Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Molecular networking and chemical similarity

GNPS

A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.

Multiple analytical platformsUntargeted metabolomicsMetabolite profilingLipidomicsWeb application
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Overview

GNPS/GNPS2 is a web-based ecosystem for analysis, annotation, visualization, curation, and reuse of tandem mass-spectrometry data. GNPS2 organizes its current infrastructure around computational workflows, interactive visualization, mass-spectrometry knowledgebase curation, and large-scale data integration. The ecosystem includes molecular networking, library searching, MASST/FASST-based public-data search, domain-specific MASST services, MassQL, Pan-ReDU, GNPS Dashboard, CMMC resources, MetaboApps, and interoperable workflows with external processing software.

Also known as: Global Natural Products Social Molecular Networking, GNPS2

What can this tool do?

Interactive dashboardSpectral-library matchingMetadata-based contextualizationNetwork visualizationProvenance trackingRepository-scale spectral search

Common uses

  • Search experimental MS/MS spectra against community and reference spectral libraries.
  • Build classical, feature-based, and ion-identity molecular networks for untargeted MS/MS datasets.
  • Search public metabolomics repositories using MASST, FASST-based services, and domain-specific MASST resources.
  • Visualize raw data and analysis results, harmonize metadata, curate knowledge resources, and launch downstream GNPS2/MetaboApps analyses.
  • Connect feature abundances to spectral similarity networks and inspect library annotations in experimental context.

Scientific fit

Primary function

Molecular networking and chemical similarity

Other functions

Metabolite annotation and identification, Spectral processing and comparison, Reference data and database search, Data management and sharing, Workflow management and reproducibility

Analysis types

Untargeted metabolomics, Metabolite profiling, Lipidomics

MS level

MS/MS, MSⁿ

Acquisition

Data-dependent acquisition (DDA), Data-independent acquisition (DIA), Targeted MS/MS, General or unspecified acquisition

Ion mobility

Ion mobility supported

Data compatibility

Inputs

Mass spectra, Feature or peak table, Sample metadata

Outputs

Mass spectra, Compound list or annotations, Human-readable report

Input formats

mzML, mzXML, MGF, MSP, CSV or TSV

Output formats

CSV or TSV, MGF, MSP, JSON

Scope and considerations

Designed for

  • MS/MS-centered annotation, molecular networking, public-data search, visualization, and community sharing of metabolomics and natural-products data.
  • Web-based workflows that integrate processed feature tables, spectra, sample metadata, and public mass-spectrometry datasets.

Not designed for

  • Establishing a confirmed compound identity solely from a network edge or spectral-library score.

Important requirements

  • Inputs depend on the selected workflow; molecular-networking workflows generally require centroided MS/MS data, while FBMN also requires a feature table and representative MS/MS spectra.
  • Appropriate metadata, feature-processing parameters, and workflow settings should be recorded for reproducible analysis.

Considerations

  • GNPS is an ecosystem rather than a single algorithm; publications should report the specific workflow, parameters, and task URL or identifier used.
  • GNPS2 is actively evolving, and workflow interfaces or recommended settings can change; consult the current documentation when reproducing older analyses.
  • Not every GNPS2 web utility is represented as a separate Navigator entry; dedicated entries are reserved for stable, reusable resources with distinct scientific functions.
  • Preserve the task identifier, input feature IDs, metadata and library information so annotations can be traced to the original data.

Education

Learn this tool

External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.

1st GNPS User MeetingDorrestein Lab · Video Workshop · Needs reviewCMFI Molecular Networking seminarFunctional Metabolomics Lab · Video Workshop · Needs reviewGC-MS deconvolution, library search and molecular networkingDorrestein Lab · Video Workshop · Needs reviewGNPS GC - Part 2Dorrestein Lab · Video Workshop · Needs reviewGNPS Library Workshop/HackathonDorrestein Lab · Video Workshop · Needs reviewGNPS Merge Polarity NetworksDorrestein Lab · Video Workshop · Needs reviewGNPS metabolomics principles + tools Portuguese Part 1Divisão de Produtos Naturais — SBQ (GNPS listing) · Video Workshop · Needs reviewGNPS metabolomics principles + tools Portuguese Part 2Divisão de Produtos Naturais — SBQ (GNPS listing) · Video Workshop · Needs reviewGNPS Nature Microbiome 2021 WorkshopMingxun Wang (GNPS workshop listing) · Video Workshop · Needs reviewGNPS Workshops/TrainingGNPS project · Training hubMANA 2021 GNPS Workshop - Networking, Dashboard, MASSTDorrestein Lab · Video Workshop · Needs reviewMetabolomics Spectrum Resolver workshopDorrestein Lab · Video Workshop · Needs reviewNTMSS2026 Day1 S3 - Daniel Petras & Ming Wang - Data Sharing and Analysis with GNPS2Functional Metabolomics Lab · Video Workshop · Needs reviewNTMSS2026 Day2 S4 - Vanessa Phelan - Molecular Networking in GNPS2Functional Metabolomics Lab · Video Workshop · Needs reviewGNPS Dashboard - OverviewDorrestein Lab · Video Workshop · Needs reviewGNPS Classical Molecular NetworkingDorrestein Lab · Video Workshop · Needs reviewSIO262 Molecular Networking IntroDorrestein Lab · Video Workshop · Needs reviewGNPS MASSTDorrestein Lab · Video Workshop · Needs reviewGNPS MolNetEnhancerDorrestein Lab · Video Workshop · Needs reviewMS-DIAL and GNPS in PortugueseData Deconvolution Lab (GNPS community listing) · Video · Needs reviewGNPS - MS2LDADorrestein Lab · Video Workshop · Needs reviewGNPS ReDUDorrestein Lab · Video Workshop · Needs review

