GNPS Theoretical/Insilico Tools and Libraries

Dereplication of Peptidic Natural Product workflow. This analysis will compare your experimental MS/MS spectra against chemical structure databases, e.g. PubChem, etc. This workflow is currently in beta development stages so any feedback is welcome to improve analysis and usability. It is available here. View documentation.

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Dereplication of peptidic natural products through database search of mass spectra, Mohimani et al., Nat Chem Biol. 2017 Jan;13(1):30-37.

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Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol. 2018 Mar;3(3):319-327.

DEREPLICATOR+ is an algorithm for in silico identification of both peptidic and non-peptidic natural products including polyketides, lipids, terpenes, benzenoids, alkaloids, flavonoids, etc. This workflow is currently in beta development stages so any feedback is welcome to improve analysis and usability. It is available here.

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Identification of Microbial Metabolites Through Database Search of Mass Spectra, Mohimani et al., Nature Communication, 2018, in press

Identification of RiPP Natural Products workflow. This analysis will compare your experimental MS/MS spectra against full genome sequences to mine them for possible RiPP natural products. This workflow is currently in beta development stages so any feedback is welcome to improve analysis and usability. It is available here.

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Automated genome mining of ribosomal peptide natural products. Mohimani et al. ACS Chem Biol. 2014 Jul 18;9(7):1545-51.

Network Annotation Propagation (NAP) uses spectral networks to propagate information from spectral library matching, in order to improve in silico fragmentation candidate structure ranking. This workflow is currently in beta development stages so any feedback is welcome to improve analysis and usability. It is available here under 'NAP_CCMS' Workflow drop down menu. View Documentation.

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da Silva, Ricardo R., et al. "Propagating annotations of molecular networks using in silico fragmentation." PLoS computational biology 14.4 (2018): e1006089.