Jul. 22, 2024, 6:38 AM","description":"Preeclampsia (PE) is a hypertensive pregnancy syndrome associated with target organ damage and higher cardiovascular sequelae and requires antihypertensive therapy. However, about 40% of patients are nonresponsive to treatment, leading to worse clinical outcomes. 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). We performed plasma protein relative quantification using mass spectrometry.","fileCount":"61","fileSizeKB":"96891396","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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;Mass Spectrometry;antihypertensive therapy responsiveness","pi":[{"name":"Bruna Cavecci Mendonca","email":"brucavecci@gmail.com","institution":"Universidade Estadual Paulista (UNESP)","country":"Brasil"},{"name":"Bruno Cesar Rossini","email":"bruno.rossini@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brazil"},{"name":"Carolina Cristina Pinto Souza","email":"caroline.cp.souza@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brasil"},{"name":"Julyane Natsumi Saito Kaihara","email":"j.kaihara@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brasil"},{"name":"Lucilene Delazari dos Santos","email":"lucilene.delazari@unesp.br","institution":"Universidade Estadual Paulista (UNESP)","country":"Brasil"},{"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":"1b1eb4339a344cb2b4b1828206b03b33","id":"146"}, {"dataset":"MSV000095400","datasetNum":"95400","title":"GNPS Example Dataset gf vs SPF Mouse duodenum","user":"khkee92","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721630537000","created":"Jul. 21, 2024, 11:42 PM","description":"these data are mouse data these data are mouse data these data are mouse data these data are mouse data these data are mouse data these data are mouse data these data are mouse ","fileCount":"17","fileSizeKB":"513349","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1000935","modification":"MS:1002864","keywords":"mouse","pi":[{"name":"Kyunghwa Kee","email":"khkee9202@gmail.com","institution":"Colleage of pharmacy, hanyang university","country":"South korea"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"27d77117c0724e0092351713d161a640","id":"147"}, {"dataset":"MSV000095399","datasetNum":"95399","title":"Haloacetonitriles Induce Structure-related Cellular Toxicity through Distinct Proteome Thiol Reaction Mechanisms","user":"KirstenYeung","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721585660000","created":"Jul. 21, 2024, 11:14 AM","description":"Raw MS files and MaxQuant txt files for \"Haloacetonitriles Induce Structure-related Cellular Toxicity through Distinct Proteome Thiol Reaction Mechanisms\" paper","fileCount":"52","fileSizeKB":"72102469","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002523","modification":"monoHAN SN2","keywords":"haloacetonitriles;SN2;thiol reaction;disinfection by products","pi":[{"name":"Hui Peng","email":"hui.peng@utoronto.ca","institution":"University of Toronto","country":"Canada"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD054084","task":"59cec508323e459f8f2f6b86023ea9a7","id":"148"}, {"dataset":"MSV000095392","datasetNum":"95392","title":"GNPS - Enviornmental Metabolomics ECOHAB 2024 DOM \/ POM ","user":"TSchramm","site":"MassIVE","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. ","fileCount":"432","fileSizeKB":"57907336","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Domoic acid","instrument":"MS:1003028","modification":"MS:1002864","keywords":"PPL;GFF;marine samples","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":"ccc307acdd364a8ea30ad972a405aba0","id":"149"}, {"dataset":"MSV000095391","datasetNum":"95391","title":"Sirt2 regulates liver metabolism in a sex-specific manner","user":"JoannaBons","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721426554000","created":"Jul. 19, 2024, 3:02 PM","description":"Sirtuin-2 (Sirt2), an NAD+-dependent lysine deacylase enzyme, has previously been implicated as a regulator of glucose metabolism, but the specific mechanisms remain poorly defined. 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. ","fileCount":"47","fileSizeKB":"93501781","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1003029","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Lysine acetylation;Data-independent acquisition (DIA);Sirtuin-2 (Sirt2);Gluconeogenesis;Quantitative proteomics;Metabolism","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":"PXD054074","task":"2b053f951e0947eba7bbd4049ae91faf","id":"150"}, {"dataset":"MSV000095388","datasetNum":"95388","title":"Targeted SuFEx-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1 ","user":"kiallsuazo","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721405535000","created":"Jul. 19, 2024, 9:12 AM","description":"Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) is complicated by the shallow catalytic pocket and the difficulties of overcoming binding interactions of substrate. 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":"MS:1002526;MS:1003029","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":"151"}, {"dataset":"MSV000095383","datasetNum":"95383","title":"GNPS - U19 Mars Wisconsin Serum Alzheimer's Disease","user":"jzemlin","site":"MassIVE","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":"807","fileSizeKB":"46467157","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","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":"152"}, {"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","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","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. Tissue samples were collected post-terminal surgery.","fileCount":"146","fileSizeKB":"15652578","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002634","modification":"MS:1002864","keywords":"Arteriovenous metabolomics;Inter-organ flux;Postprandial metabolism;Pig;Western diet","pi":[{"name":"Cholsoon Jang","email":"choljang@uci.edu","institution":"UC Irvine","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"29cb55f9395b47c38e8bca8a92991e9a","id":"154"}, {"dataset":"MSV000095379","datasetNum":"95379","title":"GNPS - Effects of light exposure on circulating metabolites in mice","user":"TSUJIT","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721342116000","created":"Jul. 18, 2024, 3:35 PM","description":"The goal of this project is to identify metabolites released from subcutaneous adipose tissue due to light exposure that regulate systemic metabolism. 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","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":"155"}, {"dataset":"MSV000095364","datasetNum":"95364","title":"GNPS - Preservative solvent 95% ethanol with ink labels - PRJ0","user":"marwa38","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1721260219000","created":"Jul. 17, 2024, 4:50 PM","description":"Solvent (95% ethanol) used to preserve fish tissues (liver, intestines and stomach) and worms with internal labels (ink printed labels) in comparison with blanks. 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":"MS:1003094","modification":"MS:1002864","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":"156"}, {"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","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":"285","fileSizeKB":"1517758723","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1003378","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":"157"}, {"dataset":"MSV000095359","datasetNum":"95359","title":"GNPS - Metabolomic analysis of Streptomyces ansochromogenes ssp. pallens aqueous fraction","user":"Rolandoo1","site":"MassIVE","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. 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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":"192"}, {"dataset":"MSV000095263","datasetNum":"95263","title":"RAW files for manuscript 'Profiling the antigen-ome of the cystic fibrosis pathogen Achromobacter xylosoxidans'","user":"csahl","site":"MassIVE","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":"MS:1002877","modification":"MS:1002864","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":"193"}, {"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":"MS:1002732","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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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. 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(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":"MS:1003152","modification":"MS:1002864","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":"201"}, {"dataset":"MSV000095232","datasetNum":"95232","title":"GNPS - Community-wide interactions sustain life in geothermal spring habitats","user":"bpbowen","site":"MassIVE","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","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":"202"}, {"dataset":"MSV000095230","datasetNum":"95230","title":"Arf1-dependent LRBA recruitment to Rab4 endosomes is required for endolysosome homeostasis","user":"verizy27","site":"MassIVE","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":"32","fileSizeKB":"79024515","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002523;MS:1003383","modification":"MS:1002864","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":"203"}, {"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","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":"MS:1002634","modification":"This term should be given if the modification was unknown.","keywords":"Heart, NAMPT, Cardiomyocyte, Metabolomics, NAD","pi":[{"name":"Joseph A. 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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]. 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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":"MS:1002634","modification":"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":"208"}, {"dataset":"MSV000095220","datasetNum":"95220","title":"GNPS_CMMC_Bile_Salt_Hydrolase_Assay_6","user":"asund42","site":"MassIVE","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","keywords":"BSH;Amino compounds;Assay","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":"a682622f3b464c7da6b130c62cd4c32e","id":"210"}, {"dataset":"MSV000095215","datasetNum":"95215","title":"Mindbomb1 is a Novel Negative Regulator of BMP Signaling","user":"TKC008","site":"MassIVE","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":"MS:1003029","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":"211"}, {"dataset":"MSV000095207","datasetNum":"95207","title":"GNPS - Synthetic interkingdom microbial consortia supported by quorum signalling for bioplastic production from agro-industrial waste","user":"bpbowen","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719890825000","created":"Jul. 1, 2024, 8:27 PM","description":"Microbial consortia have a high relevance in natural environments. 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Results show that the consortium accumulates up to 10.4 % of the total weight of the culture in form of PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells in this condition. \r\nAn interactive Shiny application has also been developed for an easy visualization and comprehension of all the trasncriptomic and metabolomic data, the application is available in the following link: https:\/\/jgf-bioinformatics.shinyapps.io\/Visualization_app\/. These results show an induction of PHA synthesis machinery of P. putida in the consortium and that trophic interaction between the microorgranisms may rely in the citric acid produced by O. piceae and glycerol liberated from WCO, which can both be consumed by P. putida. Bioreactor scale-up experiments also lay the groundwork for the implementation of an industrial consolidated bioprocess (CBP).\r\n\r\nThe work (proposal:https:\/\/doi.org\/10.46936\/10.25585\/60001228) 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":"543","fileSizeKB":"44722719","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Ophiostoma piceae CECT 20146; Pseudomonas putida KT2440","instrument":"Q Exactive","modification":"MS:1002864","keywords":"polyhydroxyalkanoates;Ophiostoma;Pseudomonas;quorum sensing;farnesol","pi":[{"name":"Jorge Barriuso","email":"jbarriuso@cib.csic.es","institution":"CIB Center for Biological Research","country":"Spain"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"2beba909267540eb8486c3aa236085e8","id":"212"}, {"dataset":"MSV000095206","datasetNum":"95206","title":"GNPS - 20240701_Alaska_soil_samples_Yu_Frank_Yang_Sudarshan_Basyal","user":"TSchramm","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719881010000","created":"Jul. 1, 2024, 5:43 PM","description":"Alaskan soil samples, for non-native MS Analysis. We have started the water extraction of the Alaska samples. Considering the 20% moisture on the samples, we conducted the extraction with 10g\/L. 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Human neuroblastoma SH-SY5Y cells were incubated with five different concentrations of A beta1-40 monomers and collected at four time points. The proteomic results found the time-course behavior of proteins involved in biological processes, such as RNA splicing, nuclear transport and protein localization. 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Only non-membrane proteins included. Samples before 7 Hidroxitropolone production and after included, along with samples with Macrophomina phaseolina micelium and without. All sample types include triplicates from SVBP6 wild type and its Tn5 gacS mutant.","fileCount":"40","fileSizeKB":"30429108","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 donghuensis (NCBITaxon:1163398)","instrument":"MS:1002523","modification":"MS:1002864","keywords":"Pseudomonas;PGPR;Antagonism","pi":[{"name":"Claudio Valverde","email":"valverdecl@hotmail.com","institution":"Universidad Nacional de Quilmes","country":"Argentina"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c2c377c1a3fb4f84a47932014d0b47a6","id":"216"}, {"dataset":"MSV000095196","datasetNum":"95196","title":"GNPS-neoflavonoid-fanshengxian","user":"gongxiaohui","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719810753000","created":"Jun. 30, 2024, 10:12 PM","description":"Exploring the mass spectrometric cleavage pathway of neoflavonoid in Dalbergia","fileCount":"9","fileSizeKB":"227156","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"neoflavonoid","instrument":"TripleTOF 5600","modification":"none","keywords":"plant","pi":[{"name":"Xiaohui Gong","email":"gongxiaohui2@jxutcm.edu.cn","institution":"Jiangxi University Of Traditional Chinese Medicine","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"412c55222e2d480fb6dec294519a1f79","id":"217"}, {"dataset":"MSV000095192","datasetNum":"95192","title":"GNPS - Alzheimer's disease postmortem brain","user":"EPishva","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719770820000","created":"Jun. 30, 2024, 11:07 AM","description":"LC-MS\/MS data for 96 postmortem prefrontal brain samples obtained from BDR cohort","fileCount":"193","fileSizeKB":"423330970","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","keywords":"Alzhimer's disease, Postmortem brain, Prefrontal cortex","pi":[{"name":"Ehsan Pishva","email":"e.pishva@maastrichtuniversity.nl","institution":"Maastricht University","country":"Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c3d24e99a49844a6b799b3a4efa5e877","id":"218"}, {"dataset":"MSV000095190","datasetNum":"95190","title":"GNPS -3',4'-hydroxy-4-methoxydalbergione","user":"gongxiaohui","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719756873000","created":"Jun. 30, 2024, 7:14 AM","description":"This compound belongs to a subclass of flavonoids, sandalwood quinone, which is a new flavonoid, and the mining of flavonoids is a new direction","fileCount":"2","fileSizeKB":"71093","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"3',4'-hydroxy-4-methoxydalbergione","instrument":"TripleTOF 5600","modification":"none","keywords":"plant","pi":[{"name":"Xiaohui Gong","email":"gongxiaohui2@jxutcm.edu.cn","institution":"Jiangxi University Of Traditional Chinese Medicine","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d1a00793686c41bc9264a2f47f68c9eb","id":"219"}, {"dataset":"MSV000095189","datasetNum":"95189","title":"GNPS -4'-hydroxy-4-methoxydal-bergione","user":"gongxiaohui","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719750632000","created":"Jun. 30, 2024, 5:30 AM","description":"This compound belongs to a subclass of flavonoids, sandalwood quinone, which is a new flavonoid, and the mining of flavonoids is a new direction","fileCount":"2","fileSizeKB":"68407","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"4'-hydroxy-4-methoxydal-bergione","instrument":"TripleTOF5600","modification":"none","keywords":"plant","pi":[{"name":"Xiaohui Gong","email":"gongxiaohui2@jxutcm.edu.cn","institution":"Jiangxi University Of Traditional Chinese Medicine","country":"China"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9ddbe7154ab94879832dc457b63d9487","id":"220"}, {"dataset":"MSV000095188","datasetNum":"95188","title":"altered proteomic events induced by a beta in SHSY5Y","user":"hubxfcxy1987","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719744477000","created":"Jun. 30, 2024, 3:47 AM","description":"To explore the physiological mechanism of A betain vitro, we employed mass spectrometry to investigate the altered proteomic events induced by lower submicromolar con-centration of A beta. Human neuroblastoma SH-SY5Y cells were incubated with five dif-ferent concentrations of A beta1-40 monomers and collected at four time points. The pro-teomic results found the time-course behavior of proteins involved in biological pro-cesses, such as RNA splicing, nuclear transport and protein localization. ","fileCount":"106","fileSizeKB":"167095950","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","keywords":"Alzheimer;a beta","pi":[{"name":"chenxi yang","email":"cyang@whut.edu.cn","institution":"wuhan university of technology","country":"china"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD053519","task":"e93b68422d184169ab62dec5b391b46f","id":"221"}, {"dataset":"MSV000095185","datasetNum":"95185","title":"Prioritisation, Identification, and Quantification of Emerging Contaminants in Recycled Textiles Using Non-Targeted and Suspect Screening Workflows by LC-ESI-HRMS","user":"drszabo","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719679753000","created":"Jun. 29, 2024, 9:49 AM","description":"Recycled textile samples obtained in Sweden, 2021. Multi-residue extraction method used. Top-5 DDA + Inclusion List employed for MS2 acquisition. mzML files converted from raw data (ProteoWizard::msConvert).","fileCount":"128","fileSizeKB":"15254850","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002523","modification":"MS:1002864","keywords":"textile","pi":[{"name":"Anneli Kruve","email":"anneli.kruve@su.se","institution":"Stockholm University","country":"Sweden"},{"name":"Drew Szabo","email":"drew.szabo@mmk.su.se","institution":"Stockholm University","country":"Sweden"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"4cc47f5a76f14137b8addcef4e6a443c","id":"222"}, {"dataset":"MSV000095179","datasetNum":"95179","title":"GNPS Maloney lab LCMS Data 062824","user":"malonekn","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719600610000","created":"Jun. 28, 2024, 11:50 AM","description":"LC-MS\/MS data from crude extracts and fractions from assorted bacteria isolated from Citrus trees","fileCount":"592","fileSizeKB":"3980264","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 - San Diego, CA","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"e077a2e98a8f4196b6b9e7e4a5a413ab","id":"223"}, {"dataset":"MSV000095178","datasetNum":"95178","title":"Mitochondrial Inorganic Polyphosphate is Required to Maintain Proteostasis Within the Organelle","user":"KanshinED1","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719596685000","created":"Jun. 28, 2024, 10:44 AM","description":"The existing literature points towards the presence of robust mitochondrial mechanisms aimed at mitigating protein dyshomeostasis within the organelle. 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. ","fileCount":"6","fileSizeKB":"1734187","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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 Elite","modification":"UNIMOD:1384 - \\\"Methionine oxidation to homocysteic acid.\\\";UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:366 - \\\"Deamidation in presence of O18.\\\"","keywords":"mitochondrial inorganic polyphosphate;PolyP;Mitochondria;protein homeostasis;proteostasis","pi":[{"name":"Beatrix Ueberheide","email":"beatrix.ueberheide@nyumc.org","institution":"NYU School of Medicine","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"1f9fa8ce158548a1b8cab685f9755be4","id":"224"}, {"dataset":"MSV000095168","datasetNum":"95168","title":"Mitochondrial proteome Wt and MitoPPX cells under control conditions and heat shock","user":"MariaESolesio","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719515605000","created":"Jun. 27, 2024, 12:13 PM","description":"Detailed methods and results are included in our published manuscript titled \"Mitochondrial Inorganic Polyphosphate is Required to Maintain Proteostasis Within the Organelle\".","fileCount":"49","fileSizeKB":"45070496","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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 Scientific","modification":"MS:1002864","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":"225"}, {"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","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":"MS:1003230","modification":"MS:1002864","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":"226"}, {"dataset":"MSV000095160","datasetNum":"95160","title":"HDL proteomics in breast cancer - Santana 2024","user":"douglasrsjr","site":"MassIVE","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":"MS:1002732","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":"227"}, {"dataset":"MSV000095157","datasetNum":"95157","title":"GNPS - ISB Gut Statin Stool Metabolomics ","user":"jzemlin","site":"MassIVE","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","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":"228"}, {"dataset":"MSV000095156","datasetNum":"95156","title":"GNPS - APOE Haddad Obesity Study Metabolomics","user":"jzemlin","site":"MassIVE","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","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":"229"}, {"dataset":"MSV000095148","datasetNum":"95148","title":"GNPS - Non-targeted Metabolomics Plant Microbiome Screen","user":"TSchramm","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"230"}, {"dataset":"MSV000095147","datasetNum":"95147","title":"GNPS - Scripps Pier Time Series 2024","user":"rrtorres","site":"MassIVE","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","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":"231"}, {"dataset":"MSV000095144","datasetNum":"95144","title":"GNPS - LIVIA_SOMAN_RESEARCH_GROUP_MICROBIAL_METABOLITES_LC_MS","user":"liviasoman","site":"MassIVE","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","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":"232"}, {"dataset":"MSV000095143","datasetNum":"95143","title":"GNPS - OAI cohort study (serum samples)","user":"helenamrusso","site":"MassIVE","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":"2426","fileSizeKB":"424302945","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","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":"233"}, {"dataset":"MSV000095141","datasetNum":"95141","title":"Label Free BioID interaction datasets, Soderling Lab","user":"es3064","site":"MassIVE","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":"MS:1002732","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":"234"}, {"dataset":"MSV000095140","datasetNum":"95140","title":"Quantitative Proteomics of Axon Regeneration in Danio rerio with Regen V Standardization","user":"sbhattacharya","site":"MassIVE","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","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":"235"}, {"dataset":"MSV000095135","datasetNum":"95135","title":"GNPS - Monotropa_MS2 Analysis for Molecular Networking","user":"kellogglab","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"236"}, {"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","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":"237"}, {"dataset":"MSV000095124","datasetNum":"95124","title":"GNPS - High mass resolution lipid MALDI imaging of rat brain ","user":"yutinlin","site":"MassIVE","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":"238"}, {"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","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":"239"}, {"dataset":"MSV000095122","datasetNum":"95122","title":"GNPS - LIVIA_SOMAN_RESEARCH_GROUP_MICROBIAL_METABOLITES_LC_MS","user":"liviasoman","site":"MassIVE","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. Natural Products.","fileCount":"194","fileSizeKB":"791232","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 wortmannii (NCBITaxon:28567);Penicillium sp. (NCBITaxon:5081);Neosetophoma sp. (NCBITaxon:1756113)","instrument":"micrOTOF-Q II","modification":"MS:1002864","keywords":"fungi 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":"05c209d67d6c428cb5cd78c4a23f4582","id":"240"}, {"dataset":"MSV000095118","datasetNum":"95118","title":"GNPS_fungi Alexandre FMVP_LBD_pos","user":"denisebrentan","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1719103664000","created":"Jun. 22, 2024, 5:47 PM","description":"Samples from fungi FMVP26, LBD22 and LBD75. 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":"241"}, {"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","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":"MS:1002634","modification":"MS:1002864","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":"242"}, {"dataset":"MSV000095110","datasetNum":"95110","title":"Presynaptic Rac1 Interactome in vivo BioID Soderling and Kim","user":"es3064","site":"MassIVE","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":"MS:1003378","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":"243"}, {"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","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":"MS:1002634","modification":"MS:1002864","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":"244"}, {"dataset":"MSV000095101","datasetNum":"95101","title":"IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport ","user":"ProteomicsCF_FLI","site":"MassIVE","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":"17","fileSizeKB":"14685824","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003028","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":"245"}, {"dataset":"MSV000095097","datasetNum":"95097","title":"GNPS - Lipidomics-based algorithms can enhance prediction of obstructive coronary artery disease","user":"mousthomai","site":"MassIVE","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":"MS:1003094","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":"246"}, {"dataset":"MSV000095093","datasetNum":"95093","title":"GNPS Ruminococcus gnavus Strains","user":"jma429njms","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718908555000","created":"Jun. 20, 2024, 11:35 AM","description":"Strains of Ruminococcus gnavus, specifically ATCC 29149 and ATCC 35913, as well as Mediterraneibacter gnavus H2-28 and AGR 2154 (formerly known as Ruminococcus gnavus), were cultured under three different conditions:\n\nMeat Broth (CTRL)\nMeat Broth with Sialic Acid (SIALIC)\nMeat Broth with 1% Porcine Mucin (PORCINE)\nThe cultures were incubated for 3 hours. 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":"MS:1002634","modification":"MS:1002864","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":"247"}, {"dataset":"MSV000095092","datasetNum":"95092","title":"GNPS - Fourier transform-Ion Mobility-Charge Detection-Mass Spectrometry","user":"michaelmarty","site":"MassIVE","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. Contains data for GroEL, ADH, and GDH, the latter with varying step size, repeats, and drift voltages.","fileCount":"203","fileSizeKB":"26624821","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003245","modification":"MS:1002864","keywords":"Charge Detection Mass Spectrometry;Native MS;Fourier transform-ion mobility","pi":[{"name":"Jennifer Brodbelt","email":"jbrodbelt@cm.utexas.edu","institution":"University of Texas-Austin","country":"United States"},{"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":"d69236e861154db78711b7c9f7747407","id":"248"}, {"dataset":"MSV000095091","datasetNum":"95091","title":"GNPS - Hadamard transform-Size Exclusion Chromatography-Charge Detection-Mass Spectrometry","user":"michaelmarty","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718898978000","created":"Jun. 20, 2024, 8:56 AM","description":"Data on multiplex HT-SEC with online CD-MS detection. 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":"MS:1003245","modification":"MS:1002864","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":"249"}, {"dataset":"MSV000095090","datasetNum":"95090","title":"GNPS Ruminococcus gnavus Strains","user":"jma429njms","site":"MassIVE","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":"MS:1002634","modification":"MS:1002864","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":"250"}, {"dataset":"MSV000095089","datasetNum":"95089","title":"GNPS Ruminococcus gnavus ATCC 29149","user":"jma429njms","site":"MassIVE","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":"MS:1002634","modification":"MS:1002864","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":"251"}, {"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","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":"57","fileSizeKB":"1888392","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002732","modification":"MS:1002864","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":"252"}, {"dataset":"MSV000095087","datasetNum":"95087","title":"Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation","user":"kojiode","site":"MassIVE","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":"MS:1003028","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":"253"}, {"dataset":"MSV000095086","datasetNum":"95086","title":"Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics","user":"jfhorner","site":"MassIVE","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":"87","fileSizeKB":"262794479","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029","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":"254"}, {"dataset":"MSV000095071","datasetNum":"95071","title":"De novo gene synthesis by an antiviral reverse transcriptase","user":"mj2794","site":"MassIVE","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":"MS:1002523","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":"255"}, {"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","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","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":"256"}, {"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","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":"MS:1002783","modification":"MS:1002864","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":"257"}, {"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","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":"MS:1002783","modification":"MS:1002864","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":"258"}, {"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","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":"1754","fileSizeKB":"35442812","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"259"}, {"dataset":"MSV000095059","datasetNum":"95059","title":"GNPS Citrus Bacteria data 06172024","user":"malonekn","site":"MassIVE","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":"260"}, {"dataset":"MSV000095058","datasetNum":"95058","title":"Effects Beta-hydroxybutyrate on human islet proteome","user":"Rogy","site":"MassIVE","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":"MS:1003230","modification":"MS:1002864","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":"261"}, {"dataset":"MSV000095055","datasetNum":"95055","title":"GNPS - LIVIA_SOMAN_RESEARCH_GROUP_MICROORGANISMS_LC_MS","user":"liviasoman","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718649996000","created":"Jun. 17, 2024, 11:46 AM","description":"Data from microorganisms investigated by Livia Soman Research Group, at UNIFESP - Diadema-Brazil","fileCount":"91","fileSizeKB":"582215","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 wortmannii (NCBITaxon:28567)","instrument":"microTOF LC","modification":"MS:1002864","keywords":"fungi metabolites","pi":[{"name":"Livia Soman de Medeiros","email":"livia.soman@unifesp.br","institution":"Unifesp","country":"Brasil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bb768eb3e66e4e85a21c9b4116667586","id":"262"}, {"dataset":"MSV000095047","datasetNum":"95047","title":"GNPS - Single cell amine metabolomics raw files","user":"JuhoH","site":"MassIVE","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","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":"263"}, {"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","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. Characterization was improved through the use of proton transfer charge reduction","fileCount":"34","fileSizeKB":"6073515","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 AAV","instrument":"MS:1003356","modification":"UNIMOD:1 - \\\"Acetylation.\\\"","keywords":"Adeno-associated viruses;proton transfer charge reduction;top-down proteomics","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":"cd381b8f36314023be3d832426902b45","id":"264"}, {"dataset":"MSV000095037","datasetNum":"95037","title":"GNPS - Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants","user":"culvej","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718374067000","created":"Jun. 14, 2024, 7:07 AM","description":"Genotyped human hepatocytes for assessing levels of Hsd17b13 in 'IsoA' donors relative to 'IsoD'","fileCount":"28","fileSizeKB":"14348871","spectra":"0","psms":"51846","peptides":"19435","variants":"26341","proteins":"3378","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002523","modification":"MS:1002864","keywords":"Human Hepatocytes","pi":[{"name":"Jeffrey Culver","email":"jeffrey.culver@pfizer.com","institution":"Pfizer","country":"United States of America"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD053125","task":"70c818d3b95641eeb6c90febbc0e39b7","id":"265"}, {"dataset":"MSV000095034","datasetNum":"95034","title":"A Closer Look at Plastic Colonisation","user":"lamesser","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718363382000","created":"Jun. 14, 2024, 4:09 AM","description":"The aim of this study was to investigate the plastic colonisation process, to identify the active taxa involved in biofilm formation and the mechanisms used to initiate colonisation. To achieve this, a marine plastisphere characterised by active hydrocarbonoclastic genera was used as the inoculum for a short-term microcosm experiment using virgin low-density polyethylene as the sole carbon source. Following incubation for 1 and 2 weeks (representing early and late colonisation, respectively), a taxonomic and comparative metaproteomic approach was used to explore shifts in diversity and function.","fileCount":"50","fileSizeKB":"24458305","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"TripleTOF 6600","modification":"MS:1002864","keywords":"plastisphere colonisation;metaproteomics;plastic microcosm","pi":[{"name":"Sabine Matallana Surget","email":"sabine.matallanasurget@stir.ac.uk","institution":"University of Stirling","country":"United Kingdom"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"PXD053111","task":"d5e9a0702d29499abc60f52c828d9960","id":"266"}, {"dataset":"MSV000095031","datasetNum":"95031","title":"GNPS-fenziwangluo-hezao-20240614-neg","user":"Liyu","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718347646000","created":"Jun. 13, 2024, 11:47 PM","description":"Ecklonia cava UHPLC-Q-Orbitrap HRMS Identification of compounds Component characterization","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":"884516fb726a4c4a8afbbaadac6609ad","id":"267"}, {"dataset":"MSV000095029","datasetNum":"95029","title":"GNPS - DonahueMauiCorals_Quinlan_Jun2024","user":"aronlabshared","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718314630000","created":"Jun. 13, 2024, 2:37 PM","description":"Non-targeted LC-MS\/MS of PPL extracts from environmental seawater samples from coral reefs collected from Maui by Dr. Megan Donahue.