Browse all education resources →

Access and documentation

Primary accessDocumentationSource repository

GNPS2 is openly available to the academic community. The current GNPS2 documentation asks industry users to contact the maintainers or UC Riverside Technology Transfer regarding organizational access.

From tool to strategy

Strategies using GNPS

Bioactivity-Based Molecular NetworkingNatural-product discovery · Journal of Natural ProductsColony-based MALDI-MS/MS dereplication with IDBac and GNPS2Natural-product discovery · Journal of Natural ProductsIon Identity Molecular Networking (IIMN)Metabolite annotation · Nature CommunicationsMass spectrometry imaging–guided molecular networkingSpatial metabolomics · Analytica Chimica ActaMetabologenomicsNatural-product discovery · ACS Central ScienceMolecular networking as a dereplication strategyDereplication · Journal of Natural ProductsMS2DECIDENatural-product discovery · Chemistry–MethodsNative MS metabolomics for metal-binding compoundsMetal-binding compound discovery · Nature ChemistryReverse metabolomicsReverse metabolomics · NatureStable-isotope labeling–assisted molecular networkingStable-isotope tracing · Analytical Chemistry

Evidence and review

Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Wang M, Carver JJ, Phelan VV, et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34, 828-837 (2016). doi:10.1038/nbt.3597
  2. Aron AT, Gentry EC, McPhail KL, et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 15, 1954-1991 (2020). doi:10.1038/s41596-020-0317-5

    Describes a reproducible workflow or method implemented within GNPS.

  3. Nothias LF, Petras D, Schmid R, et al. Feature-based molecular networking in the GNPS analysis environment. Nat Methods 17, 905-908 (2020). doi:10.1038/s41592-020-0933-6

    Describes a reproducible workflow or method implemented within GNPS.

  4. Schmid R, Petras D, Nothias LF, et al. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat Commun 12, 3832 (2021). doi:10.1038/s41467-021-23953-9

    Describes a reproducible workflow or method implemented within GNPS.

