Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Workflow management and reproducibility

MetaboApps

A modular collection of browser-based downstream analysis applications that extend GNPS2 results with targeted interpretation, statistics, metadata, and domain-specific readouts.

Multiple analytical platformsUntargeted metabolomicsMetabolite profilingWeb applicationFree web service
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Overview

MetaboApps is a GNPS2 collection of lightweight downstream applications built to make specialized post-processing analyses accessible without bespoke scripting. The current collection includes applications for post-network MassQL, multi-step MassQL, drug and food readouts, CMMC analysis, FBMN statistics, chemical proportionality, CorrOmics, conjugated-metabolome exploration, and reverse-metabolomics-style analyses. Individual apps remain separate scientific modules, while this Navigator entry represents the maintained collection as a discovery and launch layer.

What can this tool do?

Interactive dashboardProvenance tracking

Common uses

  • Launch modular downstream analyses from GNPS2/molecular-networking outputs without writing custom scripts.
  • Explore statistics, chemical pattern queries, drug/food annotations, microbial knowledge, and other specialized post-processing applications.
  • Provide a discoverable collection for rapidly evolving community analysis modules while keeping core GNPS2 workflows separate.
  • Apply an appropriate downstream app to a GNPS2 result and retain the underlying feature and sample identifiers.

Scientific fit

Primary function

Workflow management and reproducibility

Other functions

Visualization and reporting, Spectral processing and comparison, Statistical analysis, Reference data and database search

Analysis types

Untargeted metabolomics, Metabolite profiling

MS level

MS1, MS/MS

Acquisition

General or unspecified acquisition

Ion mobility

Not specified

Data compatibility

Inputs

Feature or peak table, Mass spectra, Sample metadata

Outputs

Statistical results, Human-readable report

Input formats

CSV or TSV, GNPS2 task identifier (app dependent)

Output formats

Interactive results (app dependent)

Scope and considerations

Designed for

  • Post-processing and interpretation of GNPS2 and related metabolomics analysis outputs using modular web applications.

Not designed for

  • One universal workflow with identical input formats, outputs or validation across every app.

Important requirements

  • Inputs vary by app and can include GNPS2 task identifiers, feature/network tables, spectra, or metadata.

Considerations

  • MetaboApps is a collection rather than one analytical algorithm; users should cite and document the specific app(s) used.
  • Apps can evolve or be added more rapidly than peer-reviewed methodological publications.
  • Choose the app first, then check its input contract and cited method; record its name, parameters and upstream task identifier.

Access and documentation

Primary access

Hosted access and any account or usage requirements should be checked at the linked service. Access to a web service does not establish the license of its code or reference data.

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. This is an application collection. Cite the selected application and its underlying method; no single collection-wide methods paper was identified in this pass.

No dedicated scholarly publication is listed. Follow the official documentation and resource-specific citation guidance.

Related tools

CMMC-KBIntegrates with · A community-curated knowledgebase for microbial metabolites that links reference MS/MS evidence, microbial producers, annotations, and GNPS2 analysis resources.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.GNPSPart of · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.Chemical Proportionality (ChemProp)Contains or hosts · Prioritize putative transformations between molecular-network features using abundance changes across ordered samples.CMMC DashboardContains or hosts · Visualize CMMC enrichment results alongside feature abundances, metadata and molecular-network information.Conjugated Metabolome ExplorerContains or hosts · Search public LC-MS/MS evidence for potential conjugated forms of a molecule supplied as a SMILES structure.CorrOmicsContains or hosts · Explore associations between paired metabolomics and other omics feature tables and export correlation networks.FBMN StatsContains or hosts · Clean and statistically explore feature-based molecular networking abundance tables with guided notebooks and a web app.
More related tools (5)
GNPS2 Drug ReadoutContains or hosts · Annotate GNPS2 feature-based networking results with drug and drug-metabolite context for exposure-oriented interpretation.GNPS2 Food ReadoutContains or hosts · Annotate molecular features with dietary and food-ontology context to explore potential food-derived exposures.GNPS2 Reverse MetabolomicsContains or hosts · Search public MS/MS data using spectrum identifiers and explore matched samples by their biological metadata.Multi-step MassQLContains or hosts · Apply a predefined sequence of MassQL queries to GNPS2 networking spectra to investigate bile acids and their isomers.PostMN MassQLContains or hosts · 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. 2026-09-07 · Entry update

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision
  2. 2026-08-24 · First committed entry

    Complete GNPS SIRIUS and MZmine tool ecosystems

    View change · Entry at this revision

Full GitHub history