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GNPS is the Global Natural Products Social Molecular Networking platform: a web-based mass spectrometry ecosystem for analysing, sharing and curating tandem mass spectrometry (MS/MS) data. This page explains what it does, what its main tools are, how an analysis moves from upload to results, and how to cite and deposit data. (The abbreviation is also used by an unrelated school district; this page is about the mass spectrometry platform.)
What is GNPS?
According to its documentation, GNPS (Global Natural Products Social Molecular Networking) is a web-based mass spectrometry ecosystem and an open-source, open-access knowledge base for MS/MS data. Researchers use it to organise untargeted MS/MS data into molecular networks, search spectra against reference libraries, and publish whole datasets.
What is the full form of GNPS?
Global Natural Products Social Molecular Networking. The name reflects its origin in natural products research, but the same MS/MS workflows apply to any sample type that produces tandem mass spectra, including metabolome studies.
What is GNPS metabolomics?
“GNPS metabolomics” is a search phrase, not a separate product. It refers to using GNPS to analyse untargeted LC-MS/MS metabolomics data: spectra are grouped by similarity so that related molecules cluster together, even when none of them match a known compound. For the instrument side of that workflow, see our guide to LC-MS.
What is molecular networking?
The GNPS documentation defines molecular networks as visual displays of the chemical space present in MS/MS experiments. Each spectrum is a node, and spectrum-to-spectrum alignments are edges between nodes. Nodes can carry metadata, such as dereplication matches or user-supplied information like abundance or origin, which can be reflected in a node’s size or colour. The approach can detect sets of spectra from related molecules even when the spectra are not matched to any known compound.
Who runs it and what it covers
The documentation is maintained on GitHub Pages under the CCMS-UCSD organisation (ccms-ucsd.github.io/GNPSDocumentation). The platform is described as open for the academic community; the documentation directs industry users to contact the listed people, including the UC San Diego Technology Transfer Office. The documentation lists these main components:
- Classical molecular networking with spectral library search.
- Feature-Based Molecular Networking (FBMN).
- Spectral library search and curation.
- GNPS Dashboard, for visualising mass spectrometry data.
- MassIVE (Mass Spectrometry Interactive Virtual Environment), the repository for publishing whole datasets.
How a classical molecular networking analysis works
The Quick Start in the official documentation describes this sequence. Interface labels below are quoted from it.
- Convert files. Convert vendor files to an open format with MSConvert. Molecular networking supports mzXML, mzML and mgf.
- Create an account. The registration link sits in the upper right of the GNPS page, below the login box. The sign-in is on that same page.
- Upload. Use an FTP client such as WinSCP or FileZilla to send the files to massive-ftp.ucsd.edu with your GNPS credentials.
- Open the workflow. From the main GNPS page, click “Create Molecular Network” and give the job a descriptive title so you can retrieve it later.
- Select files. Click “Select Input Files”, then place files in “Spectrum Files G1” (use G2 to G6 for other conditions, such as case versus control). You can also import a public dataset by entering a MassIVE accession in the Import Data Share box.
- Choose a preset size. The Quick Start offers Small (up to 5 LC/MS files), Medium (5 to 400) and Large (400+).
- Submit and read results. Result views include “View All Library Hits”, “View Spectral Families (In Browser Network Visualization)” and “Visualize Network”.
Two parameters worth understanding before you submit are the precursor and fragment ion mass tolerances. The documentation gives a recommended value of ±0.02 Da for high-resolution instruments (q-TOF, q-Orbitrap) and ±2.0 Da for low-resolution instruments (ion traps, QqQ) for the precursor tolerance, and says the values should be consistent with the capabilities of the mass spectrometer and the instrument method used.
Strengths and limits
Strengths
- Spectra can be organised into families without a library match, which helps when most features in a sample are unidentified.
- The same ecosystem covers analysis, library search and dataset publication (MassIVE), so data can move from processing to a public deposit.
- Importing a public MassIVE dataset by accession lets you reanalyse published data without re-uploading it.
Limits
- Input must be MS/MS data in open formats, so vendor files need conversion first.
- The basic options support six file groups (G1 to G6).
- A network groups spectra by similarity; it is a map for exploration, not by itself an identification of each compound.
- Access terms differ by user type: the documentation describes academic access and refers industry users to a contact route.
Is GNPS free?
The documentation describes GNPS as open-access and its infrastructure as open for the academic community. It does not state a price. Industry users are told to contact the people listed in the documentation, including the UC San Diego Technology Transfer Office, so commercial use should be arranged with them directly.
Citing GNPS and depositing data
The documentation’s recommended citation is Wang et al., “Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking,” Nature Biotechnology 34(8), 2016 (PMID 27504778). The documentation also describes a metadata file option for describing the experimental setup, and the MassIVE repository for publishing whole study datasets. For choosing a venue for your own data see how to choose an open data repository, and for the principles behind sharing see FAIR data principles.
Alternatives and neighbouring repositories
GNPS is an analysis and sharing platform that includes its own repository (MassIVE). The resources below serve the deposit role and are covered in separate CASRAI guides.
| Resource | Role | Operator | Guide |
|---|---|---|---|
| MassIVE | Mass spectrometry dataset repository inside the GNPS ecosystem; a ProteomeXchange member | Center for Computational Mass Spectrometry (NIH-funded) | ProteomeXchange accessions |
| Metabolomics Workbench | Metabolomics data repository | San Diego Supercomputer Center, UC San Diego; sponsored by the NIH Common Fund | Metabolomics Workbench guide |
| MetaboLights | Metabolomics data repository | See the guide | MetaboLights guide |
Frequently asked questions
What is GNPS?
A web-based mass spectrometry ecosystem and open-access knowledge base for MS/MS data, centred on molecular networking, spectral library search and dataset sharing.
What is the full form of GNPS?
Global Natural Products Social Molecular Networking.
Is GNPS free?
The documentation calls it open-access and open for the academic community, with industry users directed to a contact route. It states no price.
What is GNPS metabolomics?
Using GNPS to network and annotate untargeted LC-MS/MS metabolomics spectra.
Where is the GNPS login?
On the main GNPS page; the registration link is in the upper right, below the login box.
Sources
- GNPS Documentation, introduction: ccms-ucsd.github.io/GNPSDocumentation (checked 2026-11-07).
- GNPS Documentation, Quick Start: quickstart (checked 2026-11-07).
- GNPS Documentation, Molecular Networking: networking (checked 2026-11-07).
- Wang M. et al., Nature Biotechnology 34(8), 2016, PMID 27504778 (PubMed, citation as given in the GNPS documentation).
- MassIVE: massive.ucsd.edu (checked 2026-11-07).
- Metabolomics Workbench: metabolomicsworkbench.org/about (checked 2026-11-07).