Related tools

CMMC-KBContains or hosts · CMMC-KB is a community-curated microbial metabolite knowledge resource in the GNPS2 ecosystem.FASSTContains or hosts · FASST provides the accelerated spectral-search infrastructure used by current GNPS2 repository-search services.foodMASSTContains or hosts · foodMASST contextualizes spectra against food and beverage reference data.GNPS DashboardContains or hosts · GNPS Dashboard provides interactive visualization and exploration of raw/public MS data.MASSTContains or hosts · MASST is a repository-scale spectral search service within the GNPS ecosystem.MetaboAppsContains or hosts · MetaboApps is a modular collection of downstream GNPS2 analysis applications.microbeMASSTContains or hosts · microbeMASST contextualizes spectra against curated microbial monoculture data.microbiomeMASSTContains or hosts · microbiomeMASST maps spectral matches across harmonized microbiome study metadata.
More related tools (38)
ModiFinderContains or hosts · ModiFinder localizes structural modification sites from paired MS/MS spectra.MSMS-ChooserContains or hosts · MSMS-Chooser is a GNPS workflow for selecting reference MS/MS spectra.plantMASSTContains or hosts · plantMASST contextualizes spectra against taxonomically defined plant data.StructureMASSTContains or hosts · StructureMASST is a structure-centric pan-repository search service in the GNPS2 ecosystem.MassQLIntegrates with · An open-source, instrument-independent query language and software ecosystem for searching mass-spectrometry data using reusable MS1, MS/MS, chromatographic, and ion-mobility patterns.MS-DIALIntegrates with · A graphical and command-line workbench for untargeted metabolomics and lipidomics data processing across multiple chromatography and mass spectrometry platforms.MZmineIntegrates with · A modular mass-spectrometry environment for raw-data import, feature detection/alignment, multimodal LC/IMS/GC/MSI processing, molecular networking, annotation, lipid analysis, visualization, normalization, statistics, and downstream exports.MetGemAlternative to · Local desktop generation and exploration of MS/MS similarity networks and two-dimensional spectral projections.MolNetEnhancerComplementary to · Combine molecular networking, substructure motifs and chemical classifications into annotated networks.MS2LDAComplementary to · Find recurring patterns of fragments and neutral losses across tandem mass spectra.RAMClustRComplementary to · Cluster related mass-spectrometry features and export compound-level spectra and abundances.Everything BagelContains or hosts · Detect, align and gap-fill LC-MS features, with a GNPS2 workflow connecting raw LC-MS/MS data to feature-based molecular networking.GNPS2 Classical Molecular NetworkingContains or hosts · GNPS2 workflow for organizing MS/MS spectra into molecular families using pairwise spectral similarity and spectral-library searching.GNPS2 Cytoscape BridgeContains or hosts · Convert a GNPS2 GraphML network into a styled desktop Cytoscape session in the browser.GNPS2 Feature-Based Molecular Networking workflowContains or hosts · Dedicated GNPS2 workflow that combines an aligned LC-MS feature table with MS/MS spectra to build quantitative molecular networks.GNPS2 MassQL AnalysisContains or hosts · Hosted interface for exploring MS/MS spectral libraries with MassQL and using LLM assistance to draft or explain queries.GNPS2 MS/MS Spectrum SummaryContains or hosts · Explore recurring fragment peaks and neutral losses across selected tandem mass spectra.GNPS2 USI PlaygroundContains or hosts · Prepare spectrum references from GNPS2 jobs, public dataset identifiers and MassIVE file paths.MassQL PlaygroundContains or hosts · Browser-based MassQL query editor and runner for exploring fragmentation patterns in local mass-spectrometry files.MS2QueryContains or hosts · MS/MS analogue-search tool that combines learned spectral similarity and precursor-mass information to retrieve structurally related reference compounds.MSHub-GCContains or hosts · GC-MS processing workflow that aligns chromatographic data and deconvolves overlapping signals into spectra and quantitative tables for downstream GNPS analysis.NPClassifierContains or hosts · Deep neural-network tool that classifies natural-product structures into biosynthetic pathways, superclasses and structural classes.TinyMassContains or hosts · Hosted utility for sharing mass spectra through reusable spectrum identifiers in the GNPS2 ecosystem.CMMC DashboardIntegrates with · Visualize CMMC enrichment results alongside feature abundances, metadata and molecular-network information.Conjugated Metabolome ExplorerIntegrates with · Search public LC-MS/MS evidence for potential conjugated forms of a molecule supplied as a SMILES structure.CytoscapeIntegrates with · Desktop network visualization and analysis for exploring MS molecular networks alongside feature annotations and sample metadata.GNPS2 Drug ReadoutIntegrates with · Annotate GNPS2 feature-based networking results with drug and drug-metabolite context for exposure-oriented interpretation.GNPS2 Food ReadoutIntegrates with · Annotate molecular features with dietary and food-ontology context to explore potential food-derived exposures.GNPS2 Reverse MetabolomicsIntegrates with · Search public MS/MS data using spectrum identifiers and explore matched samples by their biological metadata.IDBacIntegrates with · Web-based MALDI-TOF mass spectrometry platform and community knowledgebase for bacterial identification, culture-collection analysis, and comparison of specialized-metabolite profiles.MassIVEIntegrates with · A public repository for depositing, preserving, browsing, downloading, and reusing mass-spectrometry datasets, including datasets connected to GNPS analyses.MS2DECIDEIntegrates with · Combine GNPS, ISDB-LOTUS and SIRIUS annotations into scores for natural-product feature prioritization.Multi-step MassQLIntegrates with · Apply a predefined sequence of MassQL queries to GNPS2 networking spectra to investigate bile acids and their isomers.NP3 MS WorkflowIntegrates with · Process LC-MS/MS data for natural-product profiling and molecular-network exploration.NPLinkerIntegrates with · Ranks candidate links between microbial biosynthetic gene clusters and MS metabolomics spectra or molecular families using paired strain data.OpenMSIntegrates with · An open-source C++ library, command-line toolkit, and Python interface for reproducible mass spectrometry data processing in metabolomics and proteomics.Pan-ReDUIntegrates with · A pan-repository metadata harmonization and search infrastructure for finding, contextualizing, downloading, and reanalyzing public metabolomics data across major repositories.PostMN MassQLIntegrates with · Run MassQL chemical-pattern queries directly on consensus spectra produced by GNPS molecular networking.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · Entry update

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision
  3. 2026-08-24 · Entry update

    Complete GNPS SIRIUS and MZmine tool ecosystems

    View change · Entry at this revision
  4. 2026-08-24 · Entry update

    Add GNPS, SIRIUS, and MZmine content batch

    View change · Entry at this revision
  5. 2026-08-24 · Entry update

    Apply v5.2 pre-population hardening

    View change · Entry at this revision
  6. 2026-08-21 · Entry update

    Add files via upload

    View change · Entry at this revision
  7. 2026-08-20 · First committed entry

    Add files via upload

    View change · Entry at this revision

Full GitHub history