Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Data management and sharing

MetaboLights

Deposit and find metabolomics studies with experimental files and structured sample and assay metadata.

Multiple analytical platformsWeb applicationFree web service
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Overview

MetaboLights is the EMBL-EBI repository for metabolomics experiments across organisms and analytical techniques. Study records connect raw and derived files to sample and assay descriptions, supporting publication-associated sharing and later reuse.

What can this tool do?

Metadata-based contextualizationProvenance tracking

Common uses

  • Deposit the files and metadata supporting a metabolomics publication.
  • Find studies by organism or analytical technology for 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

ISA-Tab, Raw and derived assay files; accepted packaging depends on file type

Output formats

ISA-Tab, Submitted study files

Scope and considerations

Designed for

  • Structured sharing of complete metabolomics experiments, with this entry focused on MS-based studies.

Not designed for

  • Automatic harmonization of measurements across unrelated studies.

Important requirements

  • Prepare sample-to-file mappings, assay details and metabolite identification tables following the submission guide.

Considerations

  • Inspect study design and processing history before combining datasets. Record the MTBLS accession and cite the original study as well as the repository.

Access and documentation

Primary accessDocumentation

Public studies can be accessed freely. Submission uses an account and the repository submission and curation process.

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. Yurekten O, Payne T, Tejera N, et al. MetaboLights: open data repository for metabolomics. Nucleic Acids Res 52, D640-D646 (2024). doi:10.1093/nar/gkad1045

Related tools

MassIVEAlternative to · A public repository for depositing, preserving, browsing, downloading, and reusing mass-spectrometry datasets, including datasets connected to GNPS analyses.Metabolomics WorkbenchAlternative to · Deposit, discover and retrieve metabolomics studies through the National Metabolomics Data Repository.MetabolomeXchangeComplementary to · Discover publicly released metabolomics studies across participating repositories.

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

    Focus shared resource entries on MS workflows

    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 · First committed entry

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision

Full GitHub history