\r\n","fileCount":"2171","fileSizeKB":"157231790","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Scleractinia (NCBITaxon:6125);Montipora (NCBITaxon:46703);Porites (NCBITaxon:46719)","instrument":"Q Exactive","modification":"MS:1002864","keywords":"Dissolved organic matter;exometabolites;coral reefs;Hawai'i;Maui;Environmental samples","pi":[{"name":"Zachary Quinlan","email":"zquinlan@gmail.com","institution":"Hawaii Institute of Marine Biology","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"051c5f6f1f8e4078bae199ab4ebaece0","id":"268"}, {"dataset":"MSV000095027","datasetNum":"95027","title":"Septin-associated protein kinase Hsl1 phosphorylates Pah1 to inhibit phosphatidate phosphatase activity and regulate lipid synthesis in Saccharomyces cerevisiae","user":"haiyanzheng","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718313179000","created":"Jun. 13, 2024, 2:12 PM","description":" In Saccharomyces cerevisiae, Pah1 phosphatidate (PA) phosphatase, which catalyzes the Mg2+-dependent dephosphorylation of PA to produce diacylglycerol, plays a key role in utilizing PA for the synthesis of membrane phospholipids or the neutral lipid triacylglycerol. 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":"MS:1003029","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":"251","fileSizeKB":"48427672","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003293","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":"270"}, {"dataset":"MSV000095016","datasetNum":"95016","title":"GNPS - Metabolomics-based LC-HRMS Analysis of Liquid Fermentation Co-culture of Penicillium sp. 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LBKURCC1 and LBKURCC2 13 June","user":"Niko160702","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718264561000","created":"Jun. 13, 2024, 12:42 AM","description":"Metabolomics analysis co-culture fungi local 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":"MS:1002791","modification":"MS:1002864","keywords":"trichoderma","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":"c017645ecbd44be7a60b73a2a318eba3","id":"272"}, {"dataset":"MSV000095013","datasetNum":"95013","title":"GNPS - Algal induction from a spotted salamander host","user":"amcaraballor","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718242751000","created":"Jun. 12, 2024, 6:39 PM","description":"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 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":"MS:1003094","modification":"MS:1002864","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":"273"}, {"dataset":"MSV000095011","datasetNum":"95011","title":"Proteomic content in metabolomic samples cause post-extraction metabolite changes","user":"ryan_sheldon","site":"MassIVE","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":"MS:1003094;MS:1003112","modification":"MS:1002864","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":"274"}, {"dataset":"MSV000095010","datasetNum":"95010","title":"Proteomic content in metabolomic samples","user":"ryan_sheldon","site":"MassIVE","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":"MS:1003029","modification":"MS:1002864","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":"275"}, {"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","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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Analyzed with 15 cm phenomenex polar C18 column, 15 minute HPLC gradient, orbitrap DDA method.","fileCount":"508","fileSizeKB":"45112809","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"Personal Care Product","pi":[{"name":"Pieter C. 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This work is included in \"The HHV-6B U20 glycoprotein binds ULBP1, masking it from recognition by NKG2D and interfering with natural killer cell activation\" by Weaver et al published in Frontiers in Immunology. (doi: 10.3389\/fimmu.2024.1363156)","fileCount":"18","fileSizeKB":"2975053","spectra":"0","psms":"12968","peptides":"2881","variants":"3715","proteins":"3707","search_psms":"0","search_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 herpesvirus 6 strain Z29 (NCBITaxon:36351)","instrument":"MS:1002732","modification":"UNIMOD:43 - \\\"N-Acetylhexosamine.\\\";UNIMOD:621 - \\\"Asn->Asp substitution.\\\"","keywords":"U20;HHV-6B;herpesvirus;roseolovirus","pi":[{"name":"Lawrence J. 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Each spectra contains up to three replicates of MALDI-MS profiles of each bacterial isolate.","fileCount":"554","fileSizeKB":"2770093","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003122;autoflex","modification":"MS:1002864","keywords":"MALDI;Bacteria;IDBac","pi":[{"name":"Brian Murphy","email":"btmurphy@uic.edu","institution":"University of Illinois at Chicago","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b89c789596fa40eeb80f903c5a51dff4","id":"284"}, {"dataset":"MSV000094967","datasetNum":"94967","title":"GSK3 inhibition reduces ECM production and prevents age-related macular degeneration-like pathology","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1718039243000","created":"Jun. 10, 2024, 10:07 AM","description":"All samples originated from ARPE-19 cultured cells. 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":"MS:1002523","modification":"MS:1002864","keywords":"EFEMP1;fibulin-3;extracellular matrix;CHIR99021;Doyne Honeycomb Retinal Dystrophy;Malattia Leventinese;age-related macular degeneration;GSK3;ARPE-19","pi":[{"name":"John D. Hulleman, Ph.D.","email":"hulleman@umn.edu","institution":"University of Minnesota","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052966","task":"9644a01a07f342e59ce6a4d71a38c00a","id":"285"}, {"dataset":"MSV000094965","datasetNum":"94965","title":"GNPS-fenziwangluo-hezao-20240610-neg","user":"Liyu","site":"MassIVE","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":"286"}, {"dataset":"MSV000094964","datasetNum":"94964","title":"GNPS-fenziwangluo-huzhang-20240610-pos","user":"Liyu","site":"MassIVE","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":"287"}, {"dataset":"MSV000094961","datasetNum":"94961","title":"GNPS TarvinETAL2024 Data and Result Files for Silverstoneia flotator and Eleutherodactylus cystignathoides","user":"jcole844","site":"MassIVE","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","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":"288"}, {"dataset":"MSV000094959","datasetNum":"94959","title":"Liver tissue proteins improve the accuracy of plasma proteins as biomarkers in diagnosing metabolic dysfunction-associated steatohepatitis","user":"brettsp1","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1717792667000","created":"Jun. 7, 2024, 1:37 PM","description":"Background: Biomarkers for metabolic dysfunction-associated steatohepatitis (MASH) have been considered based on proteomic and lipidomic data from plasma and liver tissue without clinical benefits. This study evaluated proteomics-based plasma and liver tissue biomarkers collected simultaneously from patients with metabolic dysfunction-associated steatotic liver disease (MASLD).\n\nMethods: Liver tissue samples and plasma samples were collected during liver biopsy for diagnosis. Untargeted proteomics was performed on 64 patients with MASLD.\n\nResults: Twenty plasma proteins were up or downregulated in patients with MASH compared with those without MASH. The biomarkers utilizing the best combinations of these plasma proteins had an area under the receiver operating curve (AUROC) of 0.671 for detecting those with MASH compared with those without it. However, none of the 20 plasma proteins were represented among the significantly regulated liver tissue proteins in patients with MASH. Ten of them displayed a trend and relevance in liver tissue with MASLD progression. These ten plasma proteins had an AUROC of 0.793 for MASH identification and higher positive and negative predictive values.\n\nConclusion: The plasma and liver protein expressions of patients with MASH were not directly comparable. Plasma protein biomarkers that are also expressed in liver tissue can help improve MASH detection.\n\n","fileCount":"1093","fileSizeKB":"238201746","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732","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":"289"}, {"dataset":"MSV000094955","datasetNum":"94955","title":"GNPS-fenziwangluo-hezao-20240606-pos","user":"Liyu","site":"MassIVE","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":"290"}, {"dataset":"MSV000094954","datasetNum":"94954","title":"GNPS-fenziwangluo-hezao-20240606-neg","user":"Liyu","site":"MassIVE","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":"291"}, {"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","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. ","fileCount":"137","fileSizeKB":"39339962","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003094;MS:1003029;MS:1002732","modification":"MS:1002864","keywords":"covid19;de novo;sequencing;antibody;neutralizing;polyclonal","pi":[{"name":"Thierry Le Bihan","email":"tlebihan@rapidnovor.com","institution":"Rapid Novor","country":"Canada "}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"74d1a1ff99bd419f87fe19bd06c87023","id":"292"}, {"dataset":"MSV000094949","datasetNum":"94949","title":"Raw MS data - Proximity labeling of Sucrosomes","user":"AmraSaric","site":"MassIVE","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":"MS:1002732","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":"293"}, {"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","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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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":"151","fileSizeKB":"200902089","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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","keywords":"DIA;PRM;data-independent acquisition;parallel reaction monitoring;targeted proteomics;il-2;il-15;interleukins;proteomics;ion trap;LIT;Q-LIT","pi":[{"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":"312"}, {"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","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":"38","fileSizeKB":"2360232","spectra":"0","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":"MS:1002634","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":"313"}, {"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","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":"MS:1002732","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":"314"}, {"dataset":"MSV000094896","datasetNum":"94896","title":"Paralogue-selective degradation of the lysine acetyltransferase EP300","user":"kiallsuazo","site":"MassIVE","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":"MS:1003029","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":"315"}, {"dataset":"MSV000094895","datasetNum":"94895","title":"GNPS - 2024-Mobley-collaborative-project_Fe","user":"aronlabshared","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"316"}, {"dataset":"MSV000094894","datasetNum":"94894","title":"GNPS - MS for 2-aminobenzamide-actiphenol ","user":"donghui","site":"MassIVE","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","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":"317"}, {"dataset":"MSV000094892","datasetNum":"94892","title":"Assessing and harnessing updated polyketide synthase modules...Massive dataset","user":"rayk212","site":"MassIVE","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":"MS:1002797","modification":"MS:1002864","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":"318"}, {"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","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":"319"}, {"dataset":"MSV000094885","datasetNum":"94885","title":"GNPS - Cyanobacteria Pteridines purified from Synechococcus elongatus PCC 7942 extracts","user":"Nike","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"320"}, {"dataset":"MSV000094884","datasetNum":"94884","title":"GNPS - Metabolomic approach based on mass spectrometry in plant leaf extracts of Sarcostema glaucum","user":"ValeskaLab","site":"MassIVE","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":"MS:1002791","modification":"MS:1002864","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":"321"}, {"dataset":"MSV000094883","datasetNum":"94883","title":"Molecular mechanism of Contactin 2 homophilic interaction","user":"Bill","site":"MassIVE","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":"322"}, {"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","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":"323"}, {"dataset":"MSV000094876","datasetNum":"94876","title":"Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR-T cells","user":"TKislinger","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716822988000","created":"May. 27, 2024, 8:16 AM","description":"Whole cell proteomics analysis of patient-matched glioblastoma models collected pre-treatment primary tumor (BT594) and post standard-of-care at first tumor recurrence (BT972).","fileCount":"31","fileSizeKB":"53914406","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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: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":"Glioblastoma;patient-matched;primary;recurrent","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":"2bbc776007cc478e835947965e81e5fb","id":"324"}, {"dataset":"MSV000094874","datasetNum":"94874","title":"Characterization of a monoclonal antibody by native and denaturing top-down mass spectrometry","user":"Fornelli_Lab","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716784412000","created":"May. 26, 2024, 9:33 PM","description":"Analysis of trastuzumab through both denaturing and native top-down proteomics","fileCount":"17","fileSizeKB":"154875","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029","modification":"UNIMOD:374 - \\\"Half of a disulfide bridge.\\\";UNIMOD:137 - \\\"N-linked glycan core.\\\"","keywords":"Trastuzumab;Native;Top-down","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":"adf7c3ebe0394f5a93a8a52952dee5fa","id":"325"}, {"dataset":"MSV000094870","datasetNum":"94870","title":"GNPS- metal-infusion experiments on semi-pure extract containing leptochelins A-C","user":"aronlabshared","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716590023000","created":"May. 24, 2024, 3:33 PM","description":"Direct infusion of Cu, Fe, Co, Mn, Zn was performed on semi-pure leptochelin extracts","fileCount":"13","fileSizeKB":"797719","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Leptothoe","instrument":"Q Exactive","modification":"MS:1002864","keywords":"leptochelin, leptothoe, metal-infusion","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":"1d1da501aa5d495b95b5408e1da3c0cf","id":"326"}, {"dataset":"MSV000094866","datasetNum":"94866","title":"GNPS - 20240522_Carlos_Laura_1 Bacillus Colony extracts","user":"JarmoK","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716567733000","created":"May. 24, 2024, 9:22 AM","description":"Bacillus extracts resuspended in 80\/20 MeOH\/water + 0.1% FA and run in positive mode","fileCount":"57","fileSizeKB":"5858984","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"bacterial colony","instrument":"MS:1003028","modification":"MS:1002864","keywords":"Bacillus","pi":[{"name":"Daniel Petras","email":"dpetras@ucr.edu","institution":"University of California Riverside","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"77efa218c1f0497088270b1a5cfa5406","id":"327"}, {"dataset":"MSV000094865","datasetNum":"94865","title":"Identification of proteins associated with KhpA and khpB in the bacterium Deinococcus radiodurans","user":"Runhuahan","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716566604000","created":"May. 24, 2024, 9:03 AM","description":"To examine if this is also the case in D. radiodurans and what other proteins interact with KhpA\/KhpB proteins in D. radiodurans, KhpA and KhpB were tagged with 3FLAG epitope at the C-terminus chromosomally or through expression on the pRADgro plasmid, followed by protein-protein coimmunoprecipitation (coIP) experiments. Compared to WT, only 8 proteins were enriched significantly with KhpA-3FLAG relative to the WT strain expressing untagged KhpA on pRADgro. By contrast, 28 proteins were significantly enriched with KhpB-3xFLAG.","fileCount":"25","fileSizeKB":"33459756","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Deinococcus radiodurans R1 (NCBITaxon:243230)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864","keywords":"small RNA, RNA-protein interaction, RNA binding protein, RNA regulation, Deinococcus radiodurans","pi":[{"name":"Lydia M. Contreras","email":"lcontrer@che.utexas.edu","institution":"the University of Texas at Austin","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD052557","task":"0f75463b127b4a3083a8f2ac4179e921","id":"328"}, {"dataset":"MSV000094864","datasetNum":"94864","title":"Ocotea diospyrifolia (Meisn.) Mez leaf extract in positive and negative modes","user":"matheus_fa","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716566556000","created":"May. 24, 2024, 9:02 AM","description":"Dataset of the Ocotea diospyrifolia (Meisn.) Mez leaf extract analyzed in negative and positive ionization modes, with 2 blanks samples.","fileCount":"7","fileSizeKB":"281531","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 diospyrifolia (NCBITaxon:881600)","instrument":"MS:1002634","modification":"MS:1002864","keywords":"Ocotea;Metabolic profiling;Annotation;LC-MS\/DIA","pi":[{"name":"Daniela Aparecida Chagas-Paula","email":"daniela.chagas@unifal-mg.edu.br","institution":"Federal University of Alfenas-MG","country":"Brazil "},{"name":"Matheus Fernandes Alves","email":"matheus.alves@sou.unifal-mg.edu.br","institution":"Federal University of Alfenas-MG","country":"Brazil"},{"name":"Rosana Casoti","email":"rosana.casoti@ufpe.br","institution":"Federal University of Pernambuco","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"489848de71bb49d98715475b7db958c3","id":"329"}, {"dataset":"MSV000094860","datasetNum":"94860","title":"GNPS - Australian Native fruits: Native Currant's Metabolomics profiling","user":"alsherbiny","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716516168000","created":"May. 23, 2024, 7:02 PM","description":"After screening some understudied Australian native fruits. The potential metabolites in the most active extracts (Water and ethanol extracts of Native currant) were analysed with liquid chromatography-mass spectrometry (LC-MS) driven metabolomics and chemometrics to spot differential and major metabolites. The metabolomics analysis revealed an abundance of flavonoids, fatty acyl derivatives, carbohydrates, carboxylic acids and their derivatives, and alkaloid compounds as potential bioactive metabolites in the NC extracts. ","fileCount":"27","fileSizeKB":"28371","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Acrotriche depressa","instrument":"Agilent 1290 LC coupled to 6546 Q-TOF","modification":"NA","keywords":"Australian native fruit, Acrotriche depressa, Native currant","pi":[{"name":"Maz Ali, Deep Bhuyan","email":"muhammad.alsherbiny@pharma.cu.edu.eg","institution":"Victor Chang Cardiac Research Institute, Western Sydney University, Cairo University","country":"Australia"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"7299c7d5752c40fa9835299dced95497","id":"330"}, {"dataset":"MSV000094858","datasetNum":"94858","title":"GNPS - 20240522_Carlos_Mario_2_5uL run at Functional Metabolomics Lab UCR","user":"JarmoK","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716512841000","created":"May. 23, 2024, 6:07 PM","description":"Plant and fungal extracts redissolved in 80\/20 MeOH\/water +0.1% FA. 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Cells were collected from 10 mL of each culture and harvested by centrifugation at 4000 rpm and 4 C for 10 min. The pellet was resuspended in 500 ul of 1 PBS supplemented with 1 mM PMSF (phenylmethylsulfonyl fluoride) and lysed using a sonicator (XL-2000 Microson ultrasonic liquid processor; QSonica) for ten times of 30 s bursts with 1 min of rest on ice between each burst. Following sonication, the samples were centrifuged at 12,000 rpm and 4 C for 10 min to get the soluble protein lysate in the supernatant. The protein concentration was determined using the Bradford assay.","fileCount":"19","fileSizeKB":"25734882","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"deinococcus radiodurans","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864","keywords":"small RNA, RNA-protein interaction, RNA binding protein, RNA regulation Deinococcus radiodurans","pi":[{"name":"Lydia M. 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Using this alternative approach (hereinafter referred to as 14 mer pull-down), we successfully enriched a total of 66 proteins in the 14 mer Dsr2 samples compared to the control sample. Except for several metabolic and hypothetical proteins, many of these proteins have potential nucleic acid binding functions were enriched, including three ribosomal proteins, two translation initiation factors, two TetR transcriptional regulators, five tRNA modification or processing proteins, DNA polymerase I, and five DNA repair proteins (e.g., RuvB, SbcD, and RecR). DR_2281 is one of the most enriched RBPs which contains a double stranded RNA binding motif (DSBM) but its function is unknown. In contrast, five other proteins (PNPase, RhlB, Ffh, DR_2281, KhpA and KhpB) were known as RBPs previously or contain known RNA binding domains. PNPase, RhlB, and Ffh have been revealed to play crucial roles in oxidative stress response in D. radiodurans by interacting with either oxidized RNA or Signal Recognition Particle RNA (Qpr6). PNPase also plays an indispensable role in paradoxically stabilizing sRNAs bound to other RBPs and promoting their function in gene regulation in E. coli (indicating a similar role of PNPase in D. radiodurans). ","fileCount":"13","fileSizeKB":"17546963","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Deinococcus radiodurans (NCBITaxon:1299)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864","keywords":"small RNA, RNA-protein interaction, RNA binding protein, RNA regulation Deinococcus radiodurans","pi":[{"name":"Lydia M. 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After bacterial lysis, the crude extract was loaded into an amylose-based chromatography column previously coated with the MS2 protein fused to the maltose-binding protein. This enables the specific capture of MS2-Dsr2 and its interacting protein partners. After elution, co-purified proteins were identified by LC-MS\/MS and subsequent bioinformatic analysis","fileCount":"13","fileSizeKB":"9720577","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Deinococcus radiodurans R1 (NCBITaxon:243230)","instrument":"LTQ Orbitrap Elite","modification":"MS:1002864","keywords":"small RNA;RNA-protein interaction;RNA binding protein; RNA regulation ;Deinococcus radiodurans","pi":[{"name":"Lydia M. 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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","keywords":"15N-stable isotope labeling, crop resilience, heat stress, protein turnover, proteomics","pi":[{"name":"Adrian D. 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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":"MS:1003231","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":"345"}, {"dataset":"MSV000094828","datasetNum":"94828","title":"Human_MTHR_PhosphorylationMapping_MSMS_Dataset","user":"menjdoza","site":"MassIVE","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":"MS:1003356","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":"346"}, {"dataset":"MSV000094825","datasetNum":"94825","title":"Label-free quantification of 3D MCF10A cell culture proteome (DIA)","user":"julienlab","site":"MassIVE","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":"5","fileSizeKB":"11173501","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"BioID;miniTurbo;LFQ;BAD;3D cell culture;DIA","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":"3b07aa588cc64ea68c2f35ac50f28b15","id":"347"}, {"dataset":"MSV000094819","datasetNum":"94819","title":"Protein restriction slows the development and progression of Alzheimer's disease in mice","user":"jericha66","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716325900000","created":"May. 21, 2024, 2:11 PM","description":"Untargeted lipidomics of 3xTg and non-transgenic mouse brain on protein restricted diet","fileCount":"120","fileSizeKB":"29301172","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1000937","modification":"MS:1002864","keywords":"protein restriction;lipidomics;Alzheimer's disease;3xTg mouse model;brain","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":"6c81db3c6a2249958672bb2674d12f2c","id":"348"}, {"dataset":"MSV000094818","datasetNum":"94818","title":"Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging brain","user":"malpap1","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716319482000","created":"May. 21, 2024, 12:24 PM","description":"Neuroimmune interactions mediate intercellular communication and underlie critical brain functions. Microglia, CNS-resident macrophages, modulate the brain through direct physical interactions and the secretion of molecules. One such secreted factor, the complement protein C1q, contributes to complement-mediated synapse elimination in development and disease models, yet brain C1q protein levels increase significantly throughout aging. Here we report that C1q interacts with neuronal ribonucleoprotein (RNP) complexes in an age-dependent manner. Purified C1q protein undergoes RNA-dependent liquid-liquid phase separation (LLPS) in vitro, and the interaction of C1q with neuronal RNP complexes in vivo is dependent on RNA and endocytosis. Mice lacking C1q have age-specific alterations in neuronal protein synthesis in vivo and impaired fear memory extinction. Together, our findings reveal a biophysical property of C1q that underlies RNA- and age-dependent neuronal interactions and demonstrate a role of C1q in critical intracellular neuronal processes.","fileCount":"22","fileSizeKB":"10777143","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"C-carbamidomethylation, K-TMT10, n-term-TMT10, K-TMT6, n-term-TMT6, M-oxidation, N-term acetylation, N-term pyroglutamic acid, N-deamidation, pyro carbamidomethyl Cys (N-termC)","keywords":"C1q, microglia, aging","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":"f9756d9b1ffc42f2a81cc3ce67885ae4","id":"349"}, {"dataset":"MSV000094817","datasetNum":"94817","title":"GNPS - Methylorubrum extorquens PA1 and Methylorubrum populi BJ001 data","user":"tliebergesell","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1716310071000","created":"May. 21, 2024, 9:47 AM","description":".raw and .mzML files for data from Methylorubrum extorquens PA1 and Methylorubrum populi BJ001. 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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":"353"}, {"dataset":"MSV000094811","datasetNum":"94811","title":"GNPS - CMMC_Bile_Salt_Hydrolase_Rxn_5.1","user":"asund42","site":"MassIVE","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","keywords":"BSH;Bile Acid;Amino Acid","pi":[{"name":"Pieter C. 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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":"290","fileSizeKB":"109094889","spectra":"0","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":"MS:1002877","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":"360"}, {"dataset":"MSV000094793","datasetNum":"94793","title":"GNPS - CMMC_acyl_amide_VD9_through_VD19","user":"victoriadeleray","site":"MassIVE","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","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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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":"MS:1002634;MS:1002802","modification":"MS:1002864","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":"366"}, {"dataset":"MSV000094782","datasetNum":"94782","title":"GNPS - Improving bioenergy yield under drought stress from field to lab","user":"bpbowen","site":"MassIVE","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","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":"367"}, {"dataset":"MSV000094781","datasetNum":"94781","title":"GNPS - Elucidating lignin catabolism in white rot fungi","user":"bpbowen","site":"MassIVE","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":"991","fileSizeKB":"62343411","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"368"}, {"dataset":"MSV000094780","datasetNum":"94780","title":"GNPS - Using genomics to understand microbial adaptation to soil warming - drought tolerance in Actinobacteria","user":"bpbowen","site":"MassIVE","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","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":"369"}, {"dataset":"MSV000094779","datasetNum":"94779","title":"Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance","user":"shaoen","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"370"}, {"dataset":"MSV000094778","datasetNum":"94778","title":"GNPS - Samples metabolomics, Solanaceae, GEME Max Planck","user":"EstevanGN","site":"MassIVE","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":"148","fileSizeKB":"14518408","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"371"}, {"dataset":"MSV000094777","datasetNum":"94777","title":"GNPS - Gel-assisted mass spectromety imaging","user":"ychan60","site":"MassIVE","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":"MS:1003122;4800 Plus MALDI TOF\\\/TOF;MS:1003397","modification":"MS:1002864","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":"372"}, {"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","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":"MS:1003028","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":"373"}, {"dataset":"MSV000094773","datasetNum":"94773","title":"FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer","user":"zifeng_wang","site":"MassIVE","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":"374"}, {"dataset":"MSV000094770","datasetNum":"94770","title":"GNPS - Dissolved lipidomes of three Chaetoceros diatom host virus systems","user":"edwardsbr","site":"MassIVE","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;MS:1003112","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":"375"}, {"dataset":"MSV000094769","datasetNum":"94769","title":"GNPS - LC-MS2 and BGC paired data from actinomycetes","user":"ACumsille","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1715795944000","created":"May. 15, 2024, 10:59 AM","description":"Paired genomics (.fasta) and metabolomics (.mzML) from 320 actinomycetes strains ","fileCount":"2276","fileSizeKB":"80178659","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"376"}, {"dataset":"MSV000094763","datasetNum":"94763","title":"GNPS - Metabolite release by marine nitrifiers","user":"bpbowen","site":"MassIVE","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","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":"377"}, {"dataset":"MSV000094762","datasetNum":"94762","title":"Characterization of engineered sorghum with reduced S-adenosyl-L-methionine (AdoMet) levels","user":"bpbowen","site":"MassIVE","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","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":"378"}, {"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","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;MS:1002732","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":"379"}, {"dataset":"MSV000094760","datasetNum":"94760","title":"GNPS - Plasmalogen oxidation induces the generation of excited molecules and electrophilic lipid species","user":"miyamoto_lab","site":"MassIVE","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","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":"380"}, {"dataset":"MSV000094757","datasetNum":"94757","title":"GNPS - The influence of APOE4 on the pTau interactome in sporadic Alzheimers disease","user":"Trixi","site":"MassIVE","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":"MS:1003029","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":"381"}, {"dataset":"MSV000094756","datasetNum":"94756","title":"GNPS - CROT deficiency in mice leads to an increase of omega-3 fatty acids","user":"SASINGH","site":"MassIVE","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":"773","fileSizeKB":"237410997","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1003028","modification":"MS:1002864","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":"382"}, {"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","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":"MS:1003356","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":"383"}, {"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","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":"MS:1003356","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":"384"}, {"dataset":"MSV000094749","datasetNum":"94749","title":"GNPS - Mass Spectrometry-Based Metabolomics for Siderophore Discovery","user":"marquisyazzie","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"385"}, {"dataset":"MSV000094744","datasetNum":"94744","title":"GNPS - Nose microbiota cultivated in a bioreactor under pre-established conditions ","user":"oloap1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"386"}, {"dataset":"MSV000094739","datasetNum":"94739","title":"GNPS_CMMC_KV_6_decarboxylated_amino_acids_with_various_chlorides","user":"kyvittali","site":"MassIVE","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","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":"387"}, {"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","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":"MS:1003183","modification":"MS:1002864","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":"388"}, {"dataset":"MSV000094730","datasetNum":"94730","title":"Top-Down Proteomics of Malayan Pitviper