Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Data management and sharing

Pan-ReDU Pan-ReDU

A pan-repository metadata harmonization and search infrastructure for finding, contextualizing, downloading, and reanalyzing public metabolomics data across major repositories.

Multiple analytical platformsUntargeted metabolomicsMetabolite profilingMulti-omicsWeb application
Access toolSuggest an update

Overview

Pan-ReDU is the current expansion of ReDU for harmonizing controlled sample metadata and indexing public mass-spectrometry files across repositories including MetaboLights, Metabolomics Workbench/NMDR, and GNPS/MassIVE. It links harmonized metadata with persistent run identifiers, raw-file access, and indexed MS/MS searching so researchers can discover, download, co-analyze, and contextualize public metabolomics data across repository boundaries.

Also known as: ReDU, Reanalysis of Data User Interface

What can this tool do?

Metadata-based contextualizationRepository-scale spectral search

Common uses

  • Find public metabolomics files by harmonized organism, biospecimen, disease, phenotype, and other controlled metadata.
  • Discover and download files across MetaboLights, Metabolomics Workbench/NMDR, and GNPS/MassIVE using a common metadata layer.
  • Contextualize MASST/FASST spectral matches across repositories and prepare public datasets for reanalysis or co-analysis.
  • Assemble a public-data cohort using sample metadata, then retrieve files for a documented reanalysis.

Scientific fit

Primary function

Data management and sharing

Other functions

Reference data and database search

Analysis types

Untargeted metabolomics, Metabolite profiling, Multi-omics

MS level

MS/MS

Acquisition

General or unspecified acquisition

Ion mobility

Not specified

Data compatibility

Inputs

Sample metadata

Outputs

Sample metadata, Human-readable report

Input formats

CSV or TSV

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Pan-repository discovery, contextualization, and reuse of public mass-spectrometry data using harmonized metadata and file identifiers.

Not designed for

  • Replacing primary repository records or correcting every missing or inconsistent sample annotation.

Important requirements

  • Repository records need sufficiently structured sample information to support the desired query.

Considerations

  • Metadata completeness and harmonization quality remain dependent on the information available in the source repositories and historical submissions.
  • Repository coverage and indexed file counts evolve as Pan-ReDU is updated.
  • Save the selected file identifiers and harmonized metadata with the analysis; harmonization does not make experimental strategies equivalent.

Education

Learn this tool

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

GNPS ReDUDorrestein Lab · Video Workshop · Needs review

Browse all education resources →

Access and documentation

Primary accessDocumentation

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.

From tool to strategy

Strategies using Pan-ReDU

Reverse metabolomicsReverse metabolomics · Nature

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. Jarmusch AK, Wang M, Aceves CM, et al. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods 17, 901-904 (2020). doi:10.1038/s41592-020-0916-7
  2. El Abiead Y, Strobel M, Payne T, et al. Enabling pan-repository reanalysis for big data science of public metabolomics data. Nat Commun 16, 4838 (2025). doi:10.1038/s41467-025-60067-y

Related tools

GNPSIntegrates with · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.MassIVEIntegrates with · A public repository for depositing, preserving, browsing, downloading, and reusing mass-spectrometry datasets, including datasets connected to GNPS analyses.MASSTIntegrates with · A GNPS repository-scale spectral search service for finding where a query MS/MS spectrum or related spectra occur across public metabolomics data and spectral libraries.GNPS2 Reverse MetabolomicsIntegrates with · Search public MS/MS data using spectrum identifiers and explore matched samples by their biological metadata.StructureMASSTIntegrates with · A GNPS2 web application for structure- and substructure-centric searching across public metabolomics repositories using chemical names, SMILES, SMARTS, and matched reference spectra.

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

    Audit core publications across existing tools

    View change · Entry at this revision
  3. 2026-09-07 · Entry update

    Expand and document 31 metabolomics tools and resources

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

    Complete GNPS SIRIUS and MZmine tool ecosystems

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

    Add GNPS, SIRIUS, and MZmine content batch

    View change · Entry at this revision
  6. 2026-08-21 · First committed entry

    Add files via upload

    View change · Entry at this revision

Full GitHub history