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-source and 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 LC-MS/MS data utilizing computational tools (See Molecular Networking, Spectral Library Search, etc).
- Annotate/curate identified MS/MS spectra in open-access GNPS reference spectral libraries.
- Annotate peptidic natural products in LC-MS/MS data with DEREPLICATOR/VarQuest/DEREPLICATOR+ and RiPPQuest.
- Propagate in silico annotations in your LC-MS/MS data with Network Annotation Propagation (NAP).
- NEW! Perform advanced molecular networking and spectral library search with Feature-Based Molecular Networking. See https://doi.org/10.1101/812404.
- NEW! Analyze GC-MS data with GNPS (See GC-MS deconvolution, and GC-MS library search/molecular networks).
- NEW! Annotate your LC-MS/MS data with MolNetEnhancer. See https://doi.org/10.1101/654459.
- NEW! Search spectral Mass2Motifs in your LC-MS/MS data with MS2LDA.
- NEW! Give LC-MS/MS spectra biological/environmental context by searching against all public LC-MS/MS datasets (MASST Search). See https://doi.org/10.1101/591016.
- NEW! Find and co- or re-analyze public LC-MS/MS data via systematic sample information at ReDU. See https://doi.org/10.1101/750471.
Share and Explore¶
- Publish entire study datasets with the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository (Dataset Submission).
- Browse and Reanalyze over 1500 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).
Contribute to GNPS¶
The GNPS community is always welcoming suggestions and contributions. Be part of the community and contribute ! See that page for more informations.
Mingxun Wang, Jeremy J. Carver, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen et al. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature biotechnology 34, no. 8 (2016): 828. PMID: 27504778
GNPS and MassIVE uptime¶
This is a brief overview of whether our web services are up: here.
And a more detailed functional test status page.
GNPS Documentation Site Authors¶
We would like to thank the following contributors to the documentation.
However, we want to acknowledge that we have moved documentation in 2018 to GitHub from our previous wiki and those contributions are not reflected in these numbers and were broadly subsumed into Ming Wang's contributions. These first additions to the documentation were invaluable and a few of those pioneers were Vanessa Phelan, Laura Sanchez, Laura Pace, Alexey Gurevich, and Don D. Nguyen.