Venom","user":"daniel","site":"MassIVE","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","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":"389"}, {"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","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":"390"}, {"dataset":"MSV000094721","datasetNum":"94721","title":"GNPS_CMMC_KV-5_20AminoAcids_with_C2,3,4,8","user":"kyvittali","site":"MassIVE","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","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":"391"}, {"dataset":"MSV000094718","datasetNum":"94718","title":"GNPS - Vendor-dependent mobile phase contaminants affect neutral lipid analysis in lipidomics protocols","user":"joshuaroberts","site":"MassIVE","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":"392"}, {"dataset":"MSV000094717","datasetNum":"94717","title":"GNPS Human AKR1C3 Binds Agonists of GPR84 and Participates in an Expanded Polyamine Pathway","user":"ndudkina","site":"MassIVE","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":"MS:1002783","modification":"MS:1002864","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":"393"}, {"dataset":"MSV000094716","datasetNum":"94716","title":"GNPS MS Self Service Metabolomics Spring 2024 ","user":"cmboot","site":"MassIVE","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":"MS:1002791","modification":"MS:1002864","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":"394"}, {"dataset":"MSV000094711","datasetNum":"94711","title":"Nannochloropsis oceanica red body proteome","user":"johanAR","site":"MassIVE","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":"8","fileSizeKB":"747221","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"395"}, {"dataset":"MSV000094709","datasetNum":"94709","title":"Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics","user":"melihyilmaz","site":"MassIVE","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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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":"MS:1002634","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":"398"}, {"dataset":"MSV000094700","datasetNum":"94700","title":"Aged Mouse Muscle: Sedentary or Exercised Animals with or without Nicotinamide N-methyltransferase Inhibitor Treatment","user":"RidgelineTx","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"399"}, {"dataset":"MSV000094699","datasetNum":"94699","title":"GNPS - Untargeted metabolomics of ","user":"Paul_Lubrano","site":"MassIVE","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":"400"}, {"dataset":"MSV000094698","datasetNum":"94698","title":"GNPS - Targeted metabolomics of ","user":"Paul_Lubrano","site":"MassIVE","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":"MS:1002800","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":"401"}, {"dataset":"MSV000094691","datasetNum":"94691","title":"GNPS_CMMC_BA_VITAMINS_CDCA_UDCA_CA_SA_B7_B4_B6","user":"victoriadeleray","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1715019288000","created":"May. 6, 2024, 11:14 AM","description":"MS\/MS fragmentation data of bile acids conjugated to vitamins acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\n","fileCount":"13","fileSizeKB":"2839934","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","keywords":"Bile Acid, Vitamin","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":"ece779a147904a2d8bd691b654c3eacb","id":"402"}, {"dataset":"MSV000094688","datasetNum":"94688","title":"Untargeted metabolomic analysis in developing Camelina sativa seed coat\/endosperm and embryo - GNPS","user":"macorso","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1715010046000","created":"May. 6, 2024, 8:40 AM","description":"In this study we used untargeted metabolomics (LC-MS\/MS) semi-polar specialized metabolites that are accumulated in camelina seed coat and endosperm, and in the embryo at 6 developmental and 2 germination stages.","fileCount":"109","fileSizeKB":"37151610","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Camelina sativa (NCBITaxon:90675)","instrument":"MS:1002666","modification":"MS:1002864","keywords":"specialized metabolites;seed development;seed germination","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":"31ea853122184fd39a784a0523e365b0","id":"403"}, {"dataset":"MSV000094686","datasetNum":"94686","title":"Toward a comprehensive proteomic draft map of the West Virginia Ramp (Allium tricoccum) ","user":"ben_orsburn","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1715004522000","created":"May. 6, 2024, 7:08 AM","description":"Samples of the North American wild ramp (wild leak) Allium tricoccum were harvested during the vegetative and dormant stages of the life cycle. The vegatative plant was cut into root, bulb, stem and leaf sections and homogenized in a bead mill in a solution of 35\/35\/30 LCMS grade acetonitrile, methanol, and water respectively. Centrifugation at 13,000 x g at 5 minutes was used to separate the soluble metabolome and the solid material (protein, etc.,). The soluble solution was dried by speedvac and resuspended in 5 percent acetonitrile in water for metabolomic analysis on a Q Exactive system using a 20 minute DDA method. Metabolites were analyzed in Compound Discverer 3.1. The same process was performed for dormant ramps with the exception that only bulb and root material could be obtained. The precipitate for all samples was solubilized in 1x S-trap lysis buffer and prepared with the S-Trap mini spin column kits following all vendor protocols, with the exception that reduction and alkylation were not performed. The resulting peptides were quantified and 400ng of material was analyzed using a DDA PASEF method on an EvoSep One system. ","fileCount":"255","fileSizeKB":"12461097","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 tricoccum (NCBITaxon:138334)","instrument":"MS:1003124","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Allium tricoccum;Metaproteomics;West Virginia Wild Ramp;Wild leak","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":"PXD052017","task":"1140e04b787b441a9192b28dcdbe8afc","id":"404"}, {"dataset":"MSV000094682","datasetNum":"94682","title":"GNPS.huzhang UHPLC networking UCSD 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{"dataset":"MSV000094674","datasetNum":"94674","title":"GNPS_koolengroup_microorganisms_LCMS","user":"moyses","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1714840684000","created":"May. 4, 2024, 9:38 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":"362","fileSizeKB":"3809110","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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)","instrument":"MS:1002783;micrOTOF-Q II","modification":"MS:1002864","keywords":"Fungi;Fungus;Natural Product","pi":[{"name":"Hector 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coli biotin ligase BirA* was the first developed for proximity labeling of proteins (BioID). 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":"MS:1002732;MS:1003028","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:2016;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":"MS:1002634;MS:1003124","modification":"UNIMOD:2016;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":"416"}, {"dataset":"MSV000094658","datasetNum":"94658","title":"Affinity Purification of T. vaginalis and L. donovani","user":"ljliu","site":"MassIVE","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":"MS:1003029","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":"417"}, {"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","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":"MS:1002523","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":"418"}, {"dataset":"MSV000094652","datasetNum":"94652","title":"GNPS - Rhizosphere-associated metabolites of four wetland plant species","user":"khaviland","site":"MassIVE","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","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":"419"}, {"dataset":"MSV000094651","datasetNum":"94651","title":"GNPS-fenziwangluo-2024bishe-huzhang-20240501","user":"Liyu","site":"MassIVE","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":"420"}, {"dataset":"MSV000094650","datasetNum":"94650","title":"Extraction Comparison of Cannabis sativa inflorescences","user":"kellogglab","site":"MassIVE","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":"MS:1003095;5975 Agilent GC-MS","modification":"MS:1002864","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":"421"}, {"dataset":"MSV000094648","datasetNum":"94648","title":"Cheng Zhuo raw data for ACyPs manuscript","user":"bioczz","site":"MassIVE","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 - 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Methylobacterium sp. 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Leaf119 (NCBITaxon:1736261)","instrument":"Xevo G2 Q-Tof","modification":"MS:1002864","keywords":"mass spectrometry;Inverse Stable Isotopic Labeling","pi":[{"name":"Aaron Puri","email":"awpuri@uw.edu","institution":"University of Washington","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"58d6a9b1a6a64e27995b327fdab0ad72","id":"424"}, {"dataset":"MSV000094643","datasetNum":"94643","title":"GNPS - DOM_SRFAreference_DI and LC_HRMS","user":"JessPat","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1714496519000","created":"Apr. 30, 2024, 10:01 AM","description":"Suwannee River fulvic acid (SRFA), DOM reference material, analyzed by by DI-HRMS and LC-HRMS (DIA ESI-) (Orbitrap Q-Exactive). 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The labeled peptides were mixed a=and separated into 20 fractions via HPLC","fileCount":"21","fileSizeKB":"3517944","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"galactose oxidase, glycoprotein interaction","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":"bb18220be4414a798db8027abde195a0","id":"427"}, {"dataset":"MSV000094634","datasetNum":"94634","title":"SARS-CoV-2 infection results in a unique lung proteome signature long after virus is resolved in the golden hamster ","user":"amboese","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1714421470000","created":"Apr. 29, 2024, 1:11 PM","description":"Long COVID or post-acute sequelae of COVID-19 remains an ongoing public health issue that causes impairment for those afflicted and diminishes their ability to contribute to society. To address the host response underpinning respiratory PASC, we used the golden hamster model infected with ancestral SARS-CoV-2 and examined its lung proteome in a longitudinal experiment. We infected young 6-week old male and female hamsters with 105 TCID50 of virus using a high volume intranasal inoculum and sampled the lung at 1, 3, 5, and 31 days post infection (dpi). We compared the infected lung proteome to that of uninfected sex-matched controls. We found almost no differences in protein levels at 1dpi, with hundreds at 3 dpi, and thousands at 5 dpi. Many overlapping differential protein levels and pathways were seen in both sexes at 3 and 5dpi including the Coagulation and Complement cascades. Notably, we found differences between the sexes at 31dpi which included many decreased levels of protein in the males. We also noted an increase in 7 proteins in both sexes at 31dpi including proteins responsible for airway mucosal layer integrity such as Mucin 5B and Calcium-activated chloride channel regulator 1. Longitudinally, there were more proteins changed at each timepoint in the males and only one in the females. Overall, we show that there are changes to the lung proteome at 31dpi, a time when no SARS-CoV-2 remains, and that there are sex differences in that proteome after infection with the ancestral strain. We conclude that biological sex should be examined as a variable when testing medical countermeasures for PASC in the golden hamster due to host differences between the sexes. 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See \"SARS-CoV-2 infection unevenly impacts metabolism in the coronal periphery of the lungs\" for more information on this study","fileCount":"819","fileSizeKB":"66226415","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002634","modification":"MS:1002864","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":"447"}, {"dataset":"MSV000094589","datasetNum":"94589","title":"GNPS - Atlantic salmon gut metabolites","user":"sale","site":"MassIVE","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","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":"448"}, {"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","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":"MS:1002732","modification":"MS:1002864","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":"449"}, {"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","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":"MS:1002523","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":"450"}, {"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","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":"MS:1002523","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":"451"}, {"dataset":"MSV000094584","datasetNum":"94584","title":"GNPS - Synechococcus elongatus PCC 7942","user":"Nike","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"452"}, {"dataset":"MSV000094583","datasetNum":"94583","title":"The Ubiquitin Ligase RBX2\/SAG Regulates Mitochondrial Ubiquitination and Mitophagy","user":"WW_1","site":"MassIVE","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":"MS:1003029","modification":"MS:1002864","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":"453"}, {"dataset":"MSV000094579","datasetNum":"94579","title":"A proteomic map of the life cycle stages of the spotted lanterfly (Lycorma Delicatula)","user":"ben_orsburn","site":"MassIVE","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. ","fileCount":"316","fileSizeKB":"32013107","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Lycorma delicatula (NCBITaxon:130591)","instrument":"MS:1003124","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"Spotted lanternfly;Lycorma delicatula;Instars;Invasive lanternfly","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":"PXD051612","task":"e04587dba56248c28cf674f1da614156","id":"454"}, {"dataset":"MSV000094578","datasetNum":"94578","title":"GNPS - Bile_Salt_Hydrolase_engineered strains","user":"ipmohanty","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1713680154000","created":"Apr. 20, 2024, 11:15 PM","description":"Engineered bacterial strains with bile salt hydrolase that changed in their expression levels with high diet and diurnal changes were synthesized. 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. ","fileCount":"45","fileSizeKB":"15333756","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","keywords":"Nicotinamide;NMN;NR;Anti-aging supplements","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":"518f8428662d45d1992d0b7525b2bd36","id":"456"}, {"dataset":"MSV000094573","datasetNum":"94573","title":"Proteomics of a mature female black widow spider (Latrodectus) from southeastern Pennsylvania ","user":"ben_orsburn","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1713612905000","created":"Apr. 20, 2024, 4:35 AM","description":"In 2022 a vineyard in southeastern Pennsylvania was found to be infested with black widow spiders. 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. ","fileCount":"616","fileSizeKB":"75061160","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Latrodectus (NCBITaxon:6923)","instrument":"MS:1003124","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Black widow spider;Latrodectus variolus;Latrodectus mactans","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":"PXD051601","task":"37e88c307bfd46cfb800c26231d227ae","id":"457"}, {"dataset":"MSV000094570","datasetNum":"94570","title":"GNPS - Proteomic and metabolomic analysis of multifoliolate mutants of Trifolium repens","user":"ben_orsburn","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1713563576000","created":"Apr. 19, 2024, 2:52 PM","description":"Quadrifoliolate and pentafoliolate mutants of Trifolium repens were collected at Pug Mountain Vineyards in Southern Pennsylvania in the summer of 2023 along with matched trifoliolate plants gathered within the same cubic yard. 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. ","fileCount":"375","fileSizeKB":"39111699","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Trifolium repens (NCBITaxon:3899)","instrument":"MS:1003124","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Trifolium repens;4 leaf clover;5 leaf clover;Proteomics and Metabolomics","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":"PXD051590","task":"8f5a9d5ddc554da1ad82fc79d712a7a8","id":"458"}, {"dataset":"MSV000094569","datasetNum":"94569","title":"Native gel digest of recombinantly expressed trichomonas vaginalis proteasome","user":"bhurysz","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1713547735000","created":"Apr. 19, 2024, 10:28 AM","description":"Tv20S expressed recombinantly in S frugiperda, purified, excised from native gel and digested with trypsin.","fileCount":"7","fileSizeKB":"560769","spectra":"0","psms":"443","peptides":"231","variants":"393","proteins":"40","search_psms":"0","search_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);Spodoptera frugiperda (NCBITaxon:7108)","instrument":"MS:1003029","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"recombinant;Tv20S;proteasome","pi":[{"name":"Anthony O'Donoghue","email":"ajodonoghue@ucsd.edu","institution":"UCSD","country":"USA"},{"name":"Samuel Myers","email":"sam@lji.org","institution":"La Jolla Institute for Immunology","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD051584","task":"c4d2ee52fa64426798bf3e7d7c2a3b1d","id":"459"}, {"dataset":"MSV000094566","datasetNum":"94566","title":"Cold Storage Disrupts the Proteome Landscape in Rat Kidney Transplants ","user":"sbyrum","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1713462771000","created":"Apr. 18, 2024, 10:52 AM","description":"Approximately 70% of kidney grafts are obtained from deceased donors, and these grafts must be preserved in hypothermic conditions to prolong their viability until transplantation. 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":"MS:1003029","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":"460"}, {"dataset":"MSV000094565","datasetNum":"94565","title":"A comparison of acetic and formic acid in single H358 cells analyzed by diaPASEF","user":"ben_orsburn","site":"MassIVE","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. 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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":"MS:1003095","modification":"No post-translational-modifications are been included in the identified peptides of this dataset","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":"463"}, {"dataset":"MSV000094561","datasetNum":"94561","title":"GNPS - CMMC_bile_acid_amino_acid_conjugates","user":"ipmohanty","site":"MassIVE","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. The data for each reaction mixture is acquired on stepped collision energy and at only NCE 45. 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Concurrently, peptide retention shift between 100A and 120A was more pronounced for smaller peptides. \n\nThese two findings are at odds with the general notions that (1) larger surface area leads to higher retention, (2) size exclusion effects don't happen for small (<5000 Da) peptides in this pore size range and (3) size exclusion effects are directly (not inversely) proportional to analyte size. \n\nThe 100A (col2) and 120A (col3) jurkat digest samples were run in triplicates.","fileCount":"7","fileSizeKB":"10462509","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003028","modification":"C+57.021","keywords":"hplc separation;proteomics;fundamental mechanisms","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":"e36cf255fc814db086260eb35a6d67ae","id":"467"}, {"dataset":"MSV000094553","datasetNum":"94553","title":"Electron transport chain inhibition increases cellular dependence on purine transport and salvage","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1713290150000","created":"Apr. 16, 2024, 10:55 AM","description":"H460 cells were treated with vehicle or IACS for 24 hours followed by protein isolation and TMT10plex labelling. 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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":"MS:1002732","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":"478"}, {"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","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":"66","fileSizeKB":"10412831","spectra":"0","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":"479"}, {"dataset":"MSV000094531","datasetNum":"94531","title":"GNPS 2404_Workshop_Dysidea_avaria_and_Olea_europa","user":"lfxnothias","site":"MassIVE","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","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":"480"}, {"dataset":"MSV000094528","datasetNum":"94528","title":"GNPS - MSnLib - Multi-stage fragmentation mass spectral library","user":"corinnabrungs","site":"MassIVE","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":"9553","fileSizeKB":"137895481","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003112","modification":"MS:1002864","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":"481"}, {"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","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":"5","fileSizeKB":"288136","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"482"}, {"dataset":"MSV000094520","datasetNum":"94520","title":"Molecular Mechanisms of Stress Granule Disassembly Revealed by Chemogenetic Microenvironment Mapping (MicroMap) in Living Cells","user":"RoderickPan","site":"MassIVE","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":"MS:1003230","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":"483"}, {"dataset":"MSV000094519","datasetNum":"94519","title":"GNPS - Metabolomics of Ilex guayusa leaves focused on methylxanthine","user":"LPN_IKIAM","site":"MassIVE","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":"MS:1003252","modification":"MS:1002864","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":"484"}, {"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","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":"MS:1002523","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":"485"}, {"dataset":"MSV000094516","datasetNum":"94516","title":"GNPS - Fasting in Female retina RPE with C13 glucose tracing","user":"jianhaidulab","site":"MassIVE","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","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":"486"}, {"dataset":"MSV000094515","datasetNum":"94515","title":"GNPS - U19 ADRC NCRAD 42167 Stool","user":"jzemlin","site":"MassIVE","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":"487"}, {"dataset":"MSV000094513","datasetNum":"94513","title":"GNPS - Bacteroides thetaiotaomicron Lipidomics LC-MSMS","user":"MSF_MPI_Tue","site":"MassIVE","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. ","fileCount":"294","fileSizeKB":"7529043","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002666","modification":"MS:1002864","keywords":"Lipidomics","pi":[{"name":"Ruth Ley","email":"ruth.ley@tuebingen.mpg.de","institution":"Max Planck Institute for Biology Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6800722aa363414183acce44c29603bf","id":"488"}, {"dataset":"MSV000094512","datasetNum":"94512","title":"GNPS - CMMC_VDC13milprojectreferencestandards","user":"victoriadeleray","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712787334000","created":"Apr. 10, 2024, 3:15 PM","description":"MS\/MS fragmentation data of sample VD_C13 acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.\r\n","fileCount":"16","fileSizeKB":"1888263","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","keywords":"Synthetic;Reference","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":"863893bdd0ef4ad3afb6817df8ff83b1","id":"489"}, {"dataset":"MSV000094511","datasetNum":"94511","title":"GNPS - Headspace GC-MS of ecuadorian Amazonia honey","user":"LPN_IKIAM","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712781223000","created":"Apr. 10, 2024, 1:33 PM","description":"Headspace GC-MS of ecuadorian Amazonia honey in three bee species (Melipona fuscopilosa, Tetragonisca angustula and Melipona fasciculata).","fileCount":"125","fileSizeKB":"1493121","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 fuscopilosa (NCBITaxon:486752);Tetragonisca angustula (NCBITaxon:166442);Melipona fasciculata (NCBITaxon:596912)","instrument":"GCMS-QP2020NX","modification":"MS:1002864","keywords":"Headspace;Amazonia honey;GC-MS","pi":[{"name":"Angiely Valeria Camacho Aguilar","email":"angiely.camacho@est.ikiam.edu.ec","institution":"IKIAM Amazon Regional University","country":"Ecuador"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"df68cf23735247628ae6bd9d72fc7d87","id":"490"}, {"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","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","keywords":"Autophagy, fibroblasts, lysosomal storage disorders, NAD, neurodegeneration, NPC1","pi":[{"name":"Viktor I. Korolchuk","email":"viktor.korolchuk@newcastle.ac.uk","institution":"Biosciences Institute, Faculty of Medical Sciences, Newcastle Universit","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"b426584301094c4c82bcb52e21640274","id":"491"}, {"dataset":"MSV000094504","datasetNum":"94504","title":"GNPS - U19 Wisconsin Stool Alzheimer's Disease","user":"jzemlin","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712691217000","created":"Apr. 9, 2024, 12:33 PM","description":"Corrected U19 Wisconsin fecal dataset containing roughly 333 human stool samples. 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":"912","fileSizeKB":"48142287","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","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":"7ea9007905334264a5446f22d02c02f6","id":"492"}, {"dataset":"MSV000094503","datasetNum":"94503","title":"Online Monitoring and Stable Isotope Tracing of Cancer Associated Volatiles in Murine Model Captures Oxidative Stress Markers in vivo","user":"choueiry_2","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712691186000","created":"Apr. 9, 2024, 12:33 PM","description":"In this study, we utilized advanced secondary electrospray ionization (SESI) technique coupled with a high-resolution mass spectrometer (HRMS) to non-invasively monitor lung cancer tumor volatiles in a pre-clinical mouse model in real time. 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. 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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","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":"496"}, {"dataset":"MSV000094489","datasetNum":"94489","title":"Proteome of clothianidin exposed honey bees reveals a possible mechanism behind impairment of sucrose responsiveness","user":"NadiaTs","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712592649000","created":"Apr. 8, 2024, 9:10 AM","description":"Honey bee workers were exposed to Clothianidin for 7 days. 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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":"MS:1003005","modification":"MS:1002864","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":"498"}, {"dataset":"MSV000094483","datasetNum":"94483","title":"Liver and Pancreatic-Targeted Interleukin-22 as a Therapeutic for Metabolic Dysfunction-Associated Steatohepatitis","user":"hsajiir","site":"MassIVE","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":"MS:1002634","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":"499"}, {"dataset":"MSV000094482","datasetNum":"94482","title":"GNPS - Bacteria Endophyte Extract (Strain 191, 76)","user":"nolasuryani","site":"MassIVE","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":"MS:1003002","modification":"MS:1002864","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":"500"}, {"dataset":"MSV000094479","datasetNum":"94479","title":"Comparative proteomic analysis of Arabidopsis plants treated with osmotic stress","user":"Liyongkang","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"501"}, {"dataset":"MSV000094478","datasetNum":"94478","title":"GNPS - proteomics and lipidomics of LAT1-4F2hc complex","user":"wudi1985","site":"MassIVE","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":"MS:1002877","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":"504"}, {"dataset":"MSV000094474","datasetNum":"94474","title":"GNPS - CMMC_Stearic_Acid_with_QXX_Tripeptides","user":"kyvittali","site":"MassIVE","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","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":"505"}, {"dataset":"MSV000094473","datasetNum":"94473","title":"GNPS - CMMC_Oleic_Acid_with_QXX_Tripeptides","user":"kyvittali","site":"MassIVE","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","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":"506"}, {"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","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":"MS:1002732","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":"507"}, {"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","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":"MS:1002791","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\"","keywords":"Enzymatic assay;ROCK1;Fhod1;Fhod3","pi":[{"name":"Steven G. Clarke","email":"clarke@mbi.ucla.edu","institution":"University of California - Los Angeles","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"809b1cafef2f413ab36dc726d063b288","id":"508"}, {"dataset":"MSV000094468","datasetNum":"94468","title":"GNPS - CMMC_Bile_Salt_Hydrolase_Assay","user":"Dpattynama","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712253763000","created":"Apr. 4, 2024, 11:02 AM","description":"MS\/MS fragmentation data of BSH enzyme assay of cholic glycine with a mix of 10 amino acids (Phenylalanine, Alanine, Arginine, Asparagine, Aspartic Acid, Cysteine, Glutamic Acid, Glutamine, Histidine, and Isoleucine) acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column. ","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","keywords":"Bile Salt Hydrolase;Cholic glycine;BSH Assay;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":"37700e85058c4527a6ee10e312922fd2","id":"509"}, {"dataset":"MSV000094464","datasetNum":"94464","title":"GNPS - Selenoprotein I is indispensable for ether lipid homeostasis and proper myelination","user":"aeshay","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712170691000","created":"Apr. 3, 2024, 11:58 AM","description":"Selenoprotein I (SELENOI) catalyzes the final reaction of the CDP-ethanolamine branch of the Kennedy pathway, generating the phospholipids phosphatidylethanolamine (PE) and plasmenyl-PE. Plasmenyl-PE is a key component of myelin and is characterized by a vinyl ether bond that preferentially reacts with oxidants, thus serves as a sacrificial antioxidant. 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":"MS:1002732","modification":"MS:1002864","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":"510"}, {"dataset":"MSV000094462","datasetNum":"94462","title":"GNPS Rhodococcus sp. ACT016_CultureMediaVariation","user":"carolinafmiranda","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712157438000","created":"Apr. 3, 2024, 8:17 AM","description":"ACT016 strain was growth in four different culture media: A1, TSB, TSBY and ISP2 in order to compare the metabolism production. 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;MS:1000122","modification":"MS:1002864","keywords":"bacteria soil;Rhodococcus;metabolomics;NP3_MS_Workflow","pi":[{"name":"Daniela B. B. Trivella","email":"daniela.trivella@lnbio.cnpem.br","institution":"Brazilian Center for Research in Energy and Materials","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d39c2e5050ae4ede8d20c982b80faaee","id":"511"}, {"dataset":"MSV000094461","datasetNum":"94461","title":"GNPS Streptomyces sp. ACT015_CultureMediaVariation","user":"carolinafmiranda","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712154516000","created":"Apr. 3, 2024, 7:28 AM","description":"ACT015 strain was growth in four different culture media: A1, TSB, TSBY and ISP2 in order to compare the metabolism production. AcOEt exctratcts were analysed through UPLC-MS\/MS and MS data was processed using NP3_MS_workflow. ","fileCount":"26","fileSizeKB":"1604574","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"ACQUITY UPLC H-Class;MS:1000122","modification":"MS:1002864","keywords":"bacteria soil;Streptomyces;metabolomics;NP3_MS_Workflow","pi":[{"name":"Daniela B. B. Trivella","email":"daniela.trivella@lnbio.cnpem.br","institution":"Brazilian Center for Research in Energy and Materials","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"bb2c4b0908e043cc9a4ecca38ff13955","id":"512"}, {"dataset":"MSV000094460","datasetNum":"94460","title":"GNPS Brevibacillus sp. FIR094_CultureMediaVariation","user":"carolinafmiranda","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712152842000","created":"Apr. 3, 2024, 7:00 AM","description":"FIR094 strain was growth in three different culture media: TSB, LB and R2A in order to compare the metabolism production. 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;MS:1000122","modification":"MS:1002864","keywords":"soil bacteria;brevibacillus;metabolomics;NP3_MS_Workflow","pi":[{"name":"Daniela B. B. Trivella","email":"daniela.trivella@lnbio.cnpem.br","institution":"Brazilian Center for Research in Energy and Materials","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"47f4d696913d40d282829c1c5de52c39","id":"513"}, {"dataset":"MSV000094459","datasetNum":"94459","title":"Phosphoproteomics reveals selective induction of signal transduction pathways by different lysophosphatidic acid species in macrophages","user":"Wszymanski","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1712138177000","created":"Apr. 3, 2024, 2:56 AM","description":"Lysophosphatidic acid (LPA) species, prevalent in the tumor microenvironment (TME), adversely impact various cancers. In ovarian cancer, the 18:0 and 20:4 LPA species in particular are associated with shorter relapse-free survival, indicating distinct effects on cellular signaling networks. 