Welcome to GNPS Documentation

Global Natural Products Social Molecular Networking (GNPS, https://gnps.ucsd.edu/) is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.

As there are many aspects to GNPS, it can be a bit overwhelming. Here is a quick description of main functionalities:

Analyze and Annotate

• Perform molecular networking and spectral library search of MS/MS data utilizing computational tools (e.g. Molecular Networking, Spectral Library Search, etc).
• NEW! Perform advanced molecular networking and spectral library search with Feature-Based Molecular Networking.
• Annotate/curate identified MS/MS spectra in open-access GNPS reference spectra libraries.
• Annotate peptidic natural products in MS/MS data with DEREPLICATOR/VarQuest/DEREPLICATOR+ and RiPPQuest.
• Propagate in silico annotations in your MS/MS data with Network Annotation Propagation (NAP).
• NEW! Search spectral Mass2Motifs in your MS/MS data with MS2LDA.

Share and Explore

• Publish entire study datasets with the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository (Dataset Submission).
• NEW! Give MS/MS spectra biological/environmental context by searching against all public MS/MS datasets (MASST Search).
• Browse and Reanalyze over 700 public datasets at GNPS
• Automatic reanalysis of public datasets with automated reports of new identifications (Continuous Identification).
• Explore identifications of public datasets across entire repository (Molecule Explorer).

For more detailed information, read on in the documentation, checkout the GNPS publication, and view some tutorial videos.

GNPSDocumentation

Migration to the New Documentation

Pardon our dust as we are migrating to this new documentation. During the transition, throughout the documentation we will be linking to our legacy documentation that is still relevant. Thank you for your patience.

Contributing to the New Documentation

The GitHub repository for the documentation is available here https://github.com/CCMS-UCSD/GNPSDocumentation.

• For informations/feature request, please open an "Issue" on the CCMS-UCSD/GNPSDocumentation GitHub repository.
• To contribute to the GNPS documentation, fork the CCMS-UCSD/GNPSDocumentation repository, and make a "Pull Request".

Legacy Documentation

To checkout our legacy documentation in its entirely, you can find it here.