Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Data management and sharing

Metabolomics Workbench

Deposit, discover and retrieve metabolomics studies through the National Metabolomics Data Repository.

Multiple analytical platformsWeb applicationAPIFree web service
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Overview

Metabolomics Workbench hosts study data and metadata alongside analysis and reference resources. Its repository supports different organisms and measurement platforms; REST access and the mwTab representation support programmatic reuse of study information.

Also known as: NMDR, National Metabolomics Data Repository

What can this tool do?

Repository-scale spectral searchMetadata-based contextualizationProvenance tracking

Common uses

  • Deposit metabolomics data supporting a publication.
  • Retrieve study metadata and measurements for reproducible reanalysis.

Scientific fit

Primary function

Data management and sharing

Data compatibility

Inputs

Raw instrument data, Feature or peak table, Sample metadata

Outputs

Raw instrument data, Feature or peak table, Sample metadata

Input formats

Repository submission templates and experimental files

Output formats

JSON, mwTab study representation, Submitted experimental files

Scope and considerations

Designed for

  • Study-level sharing and discovery of MS-based metabolomics data.

Not designed for

  • Guaranteeing that all deposited studies are directly comparable.

Important requirements

  • Provide experimental factors, sample identifiers, acquisition and processing details when submitting. For reuse, check the files available for each analysis.

Considerations

  • A project may contain several studies or analyses. Retain study and analysis identifiers and cite the project data DOI where provided.

Access and documentation

Primary accessDocumentation

Public study access is available through the website and REST service. Deposition requires registration and compliance with repository submission guidance.

Evidence and review

Editorial review on 7 September 2026 against official documentation and the sources listed here. Scope and practical guidance are editorial synthesis; software execution and service availability were not validated.

Core publications

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

  1. Sud M, Fahy E, Cotter D, et al. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, strategies, tutorials and training, and analysis tools. Nucleic Acids Res 44, D463-70 (2016). doi:10.1093/nar/gkv1042

Related tools

MassIVEAlternative to · A public repository for depositing, preserving, browsing, downloading, and reusing mass-spectrometry datasets, including datasets connected to GNPS analyses.MetaboLightsAlternative to · Deposit and find metabolomics studies with experimental files and structured sample and assay metadata.MetabolomeXchangeComplementary to · Discover publicly released metabolomics studies across participating repositories.METASPACEComplementary to · Annotate imaging mass-spectrometry datasets and explore community-contributed spatial metabolomes.RefMetComplementary to · Map metabolite names to a standardized reference nomenclature for cross-study comparisons.

Entry history

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

  1. 2026-09-09 · Entry update

    Use method terminology in Tool descriptions

    View change · Entry at this revision
  2. 2026-09-08 · Entry update

    Focus shared resource entries on MS workflows

    View change · Entry at this revision
  3. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  4. 2026-09-07 · First committed entry

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision

Full GitHub history