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":"MS:1003028","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":"514"}, {"dataset":"MSV000094457","datasetNum":"94457","title":"Digestion of whey peptide induces bioactivity on glial cells","user":"lucilene","site":"MassIVE","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":"515"}, {"dataset":"MSV000094447","datasetNum":"94447","title":"GNPS - CMMC_Bile_acid_derivatives_synthesis_04_01_2024","user":"apatan","site":"MassIVE","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","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":"516"}, {"dataset":"MSV000094445","datasetNum":"94445","title":"GNPS - Brain energy metabolism adenosine mediated cAMP signaling in astrocytes.","user":"viragsagikiss","site":"MassIVE","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","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":"517"}, {"dataset":"MSV000094443","datasetNum":"94443","title":"GNPS - Discovery of Biofilm Inhibitors from the Microbiota of Marine Egg Masses","user":"lkyei","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1711977565000","created":"Apr. 1, 2024, 6:19 AM","description":"Bacteria associated with marine egg masses cultured in liquid media","fileCount":"165","fileSizeKB":"76427456","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002785","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":"518"}, {"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","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":"MS:1002732","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":"519"}, {"dataset":"MSV000094439","datasetNum":"94439","title":"Coupland et al., Cryo-EM of synaptic vesicles reveals loading-induced V-ATPase dissociation","user":"Younlab_Toronto","site":"MassIVE","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":"MS:1003230","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":"520"}, {"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","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;MS:1002732;MS:1002584","modification":"MS:1002864","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":"521"}, {"dataset":"MSV000094436","datasetNum":"94436","title":"GNPS - 20240329_Aging_negative_RP_001","user":"Alesia","site":"MassIVE","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":"MS:1002674","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":"522"}, {"dataset":"MSV000094435","datasetNum":"94435","title":"GNPS - Microbial iron limitation in the ocean's twilight zone","user":"SiderophoreResearcher","site":"MassIVE","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","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":"523"}, {"dataset":"MSV000094434","datasetNum":"94434","title":"De novo nine-species benchmark peptide identifications for Casanovo and other methods","user":"melihyilmaz","site":"MassIVE","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. 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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","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":"525"}, {"dataset":"MSV000094430","datasetNum":"94430","title":"Test MassIVE Dataset for Metadata and License","user":"lhenson","site":"MassIVE","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","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":"526"}, {"dataset":"MSV000094429","datasetNum":"94429","title":"GNPS - Dataset Creation from GNPS Molcular Networking - 499f3454320146b0ac6caba3b0486ef4","user":"ndidonat","site":"MassIVE","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","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":"527"}, {"dataset":"MSV000094416","datasetNum":"94416","title":"Analysis of histone PTMs in the choanoflagellate Salpingoeca rosetta","user":"gahan","site":"MassIVE","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":"528"}, {"dataset":"MSV000094415","datasetNum":"94415","title":"Bering Strait surface water and Chukchi Sea bottom water microbiome metaproteomics ","user":"melihyilmaz","site":"MassIVE","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":"MS:1002523","modification":"UNIMOD:1 - \\\\\\\\\\\\\\\"Acetylation.\\\\\\\\\\\\\\\" | UNIMOD:4 - \\\\\\\\\\\\\\\"Iodoacetamide derivative.\\\\\\\\\\\\\\\" | UNIMOD:5 - \\\\\\\\\\\\\\\"Carbamylation.\\\\\\\\\\\\\\\" | UNIMOD:7 - \\\\\\\\\\\\\\\"Deamidation.\\\\\\\\\\\\\\\" | UNIMOD:35 - 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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":"MS:1002732","modification":"MS:1002864","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":"533"}, {"dataset":"MSV000094406","datasetNum":"94406","title":"Chemical tools to define and manipulate interferon-induced Ubl protease USP18","user":"ronholes7059","site":"MassIVE","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":"5","fileSizeKB":"5994383","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029","modification":"UNIMOD:2016;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":"534"}, {"dataset":"MSV000094405","datasetNum":"94405","title":"GNPS - Metabolomics of Bacillus subtilis interactions with SynCom","user":"scottjarmusch11","site":"MassIVE","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":"MS:1002726","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":"536"}, {"dataset":"MSV000094403","datasetNum":"94403","title":"GNPS - The role of ATP citrate lyase in myelin formation and maintenance","user":"earmstrong","site":"MassIVE","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":"537"}, {"dataset":"MSV000094401","datasetNum":"94401","title":"Proteomic profile of hippocampus regions from the pilocarpine medial temporal lobe epilepsy model","user":"amcanto","site":"MassIVE","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","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":"538"}, {"dataset":"MSV000094400","datasetNum":"94400","title":"Differences in the Cerebral Amyloid Angiopathy Proteome in Alzheimers Disease and Mild Cognitive Impairment","user":"KanshinED1","site":"MassIVE","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":"MS:1002877","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":"539"}, {"dataset":"MSV000094397","datasetNum":"94397","title":"GNPS - 20240325_Natural Products Research and Innovation Center_Metabolomics_Workshop_Dataset","user":"bciap01","site":"MassIVE","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. ","fileCount":"61","fileSizeKB":"6272492","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Persea americana (NCBITaxon:3435);Trichoderma (NCBITaxon:5543);Euclea (NCBITaxon:85201)","instrument":"MS:1002523","modification":"MS:1002864","keywords":"Fungal metabolites;natural products","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":"70b40dca2c034c30bdb1f25b3b960e87","id":"540"}, {"dataset":"MSV000094396","datasetNum":"94396","title":"Thivierge_etal_Drosha_BioID_2024","user":"gingraslab","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1711366081000","created":"Mar. 25, 2024, 4:28 AM","description":"This dataset consists of the files for 22 BioID samples: .wiff and .wiff.scan raw MS files, .mzML peak files, and MSPLIT results files; all acquired on TripleTOF 6600 mass spectrometers 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.\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":"541"}, {"dataset":"MSV000094395","datasetNum":"94395","title":"GNPS-U19_ADRC_plasma_samples_project_41945","user":"zhaohaoq","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1711341852000","created":"Mar. 24, 2024, 9:44 PM","description":"U19 ADRC 654 plasma samples project number 41945. 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":"1690","fileSizeKB":"76140434","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":"plasma;alzheimer's disease","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":"48bb46c977414441b409eca04bbaa34e","id":"542"}, {"dataset":"MSV000094394","datasetNum":"94394","title":"GNPS - Spirolactone, an unprecedented antifungal beta-lactone spiroketal macrolidemacrolides from Streptomyces iranensis","user":"yyds","site":"MassIVE","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":"MS:1002791","modification":"MS:1002864","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":"543"}, {"dataset":"MSV000094393","datasetNum":"94393","title":"GNPS - CMMC_Reactions_of_BA_Derivatives_synthesis_Set_2","user":"apatan","site":"MassIVE","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","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":"544"}, {"dataset":"MSV000094391","datasetNum":"94391","title":"GNPS - CMMC_BA_Derivatives_synthesis_1_set_of_Reactions","user":"apatan","site":"MassIVE","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","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":"545"}, {"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","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":"546"}, {"dataset":"MSV000094385","datasetNum":"94385","title":"GNPS - Annotation of DOM Metabolomes with Ultrahigh Resolution Mass Spectrometry Libraries","user":"coffe198","site":"MassIVE","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. 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\\\"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":"549"}, {"dataset":"MSV000094379","datasetNum":"94379","title":"BioID proximity labeling of interactome using BirA* tagged IRE1 ","user":"Kurt_Dejgaard2","site":"MassIVE","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":"MS:1003094","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":"550"}, {"dataset":"MSV000094370","datasetNum":"94370","title":"PPH24 - Botrytis cinerea Steroidal glycoalkaloids","user":"iris66","site":"MassIVE","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","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":"551"}, {"dataset":"MSV000094368","datasetNum":"94368","title":"Identification of 187AA unique peptides by mass spectrometry 2","user":"huzhijuan","site":"MassIVE","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":"MS:1003005","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":"552"}, {"dataset":"MSV000094366","datasetNum":"94366","title":"Identification of 187AA unique peptides by mass spectrometry","user":"huzhijuan","site":"MassIVE","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":"MS:1003005","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":"553"}, {"dataset":"MSV000094364","datasetNum":"94364","title":"GNPS - Dataset Creation from GNPS Molcular Networking - DOM metabolization from cyanobacterial and non cyanobacterial diazotrophs","user":"MarineValletMPICE","site":"MassIVE","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":"MS:1002634;Dionex instrument model","modification":"MS:1002864","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":"554"}, {"dataset":"MSV000094362","datasetNum":"94362","title":"TopDIA - temp data - file upload issue","user":"ARBasharat","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"555"}, {"dataset":"MSV000094358","datasetNum":"94358","title":"GNPS - MS2 spectra from Streptomyces bacteria containing fluorinated compounds and terminal alkynes","user":"atekel","site":"MassIVE","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":"MS:1003112","modification":"MS:1002864","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":"556"}, {"dataset":"MSV000094357","datasetNum":"94357","title":"GNPS - 2024039_KastoriaBiomass_9.8mg_25MeOH","user":"Sofia_Iliakop","site":"MassIVE","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":"MS:1002666","modification":"MS:1002864","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":"557"}, {"dataset":"MSV000094355","datasetNum":"94355","title":"GNPS - Effect of itaconate and 4-octylitaconate on the metabolome of VSV infected cells","user":"rinschen","site":"MassIVE","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":"MS:1000937","modification":"MS:1002864","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":"558"}, {"dataset":"MSV000094353","datasetNum":"94353","title":"GNPS Nostoc extracts for Cyanopeptolins detection","user":"Sofia_Iliakop","site":"MassIVE","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":"MS:1002666","modification":"MS:1002864","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":"559"}, {"dataset":"MSV000094351","datasetNum":"94351","title":"Sustained bacterial N2O reduction at acidic pH","user":"ghe3","site":"MassIVE","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":"MS:1002526","modification":"NA","keywords":"N2O reduction;acidic soils;Environmental microbiology;Microbial physiology;Co-culture EV","pi":[{"name":"Frank E. Loffler","email":"frank.loeffler@utk.edu","institution":"University of Tennessee-Knoxville","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"d5e8c12416d04749912fef56b727dc27","id":"560"}, {"dataset":"MSV000094348","datasetNum":"94348","title":"Anti-Ferroptotic Effect of Cannabidiol in Human Skin Keratinocytes Characterized by Data-Independent Acquisition-Based Proteomics","user":"Huifang123","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1710791615000","created":"Mar. 18, 2024, 12:53 PM","description":"SWATH-MS data for human keratinocytes (HaCaT cell line), sample 010-012 indicates HaCaT cells with no treatment, sample 013-015 indicates HaCaT cells induced by erastin, sample 0016-018 indicates HaCaT cells treated by erastin and CBD. 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","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":"561"}, {"dataset":"MSV000094347","datasetNum":"94347","title":"SDS22 coordinates the assembly of holoenzymes from nascent protein phosphatase-1","user":"madamo","site":"MassIVE","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":"MS:1002732","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:2016","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":"562"}, {"dataset":"MSV000094338","datasetNum":"94338","title":"GNPS - 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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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{"dataset":"MSV000094323","datasetNum":"94323","title":"Impact of Glycan Depletion, Glycan Debranching and Increased Glycan Charge on HIV-1 Neutralization Sensitivity and Immunogenicity","user":"ada1g14","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1710454633000","created":"Mar. 14, 2024, 3:17 PM","description":"Dataset for N-linked glycosylation analysis contained within 'Impact of Glycan Depletion, Glycan Debranching and Increased Glycan Charge on HIV-1 Neutralization Sensitivity and Immunogenicity'","fileCount":"28","fileSizeKB":"100388707","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029","modification":"Protein Metrics N-glycan library 308 mammalian no 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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":"572"}, {"dataset":"MSV000094311","datasetNum":"94311","title":"Top-Down Proteomics Identifies Plasma Proteoform Signatures of Liver Cirrhosis Progression","user":"mikehollas123","site":"MassIVE","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":"93","fileSizeKB":"327698572","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003029","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":"573"}, {"dataset":"MSV000094308","datasetNum":"94308","title":"Analysis of phot2 phosphorylation profiles and interaction partners involved in chloroplast accumulation and avoidance responses in Arabidopsis thaliana","user":"Urszula","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1710335659000","created":"Mar. 13, 2024, 6:14 AM","description":"The project aims to use photocycle mutants to understand the importance of phot2 autophosphorylation for signaling leading to chloroplast accumulation and avoidance. 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 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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":"580"}, {"dataset":"MSV000094298","datasetNum":"94298","title":"A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology","user":"zzyingying753","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"581"}, {"dataset":"MSV000094297","datasetNum":"94297","title":"Brain-wide alterations revealed by spatial transcriptomics and proteomics in COVID-19 infection","user":"JSha","site":"MassIVE","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":"49","fileSizeKB":"37051566","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732","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":"582"}, {"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","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":"583"}, {"dataset":"MSV000094294","datasetNum":"94294","title":"B._Raktan_Ahmed_P131_VS15_2024","user":"gingraslab","site":"MassIVE","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":"584"}, {"dataset":"MSV000094293","datasetNum":"94293","title":"Minimal Change Disease: a proteomics approach ","user":"ioanapralea","site":"MassIVE","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":"MS:1002726","modification":"MS:1002864","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":"585"}, {"dataset":"MSV000094292","datasetNum":"94292","title":"synthesized of 2H,2Cl-PFOA from 2H,2H-PFOA or from 6:2 FTOH.","user":"Bing","site":"MassIVE","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","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":"586"}, {"dataset":"MSV000094290","datasetNum":"94290","title":"Fervidibacter sacchari diferential proteomics under different growth conditions","user":"nnou","site":"MassIVE","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":"MS:1003029","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":"587"}, {"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","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":"588"}, {"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","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. The improved function of the IgGh47 subclass in two distant biological systems provides new insights into antibody function and how to enhance it for opsonic function.","fileCount":"21","fileSizeKB":"25414401","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002877","modification":"MS:1002864","keywords":"Streptococcus pyogenes;Hinge-engineering;M-protein;SARS-COV-2","pi":[{"name":"pontus nordenfelt","email":"pontus.nordenfelt@med.lu.se","institution":"Lund University","country":"Sweden"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"41bf8f3bf2c04b66aefb2ff9da02e7b2","id":"589"}, {"dataset":"MSV000094286","datasetNum":"94286","title":"Identification of host proteins implicated in Hepatitis B virus genome packaging ","user":"iwhitworth","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1710118973000","created":"Mar. 10, 2024, 6:02 PM","description":"We isolated pgRNA and characterized its protein interactome in cells transfected with packaging competent and packaging incompetent HBV plasmids to identify proteins potentially playing a role in viral packaging. 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. ","fileCount":"18","fileSizeKB":"12356816","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606);Hepatitis B virus (NCBITaxon:10407)","instrument":"Q Exactive","modification":"MS:1002864","keywords":"interactomics;RNA binding proteins;Hepatitis B Virus;viral packaging;HyPR-MS;RNA-protein interactions;host-pathogen interactions;pregenomic RNA","pi":[{"name":"Lloyd Smith","email":"smith@chem.wisc.edu","institution":"University of Wisconsin-Madison","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050509","task":"d2b666777f9b4fe7a2d45d8baa5cb451","id":"590"}, {"dataset":"MSV000094278","datasetNum":"94278","title":"GNPS - CMMC_Bile Acids_dipeptides - 3\/8\/2024","user":"Dpattynama","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709919144000","created":"Mar. 8, 2024, 9:32 AM","description":"MS\/MS fragmentation data of bile acid conjugated with dipeptides standards acquired on Q Exactive - with chromatographic separation on a Phenomenex polar C18 column.","fileCount":"8","fileSizeKB":"486075","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","keywords":"dipeptides;bile acids;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":"1dc54dd92c104f59bd78a1df2926768b","id":"591"}, {"dataset":"MSV000094277","datasetNum":"94277","title":"Hemolymph of queen honey bees at different reproductive stages","user":"amcafee","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709918801000","created":"Mar. 8, 2024, 9:26 AM","description":"Hemolymph samples were taken from queens at different ages and reproductive stages: Virgins (0-2 d old), newly mated (10-12 d old), established mated (1 month old) and banked mated (1 month old but held in a queen bank for 18 d, which restricts laying).","fileCount":"8","fileSizeKB":"98531414","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","instrument":"MS:1003230","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\"","keywords":"Hemolymph;reproduction;mating;aging","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":"","task":"41477c4f82d9450d88c422ca8d6d64f5","id":"592"}, {"dataset":"MSV000094276","datasetNum":"94276","title":"GNPS - Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease","user":"guerra","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709915360000","created":"Mar. 8, 2024, 8:29 AM","description":"Cross-linking AE-MS dataset for NDUFAF6 interactions","fileCount":"9","fileSizeKB":"8265912","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003094","modification":"MS:1002864","keywords":"Deep mutational scanning;Complex I assembly","pi":[{"name":"David Pagliarini","email":"pagliarini@wustl.edu","institution":"Washington University in St. Louis","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"c1e86a510bda4eb6a0bcaa046d31bfee","id":"593"}, {"dataset":"MSV000094271","datasetNum":"94271","title":"Analysis of ubiquitinylation sites of IDO1 after incubation of cells with iDeg-1","user":"janning","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709890003000","created":"Mar. 8, 2024, 1:26 AM","description":"IFNgamma-stimulated BxPC3 cells were treated with 20 uM iDeg-1 or DMSO as a control for 6 h prior to lysate preparation. 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Samples were fractionated using high-pH chromatograpy and analysed using nanoHPLC-MS\/MS and an LFQ approach.","fileCount":"65","fileSizeKB":"484770688","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002523","modification":"MS:1002864","keywords":"proteome profiling, iDeg-1, degrader","pi":[{"name":"Petra Janning","email":"petra.janning@mpi-dortmund.mpg.de","institution":"MPI of Molecular Physiology","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results;Study Design","status":"Partial","private":"false","hash":"","px":"PXD050474","task":"e71131fb741f410c853ac053ab75668a","id":"595"}, {"dataset":"MSV000094269","datasetNum":"94269","title":"Top-down Proteomics of Venom Gland Organoids II","user":"daniel","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709869835000","created":"Mar. 7, 2024, 7:50 PM","description":"Top-down proteomics of venom protein of venom-gland organoids aspidelaps. 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SDS was removed, and samples were digested with 1:15 of Sequencing Grade Modified Trypsin (Promega) using an S-trap micro device (Protifi) at 47 degC for 1 h. Peptides were lyophilized, and equal volumes of reconstituted samples were mixed to generate a study pool quality control (SPQC) sample. 1D-LC-MS\/MS was performed 0.75 micrograms of each sample in a block-randomized order as described in metadata. Samples were analyzed using a M-Class UPLC system (Waters) coupled to a coupled to a Fusion Lumos mass spectrometer (Thermo) via a Nanospray Flex ionization source. Samples were first trapped on a Symmetry C18 180 micrometer x 20 mm trapping column (5 microliters\/min at 99.9\/0.1 v\/v H2O\/MeCN) followed by an analytical sepa-ration using a 1.7 micrometer ACQUITY HSS T3 C18 75 micrometer x 250 mm column (Waters) with a 90 min gradient of 5 to 30% MeCN with 0.1% formic acid at a flow rate of 400 nl\/min and column temperature of 55 degC. 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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. 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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. 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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":"MS:1002523;MS:1002877;MS:1003028","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":"MS:1003230","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":"608"}, {"dataset":"MSV000094235","datasetNum":"94235","title":"The proteomics data of Aspergillus niger ATCC 1015 after spirolactone treatment","user":"yyds","site":"MassIVE","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":"609"}, {"dataset":"MSV000094234","datasetNum":"94234","title":"Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap)","user":"mwfoster","site":"MassIVE","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":"MS:1002732","modification":"UNIMOD:2016;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. 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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":"MS:1002523","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":"612"}, {"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","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":"613"}, {"dataset":"MSV000094226","datasetNum":"94226","title":"GNPS - Metabolomics data for Figure 1D-1F. 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","fileCount":"36","fileSizeKB":"7985901","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003112","modification":"MS:1002864","keywords":"metabolomics","pi":[{"name":"Zach Schafer","email":"zschafe1@und.edu","institution":"University of Notre Dame","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050289","task":"8ef3eb185986426a8196bdfcefe85625","id":"614"}, {"dataset":"MSV000094220","datasetNum":"94220","title":"GNPS - CMMC Feb 01 2024 Carboxylic Acids Conjugated with Amino Acids - 1","user":"kyvittali","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709349654000","created":"Mar. 1, 2024, 7:20 PM","description":"Amidation reaction was used. 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","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":"615"}, {"dataset":"MSV000094219","datasetNum":"94219","title":"Diagnosing and staging epithelial ovarian cancer by serum glycoproteomic profiling","user":"GX_InterVenn","site":"MassIVE","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":"616"}, {"dataset":"MSV000094218","datasetNum":"94218","title":"GNPS - Caffeine Inhibitory Effect on Catalase","user":"simonezuffa","site":"MassIVE","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","keywords":"plants;Malpighiaceae","pi":[{"name":"Pieter C. Dorrestein","email":"pdorrestein@ucsd.edu","institution":"University of California at San Diego","country":"USA"},{"name":"Vanderlan da Silva Bolzani","email":"vanderlan.bolzani@unesp.br","institution":"Sao Paulo State University (UNESP) - Araraquara","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f5ff8a2714a04b75ac839d5b99702148","id":"618"}, {"dataset":"MSV000094216","datasetNum":"94216","title":"GNPS - Ventral Tegmental Area of Murine Brain in Caffeine\/Alcohol Study","user":"simonezuffa","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709335172000","created":"Mar. 1, 2024, 3:19 PM","description":"Untargeted profiling of brain ventral tegmental area (VTA) in a mouse model looking at caffeine and alcohol interactions. Extraction with MeOH\/H2O 50\/50. Analyzed with a 5 cm C18 column and 10 minutes gradient elution. 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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). To quench the reaction, we added 2.56uL of Ammonium Bicarbonate (50mM) for 15min at room temperature (shaking at 300rpm).","fileCount":"13","fileSizeKB":"32881640","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002732","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";DMTMM","keywords":"Centrosomes;CDK5RAP2;SPD-5;Polo kinase 1;Multivalency;Phase Separation;Cross-linking Mass-spectrometry;in vitro Reconstitution;Cell Division","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":"5af0a58566074ec9ad84093550bce55b","id":"627"}, {"dataset":"MSV000094198","datasetNum":"94198","title":"Multivalent Coiled-Coil Interactions as a Conserved Design Principle for Centrosome Assembly","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709168339000","created":"Feb. 28, 2024, 4:58 PM","description":"Crosslinking reactions were prepared at room temperature with 1uM dephosphorylated SPD-5, 1uM Constitutively Active (CA) PLK-1, 0.2 mM ATP, 10 mM MgCl2, 150mM KCl, 25mM HEPES, pH7.4 and 0.5mM DTT. Samples were incubated for 2 hr at room temperature followed by addition of 1.47 uL of DMTMM (20mg\/mL) for 45min at room temperature (shaking at 300 rpm). To quench the reaction, we added 2.56uL of Ammonium Bicarbonate (50mM) for 15min at room temperature (shaking at 300rpm).","fileCount":"13","fileSizeKB":"33034567","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002732","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";DMTMM","keywords":"Centrosomes;CDK5RAP2;SPD-5;Polo kinase 1;Multivalency;Phase Separation;Cross-linking Mass-spectrometry;in vitro Reconstitution;Cell Division","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":"888fe69ee03d428193c0fad2cc839aa9","id":"628"}, {"dataset":"MSV000094197","datasetNum":"94197","title":"Quantitative proteomic analysis reveals unique Hsp90 cycle-dependent client interactions","user":"Erick_Rios2","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709165023000","created":"Feb. 28, 2024, 4:03 PM","description":"Quantitative proteomics data from DIA-MS experiments of soluble proteins in lysates of yeast expressing either Hsc82-WT or nine different temperature-sensitive alleles.","fileCount":"38","fileSizeKB":"37400921","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003028","modification":"MS:1002864","keywords":"DIA;DIA-MS;Hsp90;Mutant;cochaperone;molecular chaperone","pi":[{"name":"Jill Johnson","email":"jilljohn@uidaho.edu","institution":"University of Idaho","country":"United States of America"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"f4d2371a83f5423c8df66e7a5e70dd9f","id":"629"}, {"dataset":"MSV000094195","datasetNum":"94195","title":"Multivalent Coiled-Coil Interactions as a Conserved Design Principle for Centrosome Assembly","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709156715000","created":"Feb. 28, 2024, 1:45 PM","description":"Purified GFP-CDK5RAP2 (in Storage Buffer; 25 mM HEPES, pH 7.4, 500 mM KCl, 0.1% CHAPS, 1% glycerol) was diluted in Assembly Buffer (25 mM HEPES, pH 7.4, 150 mM KCl) to achieve a final protein concentration of 1 mM protein and final KCl concentration of 250mM. 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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Reactions were quenched with 50 mM ammonium bicarbonate and incubated at 23 C for 15 min.","fileCount":"15","fileSizeKB":"31780543","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002732","modification":"dmtmm;UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Centrosomes;CDK5RAP2;SPD-5;Polo kinase 1;Multivalency;Phase Separation;Cross-linking Mass-spectrometry;in vitro Reconstitution;Cell Division","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":"046b242dd29d4357bc56e42f47883b85","id":"632"}, {"dataset":"MSV000094191","datasetNum":"94191","title":"A central helical hairpin in SPD-5 enables centrosome strength and assembly","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709143030000","created":"Feb. 28, 2024, 9:57 AM","description":"Cross-linked samples consist of middle region of SPD-5 (541-677) plus 18 amino acids at the N-terminus (MGSSHHHHHHENLYFQSN) which we term F1. Two F1 samples (7.6 uM) were incubated with either kinase dead or constitutively active PLK-1 plus ATP-MgCl2 in a 150 mM 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 coomassie based stain. Monomer bands (LUM2_1076612, PLK-1 KD, LUM2_1076614, PLK-1 -CA) and dimer bands (LUM2_1076613, PLK-1 KD, LUM2_1076615, PLK-1 KD) were excised.","fileCount":"17","fileSizeKB":"46022698","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002732","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":"8c8fab4b4a3c46458b946ae779cde221","id":"633"}, {"dataset":"MSV000094187","datasetNum":"94187","title":"GNPS_02272024_Formaldehyde_Tolerance_dose_dependence_study_with_Marx_lab ","user":"aronlabshared","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709070579000","created":"Feb. 27, 2024, 1:49 PM","description":"Formaldehyde-conditioned M. extorquens was grown in succinate media for varying amounts of time to discover shared tolerance mechanisms. 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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. We therefore anticipate its application to a broad array of RNA phenomena.","fileCount":"254","fileSizeKB":"22683472","spectra":"0","psms":"141495","peptides":"69194","variants":"76437","proteins":"26259","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029","modification":"MS:1002864","keywords":"OMAP","pi":[{"name":"David Shechner","email":"shechner@uw.edu","institution":"University of Washington","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD050197","task":"375f98bb4a01421e853e56506271d9b0","id":"635"}, {"dataset":"MSV000094184","datasetNum":"94184","title":"Directed Evolution of Genetically Encoded LYTACs for Cell-Mediated Delivery","user":"dsroberts","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1709064779000","created":"Feb. 27, 2024, 12:12 PM","description":"Lysosome-targeting chimeras (LYTACs) are a promising therapeutic modality to drive the degradation of extracellular proteins. However, early versions of LYTAC contain synthetic glycopeptides that cannot be genetically encoded. Here we present our designs for a fully genetically encodable LYTAC (GELYTAC), making our tool compatible with integration into therapeutic cells for targeted delivery at diseased sites. To achieve this, we replaced the glycopeptide portion of LYTACs with the protein insulin like growth factor 2 (IGF2). After showing initial efficacy with wild type IGF2, we increased the potency of GELYTAC using directed evolution. Subsequently, we demonstrated that our engineered GELYTAC construct not only secretes from HEK293T cells but also from human primary T-cells to drive the uptake of various targets into receiver cells. Immune cells engineered to secrete GELYTAC thus represent a promising avenue for spatially-selective targeted protein degradation.","fileCount":"121","fileSizeKB":"568379","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002798","modification":"MS:1002864","keywords":"Targeted protein degradation; cell therapy; GELYTAC","pi":[{"name":"Carolyn Bertozzi","email":"bertozzi@stanford.edu","institution":"Stanford University","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD050196","task":"5b9f5171304d48de888c9f446e908bb9","id":"636"}, {"dataset":"MSV000094181","datasetNum":"94181","title":"GNPS - Methylobacterium sp. 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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":"MS:1003028;MS:1002732","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":"639"}, {"dataset":"MSV000094176","datasetNum":"94176","title":"mRNA-LNP HIV-1 trimer boosters elicit precursors to bnAbs","user":"sbaboo","site":"MassIVE","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":"MS:1002877","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. 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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":"MS:1002877","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":"641"}, {"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","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":"MS:1002783","modification":"MS:1002864","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":"642"}, {"dataset":"MSV000094171","datasetNum":"94171","title":"GNPS - Volatile and semivolatile compounds from the aqueous extract of Ilex guayusa leaves","user":"NPLIKIAM","site":"MassIVE","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","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":"643"}, {"dataset":"MSV000094169","datasetNum":"94169","title":"GNPS - Hand-on Microbiome course","user":"oloap1_1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"644"}, {"dataset":"MSV000094168","datasetNum":"94168","title":"Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life","user":"jeffsavas","site":"MassIVE","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;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":"645"}, {"dataset":"MSV000094160","datasetNum":"94160","title":"RNA quality control factors nucleate Clr4\/SUV39H and trigger constitutive heterochromatin assembly","user":"whaas","site":"MassIVE","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":"646"}, {"dataset":"MSV000094158","datasetNum":"94158","title":"Active site remodeling of IDH1 by tumor_relevant mutations and potential resistance mechanisms","user":"ekomives","site":"MassIVE","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","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":"647"}, {"dataset":"MSV000094156","datasetNum":"94156","title":"PRMT9 interaction proteins (WT and G189R) Nature Communications 2024","user":"Yanzhong_Yang","site":"MassIVE","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","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":"648"}, {"dataset":"MSV000094151","datasetNum":"94151","title":"GNPS Aspergillus novoparasiticus NIPE-UNIFESP Diadema positive","user":"AugustoL","site":"MassIVE","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","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":"649"}, {"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","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":"650"}, {"dataset":"MSV000094149","datasetNum":"94149","title":"Disrupted Nitric Oxide Homeostasis Impacts Fertility Through Multiple Processes Including Protein Quality Control","user":"PatrickTreffon","site":"MassIVE","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":"651"}, {"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","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":"MS:1003028","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":"652"}, {"dataset":"MSV000094142","datasetNum":"94142","title":"GNPS - Seven marine Actinomycetota from the South Pacific","user":"ACumsille","site":"MassIVE","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","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":"653"}, {"dataset":"MSV000094135","datasetNum":"94135","title":"GNPS - Lee_feline_fecal_12min_gradient","user":"ipmohanty","site":"MassIVE","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","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":"654"}, {"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","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;MS:1002874;MS:1003028","modification":"MS:1002864","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":"655"}, {"dataset":"MSV000094133","datasetNum":"94133","title":"HPK-1 Citron Homology Domain interactions with Kinase Domain","user":"btwalters","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"656"}, {"dataset":"MSV000094131","datasetNum":"94131","title":"Thylakoid Protein FPB1 Synergistically Cooperates with PAM68 to Promote CP47 Biogenesis and Photosystem II Assembly","user":"zhanglin2017","site":"MassIVE","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":"657"}, {"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","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":"658"}, {"dataset":"MSV000094128","datasetNum":"94128","title":"CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote","user":"aad100","site":"MassIVE","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":"207","fileSizeKB":"33382361","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003229","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":"659"}, {"dataset":"MSV000094124","datasetNum":"94124","title":"20240219 drug analog library mgf","user":"zhaohaoq","site":"MassIVE","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":"660"}, {"dataset":"MSV000094122","datasetNum":"94122","title":"GNPS - FVLGNPS2-Final-project-combinedfraction","user":"baldem","site":"MassIVE","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":"MS:1003112","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":"661"}, {"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","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":"MS:1003029","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":"662"}, {"dataset":"MSV000094118","datasetNum":"94118","title":"GNPS - Chevrette et al. 2022 Microbiome composition modulates secondary metabolism in a multispecies bacterial community","user":"ACumsille","site":"MassIVE","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","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":"663"}, {"dataset":"MSV000094116","datasetNum":"94116","title":"GNPS-mirror plot of new secondary bile acids","user":"qixingnie","site":"MassIVE","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","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":"664"}, {"dataset":"MSV000094115","datasetNum":"94115","title":"GNPS-alkyne probe of CA for the identification of new secondary bile acids","user":"qixingnie","site":"MassIVE","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":"11","fileSizeKB":"1291500","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"665"}, {"dataset":"MSV000094114","datasetNum":"94114","title":"Experimental viral infections in honey bee queens in queen monitoring cages","user":"abbichapman","site":"MassIVE","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":"MS:1003005","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":"666"}, {"dataset":"MSV000094113","datasetNum":"94113","title":"Experimental viral infections in honey bee queens in the field ","user":"abbichapman","site":"MassIVE","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. ","fileCount":"5","fileSizeKB":"78934084","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003005","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";N-terminal acetylation","keywords":"honey bee;queen;hemolymph;ovary;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":"1bc84a1b86f6411f8644f0bdc8378da3","id":"667"}, {"dataset":"MSV000094112","datasetNum":"94112","title":"Analysis of Synaptic Palmitoylated Proteins in a CLN1 Mouse Model","user":"tnguy214","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1708297060000","created":"Feb. 18, 2024, 2:57 PM","description":"Palmitoylation is a lipid modification that is critical for protein trafficking. 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":"668"}, {"dataset":"MSV000094097","datasetNum":"94097","title":"GNPS - Osteoarthritis diet study","user":"helenamrusso","site":"MassIVE","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":"267","fileSizeKB":"13832873","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","keywords":"osteoarthritis;diet;fecal;serum;plasma;saliva","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":"1c8f399b7e2c4726ab4e36c786a0bcc0","id":"669"}, {"dataset":"MSV000094096","datasetNum":"94096","title":"Identification of sorbitol esterification of glutamic acid by LC-MS\/MS in a monoclonal antibody stability assessment","user":"zjlinsan","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1708030844000","created":"Feb. 15, 2024, 1:00 PM","description":"The stability of monoclonal antibodies (mAbs) is vital for their therapeutic success. Sorbitol, a common mAb stabilizer used to prevent aggregation, was evaluated for any potential adverse effects on the chemical stability of mAb X. 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":"670"}, {"dataset":"MSV000094094","datasetNum":"94094","title":"MolPsy2024_YZWang_Neuron type-specific proteomics","user":"jeffsavas","site":"MassIVE","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":"671"}, {"dataset":"MSV000094092","datasetNum":"94092","title":"Anaerobic gut fungi are an untapped reservoir of natural products.","user":"bpbowen","site":"MassIVE","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","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":"672"}, {"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","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":"342","fileSizeKB":"17499907","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"673"}, {"dataset":"MSV000094090","datasetNum":"94090","title":"GNPS - Microbial regulation of soil water repellency to control soil degradation","user":"bpbowen","site":"MassIVE","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":"596","fileSizeKB":"41941711","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"674"}, {"dataset":"MSV000094089","datasetNum":"94089","title":"GNPS - Determination of metabolic changes occurring in engineered low-lignin poplar","user":"bpbowen","site":"MassIVE","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","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":"675"}, {"dataset":"MSV000094088","datasetNum":"94088","title":"GNPS - Microbial environmental feedbacks and the evolution of soil organic matter","user":"bpbowen","site":"MassIVE","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","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":"676"}, {"dataset":"MSV000094086","datasetNum":"94086","title":"Lacritin N-104 affinity purification of P. aeruginosa surface proteins","user":"anwaruddin","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"677"}, {"dataset":"MSV000094085","datasetNum":"94085","title":"Screen for proteins or peptides in human tears that are synergistic with N-104","user":"anwaruddin","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"678"}, {"dataset":"MSV000094084","datasetNum":"94084","title":"GNPS - Data files for manuscript - Selected ion monitoring for orbitrap-based metabolomics","user":"wenyunlu","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"679"}, {"dataset":"MSV000094082","datasetNum":"94082","title":"Development of an Efficient, Effective, and Economical Technology for Proteome Analysis_part II","user":"yayu","site":"MassIVE","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":"MS:1003029","modification":"MS:1002864","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":"680"}, {"dataset":"MSV000094080","datasetNum":"94080","title":"Species-specific variation in mental gland secretions of turtles revealed by proteomic and lipidomic profiling","user":"Urszula","site":"MassIVE","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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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","keywords":"Chemical signaling;Animal Microbiomes;Schistosomiasis;Snails","pi":[{"name":"J.P. 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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. MS settings were as follows - positive ion mode, 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, dynamic exclusion 0.5 s.","fileCount":"6","fileSizeKB":"160942","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 cinnamonensis (NCBITaxon:1900);Streptomyces aureoverticillatus (NCBITaxon:66871)","instrument":"Orbitrap Fusion","modification":"MS:1002864","keywords":"polyketide, monazomycin, oasomycin, seq2pks","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":"cd536d58ccb74ae6a2f33b4a8ee727f3","id":"686"}, {"dataset":"MSV000094062","datasetNum":"94062","title":"FASTMAP platform_set of raw data files","user":"Luisa_Weisbrod","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707671945000","created":"Feb. 11, 2024, 9:19 AM","description":"Set of raw data files for the FASTMAP platform (FASTMAP- A flexible and scalable immunopeptidomics platform for HLA- and antigen-specific T cell epitope mapping based on artificial antigen-presenting cells)","fileCount":"146","fileSizeKB":"122850406","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003094","modification":"MOD:01214 - \\\"modification from UniMod Chemical derivative - OBSOLETE because redundant, the difference component of MOD:01060. 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For all 'home', 'away' and control conditions for each species we also had high or low oxygen treatments. Samples were taken at day 0, 154, 257 and 354 and extracted with solid phase columns and methanol to provide extracted metabolites.","fileCount":"555","fileSizeKB":"89906991","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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);Tsuga heterophylla (NCBITaxon:3359)","instrument":"Q Exactive","modification":"MS:1002864","keywords":"decomposition;home field advantage;climate change;carbon release;leaf litter","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":"0b7a2b8abf69492185f9d979e0dd1122","id":"688"}, {"dataset":"MSV000094053","datasetNum":"94053","title":"Substrate recognition principles for PP2A-B55","user":"madamo","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707509875000","created":"Feb. 9, 2024, 12:17 PM","description":"The trimeric PP2A-B55 phosphoprotein phosphatase regulates a plethora of fundamental signaling pathways throughout eukaryotes. 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;MS:1002732;MS:1002634","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":"689"}, {"dataset":"MSV000094052","datasetNum":"94052","title":"DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity","user":"alemoff","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","keywords":"J-domain proteins;chaperone;DNAJB8;DNAJB6;tau;polyQ;LARKS;neurodegeneration;proteostasis;Alzheimers disease","pi":[{"name":"Lukasz A. 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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":"MS:1002732","modification":"MS:1002864","keywords":"Chemical Signaling;Animal Microbiome;Microeukaryote Symbiont;Schistosomiasis;Protective Symbiosis;Evolution of Multicellularity;Lipid Mediated Signaling;Hemolymph Composition;Snails;Protists","pi":[{"name":"J.P. 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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. 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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. 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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":"MS:1002634","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":"696"}, {"dataset":"MSV000094032","datasetNum":"94032","title":"Identification of Plk4 cryptic polo-box-binding proteins","user":"ronholes7059","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707328896000","created":"Feb. 7, 2024, 10:01 AM","description":"Identification of Plk4-binding proteins and investigation of the underlying mechanism of how Plk4 regulates centriole duplication.","fileCount":"31","fileSizeKB":"3428838","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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.\\\"","keywords":"Plk4, cryptic polo-box, centrosome, centriole, cell proliferation","pi":[{"name":"Dr. Kyung Lee","email":"Kyunglee@mail.nih.gov","institution":"National Cancer Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"9e6e062307f94ab1be7f2a7db40f257e","id":"697"}, {"dataset":"MSV000094030","datasetNum":"94030","title":"6 Ocotea sp. dataset analyzed in DIA mode (ESI positive and negative)","user":"matheus_fa","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707323681000","created":"Feb. 7, 2024, 8:34 AM","description":"This dataset consists of 6 Ocotea plant species analyzed in negative and positive modes, with data-independent acquisition (MSe), in a Waters Xevo G2 instrument. 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","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":"698"}, {"dataset":"MSV000094027","datasetNum":"94027","title":"HDX-MS of murine urokinase plasminogen activator and variants","user":"ekomives","site":"MassIVE","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","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":"699"}, {"dataset":"MSV000094026","datasetNum":"94026","title":"Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry","user":"jymbcrc","site":"MassIVE","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":"MS:1002732","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":"700"}, {"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","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","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":"701"}, {"dataset":"MSV000094014","datasetNum":"94014","title":"Casanovo non-enzymatic fine-tuning set","user":"melihyilmaz","site":"MassIVE","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":"702"}, {"dataset":"MSV000094010","datasetNum":"94010","title":"Molecular and Cellular Mechanisms of Teneurin Signaling in Synaptic Partner Matching","user":"malpap1","site":"MassIVE","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. ","fileCount":"20","fileSizeKB":"11334586","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002634","modification":"K-TMT6, n-term-TMT6, C-carbamidomethylation, M-oxidation, N-term acetylation","keywords":"Proximity labeling, Tem-m","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":"90171c664d2540e7b90601fc2a2b1d39","id":"703"}, {"dataset":"MSV000094008","datasetNum":"94008","title":"Proteins Can Withstand More Extensive Labeling While Providing Accurate Structural Information In Covalent Labeling-Mass Spectrometry","user":"rwvachet","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707146607000","created":"Feb. 5, 2024, 7:23 AM","description":"Increased labeling with diethylpyrocarbonate for improved protein HOS information.","fileCount":"6121","fileSizeKB":"46998421","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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);Equus caballus (NCBITaxon:9796)","instrument":"Orbitrap Fusion;amaZon ETD;micrOTOF","modification":"[H,K,S,T,Y] [72.021129]","keywords":"Covalent Labeling-MS","pi":[{"name":"Richard Vachet","email":"vachet@umass.edu","institution":"University of Massachusetts Amherst","country":"US"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a7088c857234418e81f700a37a8aa982","id":"704"}, {"dataset":"MSV000094007","datasetNum":"94007","title":"GNPS - Phenolic compounds from commonly consumed fruits in Brazil","user":"Mallmann","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707143632000","created":"Feb. 5, 2024, 6:33 AM","description":"EPC and NEPC fraction of 2 varieties of banana, apple, orange, papaya and mango and 30 phenolic compound standards. ","fileCount":"1426","fileSizeKB":"13222374","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Musa acuminata (NCBITaxon:4641);Malus domestica (NCBITaxon:3750);Citrus sinensis (NCBITaxon:2711);Carica papaya (NCBITaxon:3649);Mangifera indica (NCBITaxon:29780)","instrument":"micrOTOF-Q III","modification":"none","keywords":"phenolic;banana;apple;orange;papaya;mango","pi":[{"name":"Phenolic Lab Brazil","email":"eliseu.rodrigues@ufrgs.br","institution":"Universidade Federal do Rio Grande do Sul (UFRGS)","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"5a375a1cc3fa436c804c3c16181c39d9","id":"705"}, {"dataset":"MSV000094006","datasetNum":"94006","title":" 3day bee affected by VarroaDWV","user":"arachnid","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707126951000","created":"Feb. 5, 2024, 1:55 AM","description":"We performed a manipulative experiment in which healthy honey bees collected at the time of emergence were exposed to Varroa destructor or left untreated (control) for 72 hours. A total of 10 control and 10 Varroa-treated bees were used for label-free nano-liquid chromatography (LC)MS\/MS proteomic analysis. (k01 to k10: control; w01 to w10: Varroa exposed).","fileCount":"50","fileSizeKB":"92726111","spectra":"0","psms":"456236","peptides":"26341","variants":"35411","proteins":"10465","search_psms":"0","search_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); Deformed wing virus","instrument":"Orbitrap Fusion","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:39 - \\\"Beta-methylthiolation.\\\"","keywords":"host pathogen interaction;peroxisome","pi":[{"name":"Tomas Erban","email":"arachnid@centrum.cz","institution":"Crop Research Institute","country":"Czechia"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD049168","task":"7e5ea5ac62b4498bb920857b5861b589","id":"706"}, {"dataset":"MSV000094005","datasetNum":"94005","title":"GNPS - Untargeted Metabolomics with E.coli and S.elongatus PCC 7942 before and after heat treatment","user":"Nike","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1707118241000","created":"Feb. 4, 2024, 11:30 PM","description":"E.coli and Synechococcus elongatus PCC 7942 WT and a Mutant werde cultivated under standard growth conditions (37 or 28 degree C) and then heat shocked in a heat bath for 15 min at 58 degree C. (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","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":"707"}, {"dataset":"MSV000094002","datasetNum":"94002","title":"GNPS - KratomMitragynaSpeciosa_WVSUBBRL","user":"Djaedy","site":"MassIVE","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":"MS:1003252","modification":"MS:1002864","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":"708"}, {"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","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":"MS:1002877;MS:1003005","modification":"MS:1002864","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":"709"}, {"dataset":"MSV000093994","datasetNum":"93994","title":"Single Cell Proteoform Analysis Using scPiMS","user":"mikehollas123","site":"MassIVE","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":"710"}, {"dataset":"MSV000093982","datasetNum":"93982","title":"Delineating Bovine Milk Derived Microvesicles from Exosomes Using Proteomics","user":"AndrewCouse","site":"MassIVE","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":"MS:1002732","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":"711"}, {"dataset":"MSV000093980","datasetNum":"93980","title":"Casanovo de novo peptide sequencing immunopeptidomics, metaproteomics and dark proteome","user":"melihyilmaz","site":"MassIVE","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":"712"}, {"dataset":"MSV000093974","datasetNum":"93974","title":"GNPS - WVSU_MitragynaSpeciosaProjectBBRL","user":"Djaedy","site":"MassIVE","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":"MS:1003252","modification":"MS:1002864","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":"713"}, {"dataset":"MSV000093973","datasetNum":"93973","title":"GnRH Induces Citrullination of the Cytoskeleton in Murine Gonadotrope Cells","user":"equigle2","site":"MassIVE","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":"MS:1003029","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":"714"}, {"dataset":"MSV000093954","datasetNum":"93954","title":"PSM rescoring boosts identification of trypsin, AspN, and GluC peptides on timsTOF","user":"CAdams","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1706620329000","created":"Jan. 30, 2024, 5:12 AM","description":"To investigate whether samples digested with trypsin, GluC, or AspN benefit from PSM rescoring, we rescored a timsTOF Pro dataset that was digested using different proteases. 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":"MS:1003005","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":"715"}, {"dataset":"MSV000093951","datasetNum":"93951","title":"GNPS - AH metabolites\/zinc chelators associated with POAG identified by GC-MS-based metabolomic analysis","user":"chistyakof","site":"MassIVE","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":"59","fileSizeKB":"1036146","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"716"}, {"dataset":"MSV000093948","datasetNum":"93948","title":"GNPS Germ-Free Mice Inoculated with or without Lactobacillus rhamnosus under Tryptophan-Sufficient\/Deficient Diet","user":"jma429njms","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1706567636000","created":"Jan. 29, 2024, 2:33 PM","description":"Lacticaseibacillus rhamnosus (LGG), a promising probiotic for gastrointestinal disorders, has been found to significantly impact the host's intestinal metabolome, excluding pathobiont bacteria colonization. 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":"MS:1002634","modification":"MS:1002864","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":"717"}, {"dataset":"MSV000093930","datasetNum":"93930","title":"GNPS - The effet of siderophore on plant microbiome","user":"oloap1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"718"}, {"dataset":"MSV000093928","datasetNum":"93928","title":"Acetamiprid effect on queens and emerging bees","user":"arachnid","site":"MassIVE","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":"719"}, {"dataset":"MSV000093927","datasetNum":"93927","title":"GNPS Mara1 Heterologous expression in S. albidoflavus J1074","user":"matmal","site":"MassIVE","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":"MS:1002791","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":"720"}, {"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","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":"MS:1002728","modification":"MS:1002864","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":"721"}, {"dataset":"MSV000093919","datasetNum":"93919","title":"GNPS - Variation of terpene alkaloids in Daphniphyllum macropodum across plants and tissues","user":"trl1","site":"MassIVE","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":"MS:1002727","modification":"MS:1002864","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":"722"}, {"dataset":"MSV000093917","datasetNum":"93917","title":"Cardiac Hypertensive-Cmpd17b (therapeutic) - Cell treatment proteomics","user":"dwgree","site":"MassIVE","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":"MS:1002877","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":"723"}, {"dataset":"MSV000093916","datasetNum":"93916","title":"FGFR inhibition blocks NF-kappaB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma","user":"whaas","site":"MassIVE","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":"MS:1002732","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":"724"}, {"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","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":"MS:1003029","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":"725"}, {"dataset":"MSV000093912","datasetNum":"93912","title":"Proteogenomics analysis to identify acquired resistance-specific alterations in melanoma PDXs on MAPKi therapy","user":"sbyrum","site":"MassIVE","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":"MS:1003029","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":"726"}, {"dataset":"MSV000093910","datasetNum":"93910","title":"GNPS - Variation of terpene alkaloids in Daphniphyllum macropodum across plants and tissues","user":"trl1","site":"MassIVE","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","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":"727"}, {"dataset":"MSV000093905","datasetNum":"93905","title":"Quantitative Proteomics of axon regeneration promoted by Gangliosides and MTOR-Activating Small Molecules","user":"sbhattacharya","site":"MassIVE","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","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":"728"}, {"dataset":"MSV000093903","datasetNum":"93903","title":"Phosphoproteomic Analysis of PCB126 Impact on the Mouse Chronic-Binge Alcohol Feeding Model","user":"mmerchant","site":"MassIVE","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":"MS:1003028","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":"729"}, {"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","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":"MS:1003004","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":"730"}, {"dataset":"MSV000093898","datasetNum":"93898","title":"GNPS - Quinones identification standards analysis","user":"oloap1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"731"}, {"dataset":"MSV000093897","datasetNum":"93897","title":"PISA experiment 20 compounds test MIC concentrations 2","user":"oloap1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"732"}, {"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","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":"MS:1002877","modification":"MS:1002864","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":"733"}, {"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","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":"MS:1003028","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":"734"}, {"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","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":"MS:1003028","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":"735"}, {"dataset":"MSV000093891","datasetNum":"93891","title":"Oxidative Cyclization Reagents Reveal Tryptophan Cation-pi interactions","user":"xiaoxie","site":"MassIVE","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":"23","fileSizeKB":"17575240","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002634","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":"736"}, {"dataset":"MSV000093886","datasetNum":"93886","title":"GNPS - Charting the Cannabis plant chemical space with computational metabolomics","user":"kami_KAZE007","site":"MassIVE","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","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":"737"}, {"dataset":"MSV000093885","datasetNum":"93885","title":"GNPS - Test SynCom strains interaction 211223","user":"oloap1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"738"}, {"dataset":"MSV000093884","datasetNum":"93884","title":"GNPS - Metabolic engineering of Streptomyces peucetius for biosynthesis of N,N-dimethylated anthracyclines","user":"mbhulst","site":"MassIVE","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":"MS:1002998;MS:1003381","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":"739"}, {"dataset":"MSV000093878","datasetNum":"93878","title":"ESI-MS\/MS of ADP-ribosylated RNA to Identify Site of Modification","user":"cdoering","site":"MassIVE","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":"740"}, {"dataset":"MSV000093875","datasetNum":"93875","title":"An XIC-centric approach for improved identification and quantification in proteomic data analyses","user":"zhengzhang","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"741"}, {"dataset":"MSV000093873","datasetNum":"93873","title":"Toggling of BRD4 functions is triggered through its phosphorylation by JNK","user":"ronholes7059","site":"MassIVE","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":"15","fileSizeKB":"11814908","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029;MS:1002523","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":"742"}, {"dataset":"MSV000093872","datasetNum":"93872","title":"GNPS - HoloFish - Untargeted Metabolomics","user":"JacobAgerbo","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"743"}, {"dataset":"MSV000093869","datasetNum":"93869","title":"GNPS - KNU_NPClab-LCMS_2023_47peppers","user":"sych426","site":"MassIVE","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":"MS:1003095","modification":"MS:1002864","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":"744"}, {"dataset":"MSV000093868","datasetNum":"93868","title":"GNPS-compositae_MN library_240115","user":"cho_chae_yeon","site":"MassIVE","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":"MS:1003095","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":"745"}, {"dataset":"MSV000093867","datasetNum":"93867","title":"Automated single-cell proteomics covering over four orders of magnitude at high throughput","user":"cctortec","site":"MassIVE","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":"MS:1003231","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":"746"}, {"dataset":"MSV000093861","datasetNum":"93861","title":"Cauldrons of Bronze Age nomads","user":"Wilkin","site":"MassIVE","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":"MS:1003028","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":"747"}, {"dataset":"MSV000093857","datasetNum":"93857","title":"Pla2g12b binding proteins in Zebrafish","user":"syjung","site":"MassIVE","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":"748"}, {"dataset":"MSV000093854","datasetNum":"93854","title":"Diagnosing and staging epithelial ovarian cancer by serum glycoproteomic profiling","user":"GX_InterVenn","site":"MassIVE","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":"MS:1000937","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":"749"}, {"dataset":"MSV000093851","datasetNum":"93851","title":"SIAH3 is frequently epigenetically silenced in cancer and regulates mitochondrial metabolism - Expression Proteomics Dataset","user":"graumann","site":"MassIVE","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":"MS:1002523","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":"750"}, {"dataset":"MSV000093850","datasetNum":"93850","title":"SIAH3 is frequently epigenetically silenced in cancer and regulates mitochondrial metabolism - SIAH3 Interactomics","user":"graumann","site":"MassIVE","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":"751"}, {"dataset":"MSV000093849","datasetNum":"93849","title":" Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids","user":"aad100","site":"MassIVE","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":"MS:1003229","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":"752"}, {"dataset":"MSV000093844","datasetNum":"93844","title":"GNPS Fecal Microbiota Transplant Bile Acid","user":"Gzhang","site":"MassIVE","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":"MS:1002792","modification":"MS:1002864","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":"753"}, {"dataset":"MSV000093842","datasetNum":"93842","title":"IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma","user":"ronholes7059","site":"MassIVE","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":"MS:1003029","modification":"UNIMOD:2016;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":"754"}, {"dataset":"MSV000093840","datasetNum":"93840","title":"Osteomacs promote maintenance of murine hematopoiesis through megakaryocyte-induced upregulation of Embigin and CD166","user":"edoud","site":"MassIVE","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":"MS:1002732","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":"755"}, {"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","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":"753","fileSizeKB":"532548476","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"756"}, {"dataset":"MSV000093832","datasetNum":"93832","title":"GNPS - CCA_Exometabolites_KaneoheBay2023","user":"zquinlan","site":"MassIVE","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","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":"757"}, {"dataset":"MSV000093831","datasetNum":"93831","title":"GNPS - Evolution of the earliest stages of ovarian cancer from mutant fallopian tube epithelial cells","user":"MFJ003","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"758"}, {"dataset":"MSV000093813","datasetNum":"93813","title":"GNPS - Microbial and host compensation in a model of leucine breakdown deficiency","user":"bwf7","site":"MassIVE","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":"9","fileSizeKB":"2543872","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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;MS:1002523","modification":"MS:1002864","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":"759"}, {"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","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","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":"760"}, {"dataset":"MSV000093805","datasetNum":"93805","title":"2022 Mated-unmated honey bee queen comparison","user":"abbichapman","site":"MassIVE","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":"MS:1003005","modification":"MS:1002864","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":"761"}, {"dataset":"MSV000093803","datasetNum":"93803","title":"Bone proteomics methods optimisation for forensic investigations","user":"NUPPA","site":"MassIVE","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":"113","fileSizeKB":"67376841","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003028","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":"762"}, {"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","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":"763"}, {"dataset":"MSV000093798","datasetNum":"93798","title":"Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles","user":"trendsetter","site":"MassIVE","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":"195","fileSizeKB":"300903224","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002732;MS:1002523","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":"764"}, {"dataset":"MSV000093797","datasetNum":"93797","title":"GNPS - Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry","user":"EvoleneD","site":"MassIVE","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":"MS:1003245","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":"765"}, {"dataset":"MSV000093796","datasetNum":"93796","title":"Quantitative analysis of ribosomal protein expression in bacteria","user":"rusconi","site":"MassIVE","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":"766"}, {"dataset":"MSV000093794","datasetNum":"93794","title":"Trichomonas vaginalis 20S proteasome subunit specific MSP-MS","user":"bhurysz","site":"MassIVE","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":"767"}, {"dataset":"MSV000093787","datasetNum":"93787","title":"GNPS - LC profile of streptomyces tagetis","user":"kimkami2","site":"MassIVE","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":"768"}, {"dataset":"MSV000093785","datasetNum":"93785","title":"GNPS - RORDEPs in supernatants of Rumincoccus torques strains cultures","user":"yongfan","site":"MassIVE","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":"5","fileSizeKB":"2082072","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003028","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":"769"}, {"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","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":"MS:1003004;MS:1003094","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":"770"}, {"dataset":"MSV000093782","datasetNum":"93782","title":"GNPS - 20240105 ISS standard validation negative ionization","user":"zhaohaoq","site":"MassIVE","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":"771"}, {"dataset":"MSV000093781","datasetNum":"93781","title":"GNPS - 20240105 ISS standard validation positive","user":"zhaohaoq","site":"MassIVE","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":"772"}, {"dataset":"MSV000093780","datasetNum":"93780","title":"Analysis of ubiquitination sites in Neh2Dual-sGFP substrate","user":"DanKraut","site":"MassIVE","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":"20","fileSizeKB":"1820084","spectra":"0","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":"773"}, {"dataset":"MSV000093775","datasetNum":"93775","title":"Multivalent coiled-coil interactions enable full-scale centrosome assembly and strength","user":"alemoff","site":"MassIVE","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":"MS:1002732","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":"774"}, {"dataset":"MSV000093768","datasetNum":"93768","title":"A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival","user":"brettsp1","site":"MassIVE","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. Importantly, SG formation is significant for promoting cell survival in the physiological context of lysosomal damage inflicted by SARS-CoV-2 ORF3a, adenovirus infection, Malaria hemozoin, proteopathic tau as well as environmental hazard silica.","fileCount":"17","fileSizeKB":"25628769","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003028","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"lysosomal damage","pi":[{"name":"Jingyue Jia","email":"JJia@salud.unm.edu","institution":"Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD048258","task":"97065b7193f14f61a97e4f555a2759c8","id":"775"}, {"dataset":"MSV000093767","datasetNum":"93767","title":"Investigating honey bee nurse and forager hemolymph proteins in response to hiving in cedar and pine boxes","user":"amcafee","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1704397849000","created":"Jan. 4, 2024, 11:50 AM","description":"This dataset contains samples of honey bee worker hemolymph extracted from nurses and foragers one month after colony establishment in Western red cedar and white pine nuc boxes. ","fileCount":"3","fileSizeKB":"38681200","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","instrument":"MS:1003230","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\"","keywords":"honey bee, cedar, pine, hive, wood","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":"500a339ca52e44bd83cc95ef6601e15b","id":"776"}, {"dataset":"MSV000093759","datasetNum":"93759","title":"Evaluation of data-independent acquisition workflows for deep proteome coverage of EPS-urine","user":"TKislinger","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1704313749000","created":"Jan. 3, 2024, 12:29 PM","description":"Here, we investigated the performance of DIA-MS on a cohort of urines collected from prostate cancer patients against DDA-MS. The performance of several commonly used DIA-MS analysis approaches were examined with our cohort-specific spectral libraries, library-free and a pan-human library. 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Probes MS\/MS spectra and MZmine3 batch files are also provided. Settings: Agilent LC-qTof 6546, ACQUITY UPLC BEH C18 column, 5% to 100% ACN in H2O with 0.1% formic acid, 40eV. 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Future therapeutic attempts therefore demand targeting of both compartments in order to be effective. We show here that Dual Specificity and Tyrosine Phosphorylation-regulated Kinase 1B (DYRK1B) represents a compartment-agnostic anti-cancer target in PDAC. DYRK1B is mainly expressed by pancreatic epithelial cancer cells and modulates the influx and activity of TME-associated macrophages through effects on the cancer cells themselves as well as affecting the tumor secretome. Mechanistically, genetic ablation or pharmacological inhibition of DYRK1B strongly attracts tumoricidal macrophages and in addition downregulates the phagocytosis checkpoint and \"don't eat me\"-signal CD24 on cancer cells, resulting in enhanced tumor cell phagocytosis. Consequently, tumor cells lacking DYRK1B hardly expand in transplantation experiments despite doing so rapidly in culture. Furthermore, combining a small-molecule DYRK1B-directed therapy with mTOR inhibition and conventional chemotherapy stalls the growth of established tumors and results in significant extension of life span in a highly aggressive autochthonous model of PDAC. In light of DYRK inhibitors currently entering clinical phase testing, our data thus provide a novel and clinically translatable approach targeting the cancer cell compartment and its microenvironment, both. 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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":"MS:1002732","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":"788"}, {"dataset":"MSV000093738","datasetNum":"93738","title":"Gli3 co-IP\/MS in SAG-treated NIH\/3T3 cells","user":"pniewiadomski","site":"MassIVE","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. 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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","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":"791"}, {"dataset":"MSV000093732","datasetNum":"93732","title":"UBQLN2 Governs Lipid Metabolism Linked to Neurodegeneration in ALS\/FTD","user":"haolab","site":"MassIVE","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":"MS:1002877","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":"792"}, {"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","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":"MS:1002732","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":"793"}, {"dataset":"MSV000093724","datasetNum":"93724","title":"Essential role of STAT5 tyrosine phosphorylation in vivo","user":"ronholes7059","site":"MassIVE","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":"MS:1003029","modification":"UNIMOD:2016;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":"794"}, {"dataset":"MSV000093722","datasetNum":"93722","title":"Laser capture microdissected functional tissue units from kidney for top-down proteomic characterization using microPOTS","user":"alchemistmatt","site":"MassIVE","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":"MS:1002732","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":"795"}, {"dataset":"MSV000093721","datasetNum":"93721","title":"UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER","user":"aordureau","site":"MassIVE","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":"MS:1003028","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":"796"}, {"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","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":"MS:1003230","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":"797"}, {"dataset":"MSV000093708","datasetNum":"93708","title":"AhyBURP source data submission","user":"Rolandoo1","site":"MassIVE","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":"798"}, {"dataset":"MSV000093705","datasetNum":"93705","title":"Schreiber_2023_VS1_Exploring options for proximity-dependent biotinylation experiments","user":"Younlab_Toronto","site":"MassIVE","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":"MS:1003028","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":"799"}, {"dataset":"MSV000093703","datasetNum":"93703","title":"A chemoproteomics method for direct and comprehensive characterization of cysteine reversible oxidation","user":"xusenhan","site":"MassIVE","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;MS:1003028","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":"800"}, {"dataset":"MSV000093700","datasetNum":"93700","title":"GNPS - Native metabolomics with E.coli CutA and Isosepiapterin","user":"Nike","site":"MassIVE","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. Isosepiapterin was dissolved in 50% MeOH and run over a C18 column. ","fileCount":"9","fileSizeKB":"1550813","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002523","modification":"MS:1002864","keywords":"CutA;Isosepiapterin;Native 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":"a9103f2c12754ac4892dc31ba94b26ae","id":"801"}, {"dataset":"MSV000093698","datasetNum":"93698","title":"Chemogenetic restoration of astrocyte morphology is beneficial in obsessive-compulsive disorder","user":"adarshmayank","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1703023339000","created":"Dec. 19, 2023, 2:02 PM","description":" In vivo chemogenetic activation of astrocytes in the striatum via an engineered Gi-protein-coupled receptor was conducted in wild-type and SAPAP3 KO OCD mice. 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":"MS:1002732","modification":"MS:1002864","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":"802"}, {"dataset":"MSV000093696","datasetNum":"93696","title":"Glioblastoma Extracellular Vesicles Modulate Immune PD-L1 Expression in Accessory Macrophages upon Radiotherapy","user":"whaas","site":"MassIVE","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":"MS:1002732","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":"803"}, {"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","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","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":"804"}, {"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","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":"MS:1003028","modification":"MS:1002864","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":"805"}, {"dataset":"MSV000093692","datasetNum":"93692","title":"GNPS - IP-MS\/MS of chaperone pulldown of the CmdTAC system during T4 infection","user":"cdoering","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"806"}, {"dataset":"MSV000093682","datasetNum":"93682","title":"Analyses of Pseudoexfoliation Aqueous Humor Proteome in Homo sapiens","user":"sbhattacharya","site":"MassIVE","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":"807"}, {"dataset":"MSV000093678","datasetNum":"93678","title":"GNPS IFAS sample AM recorded on Dec 2023 ","user":"amitGNPS","site":"MassIVE","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":"MS:1002874","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":"808"}, {"dataset":"MSV000093676","datasetNum":"93676","title":"GNPS - Temporal Dynamics of Cyanobacterial Bloom Community Composition and Toxin Production from Urban Lakes","user":"mxb1224","site":"MassIVE","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","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":"809"}, {"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","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":"MS:1002791","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":"810"}, {"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","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":"MS:1002877","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":"811"}, {"dataset":"MSV000093673","datasetNum":"93673","title":"Proteomic evaluation of decellularization of porcine auricular cartilage","user":"brucepu","site":"MassIVE","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":"812"}, {"dataset":"MSV000093672","datasetNum":"93672","title":"Exploration of adult mouse Single Cardiomyocyte Proteome using Label-Free LC-MS","user":"bineka","site":"MassIVE","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":"20876","fileSizeKB":"1238461930","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1003231","modification":"MS:1002864","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":"813"}, {"dataset":"MSV000093671","datasetNum":"93671","title":"Native mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination","user":"liuweij1","site":"MassIVE","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":"MS:1003245","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":"814"}, {"dataset":"MSV000093670","datasetNum":"93670","title":"Proteomic analysis of Breast cancer spheroids responder and non-responder to Trastuzumab","user":"DavidePerico","site":"MassIVE","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":"MS:1003095","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":"815"}, {"dataset":"MSV000093666","datasetNum":"93666","title":"Chromatograms and mass spectra of high-mannose and paucimannose N-glycans for rapid isomeric identifications","user":"Rock","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1702522566000","created":"Dec. 13, 2023, 6:56 PM","description":"In this study, we constructed a database containing collision-induced dissociation (CID) mass spectra and chromatograms of high-performance liquid chromatography for the rapid\nidentification of high-mannose and paucimannose N-glycan isomers.","fileCount":"58","fileSizeKB":"13759105","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 nature products and synthetic products ","instrument":"LTQ XL","modification":"MS:1002864","keywords":"High-mannose N-glycan","pi":[{"name":"Chi-Kung Ni ","email":"ckni@po.iams.sinica.edu.tw","institution":"Academia Sinica","country":"Taiwan"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a0521495e05145448ebea261299b43c1","id":"816"}, {"dataset":"MSV000093663","datasetNum":"93663","title":"Protein interactors of Duxbl in early mouse development","user":"lisamiljenk","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1702514409000","created":"Dec. 13, 2023, 4:40 PM","description":"Duxbl is a member of the DUX (double homeobox) family of transcription factors with roles in embryonic development. 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;MS:1003028","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":"817"}, {"dataset":"MSV000093659","datasetNum":"93659","title":"Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics","user":"stephan_eckert","site":"MassIVE","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":"MS:1003029;MS:1003028","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":"818"}, {"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","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":"MS:1002732","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":"819"}, {"dataset":"MSV000093653","datasetNum":"93653","title":"GNPS - Raw data for manuscript : ","user":"aliagh81","site":"MassIVE","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":"MS:1003094;Q Exactive","modification":"MS:1002864","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":"820"}, {"dataset":"MSV000093650","datasetNum":"93650","title":"Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly","user":"brettsp1","site":"MassIVE","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":"MS:1003230;MS:1002732","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"OmpU;biofilm matrix assembly","pi":[{"name":"Fitnat H. Yildiz","email":"fyildiz@ucsc.edu","institution":"University of California-Santa Cruz","country":"USA"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"PXD047764","task":"ee437919660e4c2ca361bf0c6bd627ef","id":"821"}, {"dataset":"MSV000093645","datasetNum":"93645","title":"Characterization of YlxR\/Ssr1238, a conserved RNA binding protein in a model cyanobacterium","user":"Stholen","site":"MassIVE","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":"MS:1002634","modification":"MS:1002864","keywords":"cyanobacteria, gene expression, photosynthesis, Synechocystis sp. PCC 6803, RNA binding proteins, RNase P","pi":[{"name":"Wolfgang R. Hess ","email":"wolfgang.hess@biologie.uni-freiburg.de","institution":"Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg","country":"Germany"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047746","task":"7a8ca62d31c14da8ade4cab0fff8af7f","id":"822"}, {"dataset":"MSV000093644","datasetNum":"93644","title":"Human immune cell proteomic library","user":"Hyeon_Jeong_Lee","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1702378919000","created":"Dec. 12, 2023, 3:01 AM","description":"Comprehensive human immune cell proteomic spectral library which contain CD4+T cell, CD8+ T cell, NK cell, B cell, PBMC, Daudi, Jurkat, stimulated Jurkat, Molt-4, Ramos, and THP-1 were generated. This library includes 10,544 proteins groups, and 127,106 peptides. ","fileCount":"848","fileSizeKB":"575951845","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002634;MS:1003094","modification":"MS:1002864","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":"823"}, {"dataset":"MSV000093641","datasetNum":"93641","title":"Genome-guided isolation of Fervidibacter sacchari, an aerobic, hyperthermophilic polysaccharide-degrading specialist","user":"gabrig","site":"MassIVE","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","instrument":"MS:1003005","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":"824"}, {"dataset":"MSV000093637","datasetNum":"93637","title":"Extracellular Domains of CAR Reprogram T Cell Metabolism Without Antigen Stimulation","user":"aliyalakhani","site":"MassIVE","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":"MS:1002732","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":"825"}, {"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","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":"MS:1003094","modification":"UNIMOD:2016;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":"826"}, {"dataset":"MSV000093634","datasetNum":"93634","title":"GNPS - Ancestral allele of DNA polymerase gamma modifies antiviral tolerance","user":"zhaialek","site":"MassIVE","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":"MS:1002783","modification":"MS:1002864","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":"827"}, {"dataset":"MSV000093633","datasetNum":"93633","title":"Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate","user":"eachapman2","site":"MassIVE","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":"828"}, {"dataset":"MSV000093632","datasetNum":"93632","title":"Lu_C16orf72_APMS_U2OS_P36_Elite_VS38","user":"gingraslab","site":"MassIVE","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":"829"}, {"dataset":"MSV000093630","datasetNum":"93630","title":"Lu_C16orf72_APMS_293_P36_Elite_VS37","user":"gingraslab","site":"MassIVE","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":"830"}, {"dataset":"MSV000093628","datasetNum":"93628","title":"Lu_TP53stability_BioID_P103_6600_VS50","user":"gingraslab","site":"MassIVE","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":"831"}, {"dataset":"MSV000093627","datasetNum":"93627","title":"GNPS - 20231211_public_raw_data_invivo_sildenafil_metabolite","user":"xat007","site":"MassIVE","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":"MS:1002786","modification":"MS:1002864","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":"832"}, {"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","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":"MS:1003004;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":"833"}, {"dataset":"MSV000093624","datasetNum":"93624","title":"Phosphoproteomics of dried blood collected on Mitra devices","user":"mwfoster","site":"MassIVE","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":"MS:1003028;MS:1003094;MS:1003230","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":"834"}, {"dataset":"MSV000093623","datasetNum":"93623","title":"Identification of ubiquitin interactors in Legionella pneumophila using ubiquitin activity-based probes","user":"zhan3248","site":"MassIVE","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":"MS:1002523","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":"835"}, {"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","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. ","fileCount":"1585","fileSizeKB":"198657080","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003183","modification":"MS:1002864","keywords":"Quaternary ammonium compounds;Disinfectants;Xenobiotic metabolism;Ion mobility-mass spectrometry;Biomonitoring;COVID-19","pi":[{"name":"Libin Xu","email":"libinxu@uw.edu","institution":"University of Washington","country":"United States of America"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"f929e4005ffe4827bf0c10921b23d453","id":"836"}, {"dataset":"MSV000093620","datasetNum":"93620","title":"Multi-omics analysis of aggregative multicellularity","user":"bared","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1702152303000","created":"Dec. 9, 2023, 12:05 PM","description":"The extent to which mRNA and protein levels correlate is still not fully known, especially during development, when cells undergo a major transition in gene expression. 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":"MS:1003395","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":"837"}, {"dataset":"MSV000093618","datasetNum":"93618","title":"GNPS - Feline fecal samples (quantification of polyamine conjugated to bile acids)","user":"helenamrusso","site":"MassIVE","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","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":"838"}, {"dataset":"MSV000093615","datasetNum":"93615","title":"Proteomics of dried blood collected on Mitra devices","user":"mwfoster","site":"MassIVE","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":"MS:1003028","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":"839"}, {"dataset":"MSV000093614","datasetNum":"93614","title":"GC-MS of 4 species of plant used in Amazonia medicine recipes","user":"F4ss0","site":"MassIVE","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":"29","fileSizeKB":"456451","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"840"}, {"dataset":"MSV000093613","datasetNum":"93613","title":"Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer","user":"coonlabs","site":"MassIVE","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":"MS:1003029;MS:1003378","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":"841"}, {"dataset":"MSV000093611","datasetNum":"93611","title":"Proteostasis perturbation of N-Myc by HSP70 inhibition improves treatment in neuroendocrine prostate cancer","user":"gabrig","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1702062852000","created":"Dec. 8, 2023, 11:14 AM","description":"N-Myc is a key driver of neuroendocrine tumors, such as neuroblastoma and neuroendocrine prostate cancer. However, N-Myc is considered undruggable because it lacks clear binding sites for small molecules. One potential way to circumvent this challenge is to identify and target the protein homeostasis proteostasis systems that maintain N-Myc levels. 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. ","fileCount":"5","fileSizeKB":"21138160","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003229","modification":"UNIMOD:893 - \\\"Carbamidomethylated DTT modification of cysteine.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Prostate cancer, Neuroendocrine, Proteostasis, N-Myc, HSP70, STUB1, Ubiquitination, Therapy","pi":[{"name":"Chengfei Liu","email":"cffliu@ucdavis.edu","institution":"University Of California, Davis","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047661","task":"fbb023432d854b8c93209cd5d93c5d2b","id":"842"}, {"dataset":"MSV000093610","datasetNum":"93610","title":"Identification of complex III, NQR and SDH as pharmacologic targets in non-multiplying Pseudomonas aeruginosa cultured in urine-like conditions","user":"JuarezLab","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1702062541000","created":"Dec. 8, 2023, 11:09 AM","description":"Bacterial membrane samples (20 ug of protein) were prepared using the Filter Aided Sample Preparation protocol, employing 30 K NMWL centrifugal filter units. 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. 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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":"MS:1003029;MS:1002732","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":"845"}, {"dataset":"MSV000093605","datasetNum":"93605","title":"Heart proteomics of pathological atrial enlargement associated with atrial fibrillation","user":"dwgree","site":"MassIVE","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. 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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":"MS:1002732;MS:1003029","modification":"UNIMOD:2016","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":"852"}, {"dataset":"MSV000093593","datasetNum":"93593","title":"ARID3C acts as a regulator of monocyte to macrophage differentiation interacting with NPM1","user":"gmltn1541","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"853"}, {"dataset":"MSV000093592","datasetNum":"93592","title":"Neuronal_Notch_Exosome_YZWang_2023_Cell_Reports","user":"jeffsavas","site":"MassIVE","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":"This term should be given if the modification was unknown.","keywords":"Exosome,Alix,Neuron,Notch","pi":[{"name":"Jeffrey N. 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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","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":"858"}, {"dataset":"MSV000093586","datasetNum":"93586","title":"Detection of 187AA by mass spectrometry","user":"huzhijuan","site":"MassIVE","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":"MS:1003028;MS:1002634","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":"859"}, {"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","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":"860"}, {"dataset":"MSV000093581","datasetNum":"93581","title":"Comparison of glioblastoma cell culture platforms based on transcriptional similarity with paired tissue","user":"khj232","site":"MassIVE","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":"MS:1003028","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":"861"}, {"dataset":"MSV000093580","datasetNum":"93580","title":"Detection of 187AA by mass spectrometry","user":"huzhijuan","site":"MassIVE","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":"MS:1003028;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":"862"}, {"dataset":"MSV000093578","datasetNum":"93578","title":"Interactions between sea snails and trematodes: analysis of metabolomes","user":"egor_repkin","site":"MassIVE","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","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":"863"}, {"dataset":"MSV000093576","datasetNum":"93576","title":"AP-MS analyses of Halo- Sin3 complex subunits stably expressed in 293T cells.","user":"simrproteomics","site":"MassIVE","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":"864"}, {"dataset":"MSV000093575","datasetNum":"93575","title":"GNPS - P. fluorescens in CAA with Iron Infusion and High pH","user":"aronlabshared","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"865"}, {"dataset":"MSV000093574","datasetNum":"93574","title":"GNPS - P. fluorescens in Succinate Minimal Media","user":"aronlabshared","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"866"}, {"dataset":"MSV000093573","datasetNum":"93573","title":"Multiplexed Proteomics Analysis of Zebrafish Embryos at Early Developmental Stages","user":"simrproteomics","site":"MassIVE","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":"MS:1003029","modification":"UNIMOD:2016;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":"867"}, {"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","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","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":"868"}, {"dataset":"MSV000093571","datasetNum":"93571","title":"GNPS - 20231123_ChemProp2_Non-targeted Metabolomics of Xenobiotic Biotransformations using synthetic gut bacterial community","user":"bciap01","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"869"}, {"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","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","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":"870"}, {"dataset":"MSV000093569","datasetNum":"93569","title":"GNPS - Dataset Creation from GNPS Molcular Networking - f884a88d38134c69bb951be15ffc9f9d","user":"rboiteau","site":"MassIVE","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":"MS:1002634","modification":"MS:1002864","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":"871"}, {"dataset":"MSV000093567","datasetNum":"93567","title":"5HT - Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3","user":"ccms","site":"MassIVE","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":"MS:1002732;Q Exactive","modification":"No post-translational-modifications are been included in the identified peptides of this dataset","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":"872"}, {"dataset":"MSV000093565","datasetNum":"93565","title":"GNPS - P. fluorescens Iron Infusion in CAA","user":"aronlabshared","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"873"}, {"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","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":"MS:1003029","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":"874"}, {"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","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":"65","fileSizeKB":"46811660","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002732;MS:1003230","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":"875"}, {"dataset":"MSV000093556","datasetNum":"93556","title":"Rapid Discovery of Antitumor Substances from Marine Fungi Based on UPLC-Q-TOF-MS","user":"1234512345","site":"MassIVE","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":"876"}, {"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","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":"877"}, {"dataset":"MSV000093554","datasetNum":"93554","title":"Unveiling the Neuroprotective Potential of Nobiletin in human Neural Progenitor Cells (hNPCs)","user":"abpant","site":"MassIVE","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","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":"878"}, {"dataset":"MSV000093553","datasetNum":"93553","title":"AP-MS analyses of Halo-SAP25 transiently expressed in 293T cells.","user":"simrproteomics","site":"MassIVE","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":"879"}, {"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","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":"MS:1003028","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"Connexin 43;breast cancer;HER2;gap junction","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":"PXD047448","task":"a32bce6f826244a7baae3c9bac70121c","id":"880"}, {"dataset":"MSV000093547","datasetNum":"93547","title":"IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport","user":"ProteomicsCF_FLI","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701423242000","created":"Dec. 1, 2023, 1:34 AM","description":"Mutations in the IER3IP1 (Immediate early response-3 interacting protein 1) gene can cause MEDS1 (microcephaly with simplified gyral pattern, epilepsy, and permanent neonatal diabetes syndrome-1), a severe disease leading to death in early childhood. The small endoplasmic reticulum-membrane protein IER3IP1 has a non-essential role in ER-Golgi transport. 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":"MS:1003028","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":"881"}, {"dataset":"MSV000093542","datasetNum":"93542","title":"Alkyne-probe pull-down in LAPC4-CR cells","user":"gcraven13","site":"MassIVE","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. Biotinylated proteins were pulled down with neutravidin agarose. After the pulldown, the neutravidin agarose beads were treated with trypsin, and the tryptic peptides were labelled with TMT6 and analyzed by tandem mass spectrometry. DMSO = Reporter 126-128, alkyne-probe = Reporter 129-131. Two replicate injections.","fileCount":"6","fileSizeKB":"2678347","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003029","modification":"methionine oxidation;cysteine carbamidomethylation;TMT6plex","keywords":"TMT6","pi":[{"name":"Jack Taunton","email":"jack.taunton@ucsf.edu","institution":"University of California, San Francisco","country":"United States"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"c99e6248f76e4524af4a1ce606b4c743","id":"882"}, {"dataset":"MSV000093539","datasetNum":"93539","title":"An automated workflow for label free single cell proteomics","user":"cctortec","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701309807000","created":"Nov. 29, 2023, 6:03 PM","description":"Automated sample preparation workflows for high throughput single cell proteomics on the timsTOF platforms","fileCount":"10317","fileSizeKB":"959037054","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003231","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"single cell proteomics","pi":[{"name":"Claudia Ctortecka","email":"cctortec@broadinstitute.org","institution":"Broad Institute","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"107c422b48c44a8f988dceae85b2d59a","id":"883"}, {"dataset":"MSV000093535","datasetNum":"93535","title":"SPEED-E: A modified version of the Sample Preparation by Easy Extraction and Digestion(-free) protocol for Enamel-based sex determination","user":"tpcleland","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701274483000","created":"Nov. 29, 2023, 8:14 AM","description":"Development of the Sample Preparation by Easy Extraction and Digestion-free for Enamel (SPEED-E) for sex determination of human remains. Applied to 88 subadult and juvenile individuals from the First Baptist Church of Philadelphia assemblage of human skeletal remains from Philadelphia, Pennsylvania, USA. ","fileCount":"1283","fileSizeKB":"22914287","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"enamel;amelogenin;sex","pi":[{"name":"Timothy Cleland","email":"clelandtp@si.edu","institution":"Smithsonian Institution","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD047380","task":"5b1dd5364d0b47aca4c6a7a5a6260990","id":"884"}, {"dataset":"MSV000093533","datasetNum":"93533","title":"Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics-2","user":"cylee","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701263840000","created":"Nov. 29, 2023, 5:17 AM","description":"Kinase inhibitors (KIs) are important cancer drugs but often display polypharmacology that is molecularly not understood. 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":"MS:1002732","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":"885"}, {"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","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":"MS:1003028;MS:1003230","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":"886"}, {"dataset":"MSV000093527","datasetNum":"93527","title":"GNPS - NISTfecalRM_Astral_HypersilGoldC18_positive_2","user":"yasel","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701238070000","created":"Nov. 28, 2023, 10:07 PM","description":"NIST fecal reference material extracted with 50% MeOH and prepared in different dilutions and reconstitution solvents. The analysis was conducted using a Hypersil Gold (C18) in positive ionization mode on a Astral via different MS-modes. ","fileCount":"87","fileSizeKB":"41288221","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003378","modification":"MS:1002864","keywords":"NIST;reference material;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":"b935d74dc44344628339b3adf4689615","id":"887"}, {"dataset":"MSV000093526","datasetNum":"93526","title":"GNPS - NISTfecalRM_Astral_HypersilGoldC18_positive","user":"yasel","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701233337000","created":"Nov. 28, 2023, 8:48 PM","description":"NIST fecal reference material extracted with 50% MeOH and prepared in different dilutions and reconstitution solvents. The analysis was conducted using a Hypersil Gold (C18) in positive ionization mode on a Astral via different MS-modes (positive ionization mode). ","fileCount":"211","fileSizeKB":"106931146","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003378","modification":"MS:1002864","keywords":"NIST;fecal;reference material","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":"5b9076c6cd134284806672033569996e","id":"888"}, {"dataset":"MSV000093521","datasetNum":"93521","title":"GNPS - Hypoxylon investiens extracts obtained by Plackett Burman DOE, using epigenetic modulators","user":"sirlino","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701191091000","created":"Nov. 28, 2023, 9:04 AM","description":"Hypoxylon investiens (isolated from Asparagopsis taxiformis) extracts obtained by Plackett Burman DOE, using epigenetic modulators and varying physico-chemical conditions","fileCount":"558","fileSizeKB":"4659297","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Hypoxylon investiens (NCBITaxon:326663)","instrument":"MS:1003252","modification":"MS:1002864","keywords":"Hypoxylon investiens;Epigenetic;Plackett Burman","pi":[{"name":"Victor Hugo Lino Rufino","email":"victor.lino@unesp.br","institution":"UNESP","country":"Brazil"}],"complete":"true","quant_analysis":"Study Design","status":"Complete","private":"false","hash":"","px":"","task":"2ec2ffbb4b5743fba46496e769bd4f5a","id":"889"}, {"dataset":"MSV000093520","datasetNum":"93520","title":"Differential partitioning by disorder-mediated condensates","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701188783000","created":"Nov. 28, 2023, 8:26 AM","description":"Samples 1012398_F1-F8: Using recombinant purified mCherry-tagged FUS-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\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":"MS:1002523;MS:1002732;MS:1003029","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":"890"}, {"dataset":"MSV000093519","datasetNum":"93519","title":"MS-based Proteomics Analysis of Cerebrospinal Fluid from Niemann-Pick type C Disease Patients","user":"sebastianevw","site":"MassIVE","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":"MS:1003230","modification":"MS:1002864","keywords":"Niemann-Pick Type C Disease;proteomics","pi":[{"name":"Forbes D. Porter","email":"fdporter@mail.nih.gov","institution":"NICHD","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"c83f8a3f86334490be6493bb6644f029","id":"891"}, {"dataset":"MSV000093518","datasetNum":"93518","title":" Development of a Combined Protein and Dye Extraction Approach for the Analysis of Keratin-Based Textiles","user":"IlariaSerafini","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701186259000","created":"Nov. 28, 2023, 7:44 AM","description":"Protocol development for co-extraction of proteins and dyes from wool ","fileCount":"184","fileSizeKB":"27049544","spectra":"0","psms":"127790","peptides":"3525","variants":"11602","proteins":"2326","search_psms":"0","search_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":"LTQ Orbitrap Elite","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:5 - \\\"Carbamylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"keratins;keratin associated proteins;wool;dye","pi":[{"name":"Ilaria Serafini","email":"ilaria.serafini@uniroma1.it","institution":"Sapienza University of Rome\/ Smithsonian Institution","country":"Italy\/ USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047336","task":"9f2de51421194c699e2206059abb0dec","id":"892"}, {"dataset":"MSV000093517","datasetNum":"93517","title":"Chondrodysplasia-inducing COL2A1 p.Gly1170Ser causes an ER storage defect without associated unfolded protein response in a human cartilage model","user":"rpschiav","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701179753000","created":"Nov. 28, 2023, 5:55 AM","description":"10-plex TMT dataset generated by immunoprecipitation of epitope-tagged COL2A1 constructs along with DSP-crosslinked interactors. This experiment allows for quantitative comparison of wild-type and Gly1170Ser 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":"6","fileSizeKB":"995955","spectra":"0","psms":"3103","peptides":"1382","variants":"1805","proteins":"147","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003028","modification":"UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:34 - \\\"Methylation.\\\"","keywords":"COL2A1;Quantitative Proteomics; TMT Labeling,","pi":[{"name":"Matthew Shoulders","email":"mshoulde@mit.edu","institution":"MIT","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047329","task":"da2754ec8b8d4121a365babbf46dc1d2","id":"893"}, {"dataset":"MSV000093516","datasetNum":"93516","title":"In-depth analysis of molecular network based on LC-MS\/MS in complex systems","user":"ZYH159951","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701139916000","created":"Nov. 27, 2023, 6:51 PM","description":"Ginseng Radix et Rhizoma (GR), Bufonis Venenum (BV), Epimedii Folium (EF), Aconiti Lateralis Radix Praeparata (AL) and Salviae Miltiorrhizae Radix et Rhizoma (SM)","fileCount":"27","fileSizeKB":"3566347","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002726","modification":"NA","keywords":"Natural products;In-depth analysis","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":"8c483a6a04b44d74b3d1d90c1fdf6af7","id":"894"}, {"dataset":"MSV000093515","datasetNum":"93515","title":"Myeloid Cell MHC1 regulates CD8 T cells and NASH","user":"Kennedy2021","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701135795000","created":"Nov. 27, 2023, 5:43 PM","description":"Isolated H2KB peptides from control and NASH livers from LDLRKO and Sucrose fed mice.","fileCount":"18","fileSizeKB":"8498847","spectra":"0","psms":"6705","peptides":"1127","variants":"1283","proteins":"1082","search_psms":"0","search_peptides":"0","search_variants":"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":"Thermo Orbitrap Explores 480","modification":"MS:1002864","keywords":"Liver, H2KB peptides","pi":[{"name":"Arion Kennedy","email":"akmidget@ncsu.edu","institution":"North Carolina State University","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD047295","task":"1b8aecd78505492b9c254241d96de1c6","id":"895"}, {"dataset":"MSV000093514","datasetNum":"93514","title":"GNPS Scripps Pier Hurricane 2023 Samples Positive and Negative Mode","user":"rrtorres","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701113394000","created":"Nov. 27, 2023, 11:29 AM","description":"Acidified and untreated PPL SPE extracted DOM samples taken before during and after Hurricane Hillary 2023 at the Scripps Pier in La Jolla, CA (Non-targeted LC-MS\/MS, positive and negative mode)","fileCount":"192","fileSizeKB":"9416158","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 Elite","modification":"MS:1002864","keywords":"marine;DOM;Non-targeted MS\/MS","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":"2992cc8f4e3e4b50b3223a3d53c5945a","id":"896"}, {"dataset":"MSV000093513","datasetNum":"93513","title":"Alcoholic hepatitis plasma degradome","user":"mmerchant","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701109154000","created":"Nov. 27, 2023, 10:19 AM","description":"It was hypothesized that the severe inflammatory liver injury caused by alcoholic hepatitis (AH) would yield a unique peptidome profile in human patient plasma, and degraded fragments (degradome) of hepatic and extracelluar proteomes would change between AH patient groups defined by MELD scores. 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. TIC-normalized XIC data were used for statistical analyses.","fileCount":"129","fileSizeKB":"34883020","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"de novo sequencing;biomarker;degradome;alcoholic hepatitis","pi":[{"name":"Michael L. Merchant, PhD","email":"mlmerc02@louisville.edu","institution":"University of Louisville","country":"USA"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"3a1e77b7fdf649cdb18e51be2661f6f1","id":"897"}, {"dataset":"MSV000093512","datasetNum":"93512","title":"Quantitative proteomics with Regen V standardization of PTEN deletion-induced optic nerve regeneration mouse models and controls.","user":"sbhattacharya","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701108182000","created":"Nov. 27, 2023, 10:03 AM","description":"A quantitative proteomic profiling was performed on PTEN deletion-induced optic nerve regeneration mouse models and controls. At postnatal day 28 (week 4), PTENloxP\/loxP mice were subjected to intravitreal injection (2-3ul) of adeno-associated viruses expressing Cre (AAV2-Cre) or control placenta alkaline phosphatase (AAV2-PLAP). 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. The Normalization was set to total peptide amount and confidence to low.\n","fileCount":"56","fileSizeKB":"74871396","spectra":"0","psms":"49894","peptides":"35341","variants":"36872","proteins":"21224","search_psms":"0","search_peptides":"0","search_variants":"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","keywords":"PTEN KO, Axon Regeneration, Mouse, Optic Nerve, Quantitative Proteomics, 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":"PXD047286","task":"6fc1db91a04b4adf906cb5ae11dc2ee1","id":"898"}, {"dataset":"MSV000093511","datasetNum":"93511","title":"Zhang Plasma Extracellular Vesicle Proteomics in Healthy Donors","user":"es3064","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1701107640000","created":"Nov. 27, 2023, 9:54 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. 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Index of MS supporting files uploaded: - Related to Fig. 1a and Extended Data Fig. 1a (AO3435-AO3440: TMT proteomics (Unimod: 35; 737; 4)). - Related to Fig. 1b, c (see MSV000093721).","fileCount":"7","fileSizeKB":"2052186","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732;MS:1003028","modification":"UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:737 - \\\"Sixplex Tandem Mass Tag.\\\"","keywords":"Label Free;TMT;UFM1;UFMylation","pi":[{"name":"Alban Ordureau","email":"OrdureaA@mskcc.org","institution":"Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center","country":"USA"},{"name":"Joao A. 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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","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":"902"}, {"dataset":"MSV000093498","datasetNum":"93498","title":"GNPS - Brittonodoxa subpinnata Insoluble extract","user":"Wilton","site":"MassIVE","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","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":"903"}, {"dataset":"MSV000093497","datasetNum":"93497","title":"GNPS - Brittonodoxa subpinnata soluble extract","user":"Wilton","site":"MassIVE","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","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":"904"}, {"dataset":"MSV000093496","datasetNum":"93496","title":"GNPS - Brittonodoxa subpinnata non-polar extract","user":"Wilton","site":"MassIVE","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","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":"905"}, {"dataset":"MSV000093495","datasetNum":"93495","title":"GNPS - Brittonodoxa subpinnata polar extracts","user":"Wilton","site":"MassIVE","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","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":"906"}, {"dataset":"MSV000093494","datasetNum":"93494","title":"nPOP_ProtocolPaper_Dataset_celllines","user":"andrewleduc95","site":"MassIVE","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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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":"916"}, {"dataset":"MSV000093466","datasetNum":"93466","title":"Protection of beta cells against pro-inflammatory cytokine stress by GDF15-ERBB2 signaling","user":"alchemistmatt","site":"MassIVE","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":"MS:1002634","modification":"UNIMOD:2016;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":"917"}, {"dataset":"MSV000093465","datasetNum":"93465","title":"Quantitative proteomics with Regen V standardization in axon regeneration of Xenopus Laevis.","user":"sbhattacharya","site":"MassIVE","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","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":"918"}, {"dataset":"MSV000093464","datasetNum":"93464","title":"GNPS_Korean_Medicinal_Plants_reprocess_ENPKG","user":"pmallard","site":"MassIVE","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","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":"919"}, {"dataset":"MSV000093463","datasetNum":"93463","title":"GNPS - Senegal Mangrove spcecies Raw data extract","user":"khadime","site":"MassIVE","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","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":"920"}, {"dataset":"MSV000093458","datasetNum":"93458","title":"GNPS - LC-MSe Data from the Berries and Roots of 60 Panax ginseng Genotypes","user":"kbkang","site":"MassIVE","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","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":"921"}, {"dataset":"MSV000093457","datasetNum":"93457","title":"Structure-function analysis of the cyclic b-1,2-glucan synthase from Agrobacterium tumefaciens","user":"klemens_froehlich","site":"MassIVE","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":"MS:1002523","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":"922"}, {"dataset":"MSV000093456","datasetNum":"93456","title":"Ttttttttttttttttttttttttttttttttttttttteszt15","user":"KecskemetiGabor2","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"923"}, {"dataset":"MSV000093453","datasetNum":"93453","title":"O-GlcNAc Containing Proteins in Normal and Idiopathic Pulmonary Fibrosis Human Fibroblasts","user":"alchemistmatt","site":"MassIVE","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":"30","fileSizeKB":"12179009","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002877","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":"924"}, {"dataset":"MSV000093452","datasetNum":"93452","title":"Quantitative proteomics with Regen V standardization of optogenetics induced axon regeneration.","user":"sbhattacharya","site":"MassIVE","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","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":"925"}, {"dataset":"MSV000093443","datasetNum":"93443","title":"20210223_new_timedependent_human_fbmn_data","user":"xat007","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1700528126000","created":"Nov. 20, 2023, 4:55 PM","description":"In vitro metabolite data of sildenafil using LC-QTOF\/MS and human liver microsome at 2021. because of new policy of storage.","fileCount":"70","fileSizeKB":"833568","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002786","modification":"FBMN","keywords":"sildenafil;metabolite","pi":[{"name":"Junsang Yu","email":"wowxat@naver.com","institution":"Hanyang University","country":"South Korea"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"9615726736cb48f59ec0de0510fcff5e","id":"926"}, {"dataset":"MSV000093442","datasetNum":"93442","title":"GNPS - NISTfecal - KinetexC18 column - pos","user":"yasel","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1700521697000","created":"Nov. 20, 2023, 3:08 PM","description":"Fecal NIST reference material, Kinetex C18 50mm*2.1mm, positive. \n400 mg fecal extracted in 4 mL of 50% MeOH without beads. 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","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":"927"}, {"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","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":"MS:1002732","modification":"MS:1002864","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":"928"}, {"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","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. 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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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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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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). 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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. 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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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However, there is no existing contaminant assay to test and quantify contaminants prior to MS analysis. Here, we developed a rapid and sensitive contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in MS sample preparation workflow. 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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":"8","fileSizeKB":"3777584","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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. 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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. 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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":"MS:1002732","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":"951"}, {"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","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. 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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. 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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":"66","fileSizeKB":"44355676","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003356","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":"956"}, {"dataset":"MSV000093347","datasetNum":"93347","title":"GNPS - Fecal metabolites identify liver transplant recipients at risk for peri-operative infection","user":"jess_cleary","site":"MassIVE","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. 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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":"MS:1002732","modification":"MS:1002864","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":"960"}, {"dataset":"MSV000093339","datasetNum":"93339","title":"Proteome analysis of the retina from RhoQ344X\/+ mouse","user":"ShimpeiTakita","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"961"}, {"dataset":"MSV000093337","datasetNum":"93337","title":"Dendrobates auratus PDMS in vivo temporal sampling","user":"mabel_gonzalez","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1699470943000","created":"Nov. 8, 2023, 11:15 AM","description":"In vivo analysis of skin secretions from D. auratus","fileCount":"82","fileSizeKB":"21335129","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"962"}, {"dataset":"MSV000093335","datasetNum":"93335","title":"Mitochondrial ribosomal protein L12 (MRPL12) post-translational modifications","user":"dittenhaferreed","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1699468392000","created":"Nov. 8, 2023, 10:33 AM","description":"Analysis of post-translational modifications on mitochondrial protein L12 (MRPL12). 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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":"343","fileSizeKB":"42408371","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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","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":"966"}, {"dataset":"MSV000093323","datasetNum":"93323","title":"The ALPHA Phase 1 Study: Pulmonary ArteriaL Hypertension Treated with CardiosPHere-Derived Allogeneic Stem Cells","user":"NivedaS5","site":"MassIVE","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":"MS:1003028","modification":"MS:1002864","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":"967"}, {"dataset":"MSV000093320","datasetNum":"93320","title":"Essential role of STAT5 tyrosine phosphorylation in vivo","user":"ronholes7059","site":"MassIVE","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":"MS:1002732","modification":"UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:2016;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":"968"}, {"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","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":"MS:1003252","modification":"MS:1002864","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":"969"}, {"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","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":"MS:1003252","modification":"MS:1002864","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":"f02ad2abab43446c928e0257c8aed9ec","id":"970"}, {"dataset":"MSV000093317","datasetNum":"93317","title":"GNPS - 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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":"974"}, {"dataset":"MSV000093307","datasetNum":"93307","title":"GNPS - Celastraceae_plant_extracts_library_graphknowledge","user":"quirosgu","site":"MassIVE","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","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":"975"}, {"dataset":"MSV000093306","datasetNum":"93306","title":"Egg MVBs elicit an LC3-associated phagocytosis-like pathway to degrade paternal mitochondria after fertilization ","user":"ylevinwis","site":"MassIVE","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":"MS:1002732","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":"976"}, {"dataset":"MSV000093305","datasetNum":"93305","title":"GNPS - Dyrehaven Streptomyces P9-A2 monoculture and coculture data with Aspergillus tubingensis","user":"scottjarmusch11","site":"MassIVE","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":"MS:1002791","modification":"MS:1002864","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":"977"}, {"dataset":"MSV000093304","datasetNum":"93304","title":"Ttttttttttttttttttttttttttttttttttttttteszt9","user":"KecskemetiGabor2","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"978"}, {"dataset":"MSV000093302","datasetNum":"93302","title":"GNPS - Methanolic extracts of Amycolatopsis spp. on ISP2 - 8cae4ec6622e4cc0959042f087315336","user":"ka26lul","site":"MassIVE","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":"MS:1002634","modification":"MS:1002864","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":"979"}, {"dataset":"MSV000093301","datasetNum":"93301","title":"A mammalian-specific Alex3\/Galphaq protein complex regulating mitochondrial dynamics, dendritic complexity, and neuronal survival","user":"CBeninca","site":"MassIVE","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":"MS:1002523","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":"980"}, {"dataset":"MSV000093299","datasetNum":"93299","title":"mitochondrial and dengue virus_2023","user":"marjollycb","site":"MassIVE","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","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":"981"}, {"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","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":"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":"982"}, {"dataset":"MSV000093297","datasetNum":"93297","title":"20231103 DDA analysis of various rubber products with Agilent q-TOF","user":"zhaohaoq","site":"MassIVE","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":"MS:1002787","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":"983"}, {"dataset":"MSV000093296","datasetNum":"93296","title":"GNPS - Characterization of molecular factors involved in plant metabolic and morphological reprogramming during gall formation","user":"bpbowen","site":"MassIVE","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":"762","fileSizeKB":"50762827","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"984"}, {"dataset":"MSV000093294","datasetNum":"93294","title":"Genetic, community, and ecosystem consequences of co-introduction of mycorrhizal fungiwith exotic pines","user":"bpbowen","site":"MassIVE","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","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":"985"}, {"dataset":"MSV000093293","datasetNum":"93293","title":"MSX Spleen DIA and DDA Proteomics","user":"seeramlab","site":"MassIVE","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","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":"986"}, {"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","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","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":"987"}, {"dataset":"MSV000093287","datasetNum":"93287","title":"Detection of a Mitochondrial Stress Phenotype using the Cell Painting Assay","user":"janning","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"988"}, {"dataset":"MSV000093286","datasetNum":"93286","title":"GNPS - Pseudoalteromonas and Phaeobacter coexistence study","user":"PeterSvend","site":"MassIVE","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":"MS:1002791","modification":"MS:1002864","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":"989"}, {"dataset":"MSV000093282","datasetNum":"93282","title":"A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling","user":"Natalie_1234","site":"MassIVE","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":"62","fileSizeKB":"65673222","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1003029","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:21 - \\\"Phosphorylation.\\\";UNIMOD:2016;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":"990"}, {"dataset":"MSV000093279","datasetNum":"93279","title":"Multiplex substrate profiling by mass spectrometry Nf20S marizomib","user":"elanybs","site":"MassIVE","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","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":"991"}, {"dataset":"MSV000093278","datasetNum":"93278","title":"20231102_RAD_KRAS4B_TD_Assay_Submission","user":"dippolitora","site":"MassIVE","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":"MS:1002732;MS:1002526","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":"992"}, {"dataset":"MSV000093277","datasetNum":"93277","title":"GNPS - Comparative and Population Genomics of Xylariaceae","user":"bpbowen","site":"MassIVE","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","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":"993"}, {"dataset":"MSV000093276","datasetNum":"93276","title":"GNPS - Metabolite profiles of two Pantoea species with divergent traits for onion virulence.","user":"bpbowen","site":"MassIVE","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","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":"994"}, {"dataset":"MSV000093275","datasetNum":"93275","title":"GNPS - A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites","user":"bpbowen","site":"MassIVE","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","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":"995"}, {"dataset":"MSV000093274","datasetNum":"93274","title":"GNPS - Global metabolic profile comparison between 2 ecotypes upon inoculation with Azoarcus olearius","user":"bpbowen","site":"MassIVE","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","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":"996"}, {"dataset":"MSV000093273","datasetNum":"93273","title":"GNPS - Elucidate metabolism of bioenergy-relevant Clostridial and Streptomyces species","user":"bpbowen","site":"MassIVE","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","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":"997"}, {"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","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","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":"998"}, {"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","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","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":"999"}, {"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","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":"795","fileSizeKB":"48194982","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","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":"1000"}, {"dataset":"MSV000093269","datasetNum":"93269","title":"GNPS - Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours Postinoculation","user":"bpbowen","site":"MassIVE","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","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":"1001"}, {"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","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","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":"1002"}, {"dataset":"MSV000093267","datasetNum":"93267","title":"GNPS - Botryococcus braunii circadian time course","user":"bpbowen","site":"MassIVE","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","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":"1003"}, {"dataset":"MSV000093265","datasetNum":"93265","title":"GNPS - LC-MS2 and BGC paired data from actinomycetes","user":"amcaraballor","site":"MassIVE","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","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":"1004"}, {"dataset":"MSV000093263","datasetNum":"93263","title":"GNPS - MS2 data of zwitterionic metabolites from phyto- and bacterioplankton using ZIC-HILIC column","user":"Muhaiminatul","site":"MassIVE","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","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":"1005"}, {"dataset":"MSV000093262","datasetNum":"93262","title":"GNPS - Bile Acid Standards for MSV000093200","user":"spthomasGNPS","site":"MassIVE","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":"1006"}, {"dataset":"MSV000093257","datasetNum":"93257","title":"The effect of abiotic stress on rhizosphere microbiota","user":"bpbowen","site":"MassIVE","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","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":"1007"}, {"dataset":"MSV000093248","datasetNum":"93248","title":"The effect of abiotic stress on rhizosphere microbiota","user":"bpbowen","site":"MassIVE","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","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":"1008"}, {"dataset":"MSV000093247","datasetNum":"93247","title":"GNPS - Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces","user":"bpbowen","site":"MassIVE","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","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":"1009"}, {"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","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","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":"1010"}, {"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","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":"1011"}, {"dataset":"MSV000093230","datasetNum":"93230","title":"GNPS - 3XTG AGMP QiitaID 14748","user":"amcaraballor","site":"MassIVE","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","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":"1012"}, {"dataset":"MSV000093227","datasetNum":"93227","title":"Human Keratinocyte Responses to Woodsmoke","user":"brettsp1","site":"MassIVE","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":"MS:1002634","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":"1013"}, {"dataset":"MSV000093224","datasetNum":"93224","title":"GNPS - ","user":"klongnecker","site":"MassIVE","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":"MS:1002732","modification":"MS:1002864","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":"1014"}, {"dataset":"MSV000093223","datasetNum":"93223","title":"Stable-isotope analysis of nitrate using ESI-Orbitrap IRMS","user":"isoorbi","site":"MassIVE","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":"800","fileSizeKB":"6782056","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"1015"}, {"dataset":"MSV000093222","datasetNum":"93222","title":"Stable-isotope analysis of TFA and MRFA using ESI-Orbitrap IRMS","user":"isoorbi","site":"MassIVE","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":"24","fileSizeKB":"182589","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"1016"}, {"dataset":"MSV000093220","datasetNum":"93220","title":"NAK-associated protein 1\/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis.","user":"aordureau","site":"MassIVE","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":"MS:1003029","modification":"UNIMOD:2016;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":"1017"}, {"dataset":"MSV000093217","datasetNum":"93217","title":"GNPS - Streptomyces leeuwenhoekii C34 mutasynthesis","user":"scottjarmusch11","site":"MassIVE","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","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":"1018"}, {"dataset":"MSV000093216","datasetNum":"93216","title":"GNPS - honey quechers data submission","user":"Wang_1999","site":"MassIVE","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":"MS:1003095","modification":"MS:1002864","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":"1019"}, {"dataset":"MSV000093215","datasetNum":"93215","title":"GNPS - Glutathione adduct_in vitro_human liver microsomes","user":"jyoungheun","site":"MassIVE","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","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":"1020"}, {"dataset":"MSV000093214","datasetNum":"93214","title":"GNPS_LCMSMS_metabolomics approach ","user":"Nathareen","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1698818327000","created":"Oct. 31, 2023, 10:58 PM","description":"Testing pooled samples and samples for metabolomics approach","fileCount":"99","fileSizeKB":"12525977","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1002789","modification":"MS:1002864","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":"1021"}, {"dataset":"MSV000093213","datasetNum":"93213","title":"The modified RNA base acp3U is an attachment site for N-glycans in glycoRNA","user":"xie753951","site":"MassIVE","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":"MS:1003293","modification":"MS:1002864","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":"1022"}, {"dataset":"MSV000093211","datasetNum":"93211","title":"Proteomic analysis of ARF regulatory molecules co-immunoprecipitating with human SDC4 (huSDC4) ","user":"HoracioML","site":"MassIVE","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":"1023"}, {"dataset":"MSV000093210","datasetNum":"93210","title":"MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons","user":"fschulte","site":"MassIVE","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":"1024"}, {"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","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","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":"1025"}, {"dataset":"MSV000093206","datasetNum":"93206","title":"Recruitment of FBXO22 for Targeted Degradation of NSD2","user":"jonstgermain","site":"MassIVE","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":"319","fileSizeKB":"68361512","spectra":"0","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":"MS:1002523","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":"1026"}, {"dataset":"MSV000093204","datasetNum":"93204","title":"Mitochondrial RNA Polymerase Post-translational Modifications","user":"dittenhaferreed","site":"MassIVE","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":"MS:1002791","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":"1027"}, {"dataset":"MSV000093203","datasetNum":"93203","title":"An Improved Sample Preparation Method for Protein and Peptide Identification from Human Hair","user":"zhengzhang","site":"MassIVE","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":"8","fileSizeKB":"11881094","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732","modification":"MS:1002864","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":"1028"}, {"dataset":"MSV000093202","datasetNum":"93202","title":"Poirson_TPD_timsTOFPro2_VS13_14","user":"gingraslab","site":"MassIVE","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":"MS:1003230","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":"1029"}, {"dataset":"MSV000093201","datasetNum":"93201","title":"COQ4 Affinity Enrichment Mass Spectrometry","user":"guerra","site":"MassIVE","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":"MS:1003094","modification":"MS:1002864","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":"1030"}, {"dataset":"MSV000093200","datasetNum":"93200","title":"GNPS_Sepsis_LP2_Trial_Untargeted_Metabolomics","user":"spthomasGNPS","site":"MassIVE","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. 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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","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":"1033"}, {"dataset":"MSV000093196","datasetNum":"93196","title":"Antigen-specific Fab profiling achieves molecular resolution of human autoantibody repertoires in rheumatoid arthritis ","user":"DaniquevanRijswijck","site":"MassIVE","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":"26","fileSizeKB":"2695301","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1003028;MS:1002732","modification":"MS:1002864","keywords":"IgG1 clonal profiling, Rheumatoid arthritis, ACPA, Autoimmune disease, Antibodies, LC-MS","pi":[{"name":"Albert J.R. 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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":"MS:1003005","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":"1035"}, {"dataset":"MSV000093192","datasetNum":"93192","title":"GNPS_Mouse_Maternal_Infant_Antibiotic_Administration","user":"spthomasGNPS","site":"MassIVE","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. 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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":"MS:1002732","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":"1037"}, {"dataset":"MSV000093186","datasetNum":"93186","title":"2022_Corsican_Bryophyta_collection","user":"anaisP2A","site":"MassIVE","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":"No post-translational-modifications are been included in the identified peptides of this dataset","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":"1038"}, {"dataset":"MSV000093184","datasetNum":"93184","title":"GNPS - Effects of Dapensutrile and Glycine on mice QiitaID 15108 and 14472","user":"amcaraballor","site":"MassIVE","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. 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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. These results reveal that the metabolic flexibility imparted by the stroma-derived acetate enabled cancer cell survival under acidosis via the ACSS2-SP1-SAT1 axis.","fileCount":"9","fileSizeKB":"2673428","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732","modification":"UNIMOD:1 - \\\"Acetylation.\\\";UNIMOD:4 - \\\"Iodoacetamide derivative.\\\";UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\"","keywords":"ACLY, ACSS2, Cancer-associated fibroblasts, Pancreatic cancer, Acidosis, Cancer 48 metabolism","pi":[{"name":"Pankaj K Singh","email":"Pankaj-Singh@ouhsc.edu","institution":"University of Oklahoma Health Sciences Center","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046270","task":"cc6377649ca547699fb16e230cb06609","id":"1049"}, {"dataset":"MSV000093153","datasetNum":"93153","title":"ERBB2 R599C variant is associated with left ventricular outflow tract obstruction defects in human","user":"ichowdhu","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697729346000","created":"Oct. 19, 2023, 8:29 AM","description":"Non-syndromic congenital heart defects (CHD) are occasionally familial and left ventricular out flow tract obstruction (LVOTO) defects are among the subtypes with the highest hereditability. 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We used this data to standardize our milk extractions to 75:25 MeOH:MTBE.","fileCount":"190","fileSizeKB":"9018456","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":"human milk;methods","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":"3e200c6f40b34ddcbb5ed8e87d95cc1c","id":"1052"}, {"dataset":"MSV000093144","datasetNum":"93144","title":"GNPS - Bacterial Bile Acid Amidates (BBAAs) data set","user":"haihaba","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697644125000","created":"Oct. 18, 2023, 8:48 AM","description":"Data acquired for conjugated bile acids with amino acids analysis of human fecal samples by targeted LC-MS. 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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":"MS:1002634","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":"1054"}, {"dataset":"MSV000093140","datasetNum":"93140","title":"GNPS - Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life","user":"kkleigrewe","site":"MassIVE","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":"1055"}, {"dataset":"MSV000093137","datasetNum":"93137","title":"Identification of non-conventional small molecule degraders and stabilizers of squalene synthase","user":"joseho","site":"MassIVE","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). 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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. 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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":"MS:1002732","modification":"MS:1002864","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":"1062"}, {"dataset":"MSV000093124","datasetNum":"93124","title":"GNPS - klebsiella pneumoniae serum exposure","user":"lsanti","site":"MassIVE","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","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":"1063"}, {"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","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. 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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","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":"1065"}, {"dataset":"MSV000093120","datasetNum":"93120","title":"GNPS - 20231016_RIA_ApF5_secondary-metabolites_2","user":"iaco","site":"MassIVE","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":"MS:1002634","modification":"MS:1002864","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":"1066"}, {"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","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","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":"1067"}, {"dataset":"MSV000093117","datasetNum":"93117","title":"Logan Smith Revised MSc Thesis","user":"logansmith851","site":"MassIVE","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":"1068"}, {"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","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":"MS:1003028","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":"1069"}, {"dataset":"MSV000093115","datasetNum":"93115","title":"Myrsine guianensis (syn. Rapaneae guianensis) - UHPLC-ESI(+)-Q-tof","user":"fcassas88","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697385794000","created":"Oct. 15, 2023, 9:03 AM","description":"Chemical Profile of Myrsine guianensis Extracts obtained from floewrs, leaves and brunchs in EtOH, AcOEt and EtOH.","fileCount":"12","fileSizeKB":"190979","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Myrsine guianensis","instrument":"micrOTOF-Q","modification":"None","keywords":"Myrsine guianensis;Myrsinoic Acids;Flavonoids","pi":[{"name":"Fernando Cassas","email":"fernando.machado@unifesp.br","institution":"UNIFESP","country":"Brazil"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"12676e13f54144b68f7b2af9548abea3","id":"1070"}, {"dataset":"MSV000093113","datasetNum":"93113","title":"Development of a Semi-Automated MHC Associated Peptide Proteomics (MAPPs) Method Using Streptavidin Bead-Based Immunoaffinity Capture and Nano LC-MS\/MS to Support Immunogenicity Risk Assessment in Drug Development","user":"mvlee","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697316615000","created":"Oct. 14, 2023, 1:50 PM","description":"Proteomics data corresponding to the development of semi-automated MAPPs method. 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":"MS:1002732","modification":"UNIMOD:35 - \\\"Oxidation or Hydroxylation.\\\";UNIMOD:7 - \\\"Deamidation.\\\"","keywords":"MHC II;MAPPs;Biotherapeutic;Immunogenicity;PBMCs","pi":[{"name":"M. Violet Lee","email":"lee.manjui@gene.com","institution":"Genentech","country":"United States"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"7ada394f2e0745658fcea8257a65e61a","id":"1071"}, {"dataset":"MSV000093111","datasetNum":"93111","title":"Self-assembly of nanofilaments in cyanobacteria for protein co-localization","user":"david_prot","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697287861000","created":"Oct. 14, 2023, 5:51 AM","description":"Shotgun proteomics of Synechocystis sp. PCC 6803 and Synechococcus elongatus UTEX 2973 expressing PduA*","fileCount":"273","fileSizeKB":"607276849","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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);Synechococcus sp. UTEX 2973 (NCBITaxon:1350461)","instrument":"MS:1003005","modification":"MS:1002864","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":"1072"}, {"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","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":"MS:1003004","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":"1073"}, {"dataset":"MSV000093105","datasetNum":"93105","title":"GNPS - Integrated analysis of transcriptomics, metabolomics and proteomics approach to understand the importance of ABA-dependent pathways in facultative plant Mesembryanthemum Crystallinum leaf during the salt induced C 3 to CAM transition to explore the mechanism of this shift.","user":"takter3","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697222692000","created":"Oct. 13, 2023, 11:44 AM","description":"Mesembryanthemum crystallinum, a facultative CAM plant, shifts from C3 to CAM photosynthesis under salt stress, enhancing water use efficiency due to inverse stomatal patterns. 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":"MS:1002634","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":"1074"}, {"dataset":"MSV000093104","datasetNum":"93104","title":"GNPS melHKO Mm untargeted metabolomics","user":"Vitayo","site":"MassIVE","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":"MS:1002666","modification":"MS:1002864","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":"1075"}, {"dataset":"MSV000093103","datasetNum":"93103","title":"Hesketh_GIGYF1_P116_Sciex6600_VS11","user":"gingraslab","site":"MassIVE","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. The dataset consists of 12 raw MS files and associated peak lists and result files, all acquired on a SCIEX TripleTOF 6600 mass spectrometer. Geoffrey Hesketh generated samples, performed affinity purification and mass spectrometric acquisition. \r\n\r\nWithin the Tables:\r\nTable 1 describes the composition of this dataset\r\nTable 2 describes search parameters\r\nTable 3 provides SAINT output file\r\n","fileCount":"67","fileSizeKB":"27665558","spectra":"0","psms":"274802","peptides":"44630","variants":"53560","proteins":"30659","search_psms":"0","search_peptides":"0","search_variants":"0","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;mRNA translation initiation;GIGYF1","pi":[{"name":"Seyed Mehdi Jafarnejad","email":"sm.jafarnejad@qub.ac.uk","institution":"Queen's University Belfast","country":"UK"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"PXD046126","task":"37876cfc75d44b99a9192826e8e28138","id":"1076"}, {"dataset":"MSV000093102","datasetNum":"93102","title":"GNPS - Convergent and divergent responses of the rhizosphere chemistry and bacterial communities to a stress gradient in the Atacama Desert.","user":"ThomasDussarrat","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697204285000","created":"Oct. 13, 2023, 6:38 AM","description":"Untargeted analysis of plant and rhizosphere samples from the Atacama Desert. ","fileCount":"117","fileSizeKB":"6918146","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Jarava frigida (Phil.) F. Rojas;Atriplex imbricata (Moq.) D.Dietr.;Hoffmannseggia doellii Phil.;Adesmia spinosissima Meyen ex Vogel","instrument":"LTQ Orbitrap","modification":"MS:1002864","keywords":"Predictive metabolomics;rhizosphere chemistry;plants;Atacama Desert;soil microbiome","pi":[{"name":"Pierre Petriacq","email":"Pierre.Petriacq@inrae.fr","institution":"Universite de Bordeaux, INRAE, UMR1332 BFP","country":"France"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"17f668eb8679400db7d2490b4500fe03","id":"1077"}, {"dataset":"MSV000093101","datasetNum":"93101","title":"A modular turn-on strategy to profile E2-specific ubiquitination events in living cells","user":"suprama","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697203020000","created":"Oct. 13, 2023, 6:17 AM","description":"This dataset describes label-free quantification of E2-specific ubiquitinated species identified by a chemically-induced proximity approach, tCUbE.","fileCount":"113","fileSizeKB":"83906333","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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 Discovery;MS:1003094","modification":"MS:1002864","keywords":"chemically-induced proximity;E2-E3-substrates;label-free quantification;tCUbE;E2-specific ubiquitination","pi":[{"name":"Rebecca Scheck","email":"Rebecca.Scheck@tufts.edu","institution":"Tufts University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"6a7e76e7f1a94d95be44bd1fcaba3a37","id":"1078"}, {"dataset":"MSV000093092","datasetNum":"93092","title":"GNPS - Priestia endophytica fluorescent pigments","user":"alina_kharchuk","site":"MassIVE","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","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":"1079"}, {"dataset":"MSV000093090","datasetNum":"93090","title":"Janer_et_al_ESYT1_mitochondria_ER_contacts_P129","user":"gingraslab","site":"MassIVE","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":"1080"}, {"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","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":"MS:1002732","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":"1081"}, {"dataset":"MSV000093088","datasetNum":"93088","title":"SaLT&PepPr is an Interface-Predicting Language Model for Designing Peptide-Guided Protein Degraders","user":"mwfoster","site":"MassIVE","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":"MS:1003028","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":"1082"}, {"dataset":"MSV000093086","datasetNum":"93086","title":"Selective inhibition of OSBP blocks retrograde trafficking by inducing partial Golgi degradation","user":"niahedtu","site":"MassIVE","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","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":"1083"}, {"dataset":"MSV000093084","datasetNum":"93084","title":"Binding partners of Annexin A2 in MDA-MB-231 cells","user":"amira_mahdi","site":"MassIVE","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","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":"1084"}, {"dataset":"MSV000093083","datasetNum":"93083","title":"PHF6 cooperates with SWI\/SNF complexes to facilitate transcriptional progression","user":"mittal","site":"MassIVE","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":"1085"}, {"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","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. Arthritis Res Ther 25, 234 (2023). https:\/\/doi.org\/10.1186\/s13075-023-03204-6\r\n","fileCount":"11","fileSizeKB":"491232","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002582;ExionLC","modification":"MS:1002864","keywords":"lipidomics;hyperuricemia;gout;urate-lowering therapy","pi":[{"name":"Blanka Stiburkova","email":"stiburkova@revma.cz","institution":"Institute of Rheumatology, Prague","country":"Czech Republic"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"7ec8698c6db84cd9b68525d0547a9f35","id":"1086"}, {"dataset":"MSV000093079","datasetNum":"93079","title":"GNPS - Metabolomics data from Corallococcus coralloides","user":"Anton_Lindig","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1697015633000","created":"Oct. 11, 2023, 2:13 AM","description":"These are metabolomics data from a Bivariate OSMAC of Corallococcus coralloides. These data are part of the publication: Bivariate OSMAC Designs Expand the Secondary Metabolite Production Space in Corallococcus Coralloides\r\n","fileCount":"5","fileSizeKB":"229","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Corallococcus coralloides (NCBITaxon:184914)","instrument":"compact","modification":"MS:1002864","keywords":"Bivariate OSMAC","pi":[{"name":"Anton Lindig","email":"anton.lindig@tu-dortmund.de","institution":"TU Dortmund","country":"Germany"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"d9deebf9b5224e44ac9f72a51ebcd0e2","id":"1087"}, {"dataset":"MSV000093078","datasetNum":"93078","title":"Fremont et al 2023 - Arsenic stress triggers active exudation of arsenic-phytochelatin complexes from Lupinus albus roots ","user":"AdrienFremont","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696972941000","created":"Oct. 10, 2023, 2:22 PM","description":"Arsenic stress triggers active exudation of arsenic-phytochelatin complexes from Lupinus albus roots ","fileCount":"83","fileSizeKB":"8669177","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 albus (NCBITaxon:3870)","instrument":"MS:1002786","modification":"MS:1002864","keywords":"White Lupin;LC-MS\/MS;Arsenic;Phytochelatin","pi":[{"name":"Nicholas J. B. Brereton","email":"nicholas.brereton@umontreal.ca","institution":"University of Montreal","country":"Canada"}],"complete":"false","quant_analysis":"Study Design","status":"Partial","private":"false","hash":"","px":"","task":"9ef2f012cea54f86a968720658bff4d8","id":"1088"}, {"dataset":"MSV000093077","datasetNum":"93077","title":"GNPS - Tryptophan metabolite analysis of mouse serum by targeted LCMS","user":"djakob","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696966074000","created":"Oct. 10, 2023, 12:27 PM","description":"Tryptophan metabolite analysis of mouse serum by targeted LCMS.\r\nData are associated with publication in prep \"Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice\"","fileCount":"3392","fileSizeKB":"148573129","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"MS:1002666","modification":"MS:1002864","keywords":"LCMS;Tryptophan metabolites;mouse;targeted Metabolomics","pi":[{"name":"Ruth Ley","email":"ruth.ley@tuebingen.mpg.de","institution":"Max Planck Institute for Biology Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"35bdf5b1727f4084877df2e3cd8b0a25","id":"1089"}, {"dataset":"MSV000093076","datasetNum":"93076","title":"Short & branched-chain fatty acids analysis of mouse cecum by GCMS.","user":"djakob","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696964757000","created":"Oct. 10, 2023, 12:05 PM","description":"Short & branched-chain fatty acids analysis of mouse cecum by GCMS.","fileCount":"1340","fileSizeKB":"153766","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"5977 Agilent GCMS","modification":"MS:1002864","keywords":"GCMS;SCFA;cecum;mouse;BCFA","pi":[{"name":"Ruth Ley","email":"ruth.ley@tuebingen.mpg.de","institution":"Max Planck Institute for Biology Tuebingen","country":"Germany"}],"complete":"false","quant_analysis":"Quantification Results","status":"Partial","private":"false","hash":"","px":"","task":"f5472bbbff6e437e96cd14e329806433","id":"1090"}, {"dataset":"MSV000093074","datasetNum":"93074","title":"(N)1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting","user":"Mass4Tox","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696959712000","created":"Oct. 10, 2023, 10:41 AM","description":"To investigate how (N)1-methyl-phi affects out-of-frame mRNA translation","fileCount":"10","fileSizeKB":"1509518","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003029","modification":"MS:1002864","keywords":"mRNA translation; Synthetic mRNA; Protein synthesis","pi":[{"name":"Anne E Willis","email":"tls36@cam.ac.uk","institution":"MRC Toxicology Unit, University of Cambridge","country":"United Kingdom"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"PXD046038","task":"1688cb0e871c4f5f9de6a76ab631155a","id":"1091"}, {"dataset":"MSV000093073","datasetNum":"93073","title":"GNPS_Feline_fecal_Samples_OrbitrapMSdata","user":"mohantyipsita92","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696925821000","created":"Oct. 10, 2023, 1:17 AM","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","fileCount":"65","fileSizeKB":"8618226","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","keywords":"Polyamine 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":"762cc3c85e514b11a0e34f097bba238b","id":"1092"}, {"dataset":"MSV000093072","datasetNum":"93072","title":"GNPS - EthaNASH_study__healthy_plasma","user":"hfaassen","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696899558000","created":"Oct. 9, 2023, 5:59 PM","description":"This dataset consists of plasma from patients with NASH disease and healthy age- and BMI- matched healthy volunteers with data acquired on Orbitrap in positive ionization mode.","fileCount":"97","fileSizeKB":"13687563","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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":" Modifications MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset","keywords":"human, NAFLD, NASH, antibiotics;metabolomics","pi":[{"name":"Pieter Dorrestein","email":"pdorrestein@ucsd.edu","institution":"UCSD","country":"United States"},{"name":"Stijn Abraham Meijnikman","email":"a.s.meijnikman@amsterdamumc.nl","institution":"Amsterdam UMC","country":"The Netherlands"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a958842cc4b84ad2907a7453b23f870f","id":"1093"}, {"dataset":"MSV000093071","datasetNum":"93071","title":"RIME Analysis of HNF4A binding partners in the intestinal epithelium","user":"kvemuri","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696882913000","created":"Oct. 9, 2023, 1:21 PM","description":"The mechanisms driving gene expression changes during intestinal differentiation are unclear. Our studies have shown differential recruitment and occupancy of Pol II to be a major driver of these gene expression changes. Additionally, we have identified the transcription factor HNF4 as a key player in shaping this phenomenon. To gain insights into the protein-based mechanisms underlying HNF4-mediated Pol II recruitment, we performed RIME (Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins) using anti-HNF4A antibodies in primary mouse epithelium. ","fileCount":"15","fileSizeKB":"272719","spectra":"0","psms":"56401","peptides":"17322","variants":"21177","proteins":"6439","search_psms":"0","search_peptides":"0","search_variants":"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":"Unknown","modification":"MS:1002864","keywords":"RIME, HNF4A, Intestine","pi":[{"name":"Michael P Verzi","email":"mv347@biology.rutgers.edu","institution":"Rutgers, The State University of New Jersey","country":"USA"}],"complete":"true","quant_analysis":"null","status":"Complete","private":"false","hash":"","px":"","task":"c842f37e24f94ff985c8438850a9593e","id":"1094"}, {"dataset":"MSV000093070","datasetNum":"93070","title":"Simultaneous monitoring of active drug concentrations and proteomics within single human cells of typical size","user":"ben_orsburn","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696877263000","created":"Oct. 9, 2023, 11:47 AM","description":"PANC 02.03 cells were treated with MRTX1133 for 48 hours and the cells were lysed using a simplistic method. A TIMSTOF SCP system was optimized to allow both the drug concentration and the proteomics data to be measured simultaneously. 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Both High resolution data and low resolution data. Raw files and mzXML files have been submitted for each sample and sample information can be found in the published work.","fileCount":"58","fileSizeKB":"3473398","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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 thiebautii (NCBITaxon:1208)","instrument":"LTQ Orbitrap XL;LTQ XL","modification":"MS:1002864","keywords":"Cyanobacteria;PKS-NRPS","pi":[{"name":"Matt Bertin","email":"mbertin@uri.edu","institution":"University of Rhode Island","country":"United States"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"a4dbcd79ba3b48c188e30ba4aa86b7d5","id":"1096"}, {"dataset":"MSV000093068","datasetNum":"93068","title":"Identification of PIP5K1a-associated proteins in human Th17 cells by IP-MS ","user":"mandymcgeachy","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696873091000","created":"Oct. 9, 2023, 10:38 AM","description":"human Th17 cells generated in vitro from naive T cells + anti-CD3+IL-23+IL1b for 5 days, then immunopreciptation performed with anti-PIP5K1a or IgG controls and submitted to MSBioworks for LC-MS analysis. 3 individual experiments with 3 unique donors. \t\t\t\t\t\t\t\t","fileCount":"42","fileSizeKB":"9084474","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002732","modification":"MS:1002864","keywords":"Human;Th17;PIP5K1a","pi":[{"name":"Mandy McGeachy","email":"mandymcgeachy@cornell.edu","institution":"Cornell University","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"fa60b54d9f6f42be8d12a4be1feb49af","id":"1097"}, {"dataset":"MSV000093065","datasetNum":"93065","title":"GNPS - Integrated analysis of transcriptomics and proteomics approach the importance of ABA-dependent pathways in Mesembryanthemum Crystallinum leaf during the salt induced C 3 to CAM transition","user":"takter3","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696702299000","created":"Oct. 7, 2023, 11:11 AM","description":"Mesembryanthemum Crystallinum, a facultative CAM plant, shifts from C 3 to CAM photosynthesis under\r\nsalt stress, enhancing water use efficiency due to inverse stomatal patterns. Exploring the mechanisms\r\nof this transition could improve salt tolerance in C 3 crops. We used transcriptomics, proteomics, and\r\ntargeted metabolomics every 8 hours to track molecular shifts during this transition.","fileCount":"79","fileSizeKB":"590366","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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","instrument":"Vanquish LC and Altis mass spectrometer (Thermo Scientific, Bremen, Germany)","modification":"free text","keywords":"Mesembryanthemum crystallinum;C 3 to CAM transition;transcriptomics;proteomics;metabolomics;ABA-dependent stomatal movement","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":"7abee22a9135490fb93dc02556792cc7","id":"1098"}, {"dataset":"MSV000093064","datasetNum":"93064","title":"AqpZ Single Mutant and Double Mutant Cycle Native MS","user":"michaelmarty","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696629558000","created":"Oct. 6, 2023, 2:59 PM","description":"Native MS analysis of single mutant and double mutant cycle experiments. See: https:\/\/www.biorxiv.org\/content\/10.1101\/2023.09.19.558516v1","fileCount":"1516","fileSizeKB":"592922","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_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":"MS:1003245","modification":"MS:1002864","keywords":"Aquaporin;Membrane Protein;Native MS;Double Mutant Cycle;Mutagenesis;Protein-Lipid Interactions","pi":[{"name":"Michael Marty","email":"mtmarty@arizona.edu","institution":"University of Arizona","country":"United States"}],"complete":"false","quant_analysis":"Differential Abundance Results","status":"Partial","private":"false","hash":"","px":"","task":"dd5ccf3981e74e73aeb119f972071727","id":"1099"}, {"dataset":"MSV000093062","datasetNum":"93062","title":"Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696618945000","created":"Oct. 6, 2023, 12:02 PM","description":"Identification of tryptic and non tryptic fragments in ATTRv-I84S and wild type control sample (Supplementary table 2).\n\nSample ID 1120233: wild type\nSample ID 1123799: I84S, Patient 2\nSample ID 1123800: I84S, Patient 3\nSample ID1123801: I84S, Patient 1\n","fileCount":"9","fileSizeKB":"3540618","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","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:1002523","modification":"MS:1002864","keywords":"Transthyretin;ATTRv-I84S;fragments","pi":[{"name":"Lorena Saelices","email":"lorena.saelices@utsouthwestern.edu","institution":"University of Texas Southwestern Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"3f0caffc5cb74a1f85e5b9e6ce8a8b5a","id":"1100"}, {"dataset":"MSV000093061","datasetNum":"93061","title":"Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy","user":"alemoff","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696618661000","created":"Oct. 6, 2023, 11:57 AM","description":"Identification of ATTR C-terminal fragment by LC\/MS QTOF in ATTRv-I84S \nsamples (Supplementary Fig.3 and supplementary table 1)\n\n1126546: Patient 2\n1126547: Patient 3\n1126548 :Patient 1\n","fileCount":"10","fileSizeKB":"256272","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"0","search_proteins":"0","search_spectra":"0","reanalysis_psms":"0","reanalysis_peptides":"0","reanalysis_variants":"0","reanalysis_proteins":"0","species":"Homo sapiens (NCBITaxon:9606)","instrument":"Sciex X500B QTOF","modification":"MS:1002864","keywords":"Transthyretin;ATTRv-I84S;fragments","pi":[{"name":"Lorena Saelices","email":"lorena.saelices@utsouthwestern.edu","institution":"University of Texas Southwestern Medical Center","country":"USA"}],"complete":"false","quant_analysis":"null","status":"Partial","private":"false","hash":"","px":"","task":"019f119d13b747d09e22bc352e41b7d6","id":"1101"}, {"dataset":"MSV000093060","datasetNum":"93060","title":"test upload need at least 30 characters ","user":"jianhaidulab","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696618524000","created":"Oct. 6, 2023, 11:55 AM","description":"test for upload need to now make minimum 50 characters in description,,,,,,,,,","fileCount":"3","fileSizeKB":"380","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"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":"QTRAP 5500","modification":"MS:1002864","keywords":"test","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":"4e66fb547d8046cd94df7dbe7da1bb60","id":"1102"}, {"dataset":"MSV000093059","datasetNum":"93059","title":"20231006 mice urine and tissue samples with 6PPD and 6PPDQ exposure","user":"zhaohaoq","site":"MassIVE","flowname":"MASSIVE-COMPLETE","createdMillis":"1696615497000","created":"Oct. 6, 2023, 11:04 AM","description":"Time series of urine samples collected from male and female mice after exposure to 6PPD and 6PPDQ. Analyzed with LC-DDA-MS\/MS. Rerun of tissue samples from pregnant mice exposed to 6PPD and 6PPDQ.","fileCount":"772","fileSizeKB":"61742244","spectra":"0","psms":"0","peptides":"0","variants":"0","proteins":"0","search_psms":"0","search_peptides":"0","search_variants":"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":"urine;tissue;6PPD;6PPDQ","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":"f4c7e8857a5f43b78877121182b93bbe","id":"1103"}, {"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","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":"MS:1002634","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":"1104"}, {"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","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":"MS:1003094","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":"1105"}, {"dataset":"MSV000093051","datasetNum":"93051","title":"A carboxy-terminal ubiquitylation site regulates androgen receptor activity","user":"mnouri","site":"MassIVE","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":"1106"}, {"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","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":"1107"}, {"dataset":"MSV000093046","datasetNum":"93046","title":"CSF shotgun proteomics in human sCAA patients","user":"marcvervuurt","site":"MassIVE","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":"MS:1003005","modification":"MS:1002864","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":"1108"}, {"dataset":"MSV000093045","datasetNum":"93045","title":"GNPS - Eva and Anil first test - polymer contaminations","user":"oloap1","site":"MassIVE","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":"MS:1002523","modification":"MS:1002864","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":"1109"}, {"dataset":"MSV000093041","datasetNum":"93041","title":"CPTAC CCRCC Discovery Study - DIA Proteome","user":"cptac","site":"MassIVE","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