Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

METASPACE

Annotate imaging mass-spectrometry datasets and explore community-contributed spatial metabolomes.

Imaging mass spectrometryWeb applicationPython packageAPIFree web service
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Overview

METASPACE combines a cloud annotation engine with a public knowledgebase and interactive ion-image exploration. Its Python client supports programmatic analysis of annotations.

What can this tool do?

Metadata-based contextualizationInteractive dashboard

Common uses

  • Find public spatial metabolomics datasets.
  • Inspect molecular annotations alongside tissue ion images.

Scientific fit

Primary function

Reference data and database search

Data compatibility

Inputs

Imaging data, Sample metadata

Outputs

Imaging data, Compound list or annotations

Input formats

Other, Imaging-MS files and acquisition metadata

Output formats

Other, Ion images and annotation records

Scope and considerations

Designed for

  • Find public spatial metabolomics datasets.

Not designed for

  • Treating a spatial annotation as complete isomer or stereochemical confirmation.

Important requirements

  • For new analyses, compatible imaging-MS data and acquisition metadata; browsing public results is a separate workflow.

Considerations

  • Review annotation confidence, adduct assumptions and database choice; spatial colocalization does not by itself imply a biological interaction.

Access and documentation

Primary accessDocumentation

Public platform with Apache-2.0 source code; dataset access and reuse depend on the individual deposit.

Evidence and review

Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.

Core publications

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

  1. Preprint · not peer reviewed Alexandrov T, Ovchinnikova K, Palmer A, et al. METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease. bioRxiv (2019). Preprint; not peer reviewed. doi:10.1101/539478

Related tools

Metabolomics WorkbenchComplementary to · Deposit, discover and retrieve metabolomics studies through the National Metabolomics Data Repository.CardinalComplementary to · Open-source R/Bioconductor toolbox for preprocessing, statistical analysis, segmentation, classification and visualization of mass spectrometry imaging data.MSiReaderComplementary to · Vendor-neutral desktop software for visualization, analysis and interpretation of high-resolution mass spectrometry imaging datasets.SCiLS LabComplementary to · Commercial software suite for processing, statistical analysis, segmentation, annotation and 2D/3D visualization of mass spectrometry imaging data.SpaMTPComplementary to · Open-source framework for joint analysis, annotation, alignment, integration and visualization of spatial metabolomics and spatial transcriptomics.

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 · First committed entry

    Add 50 documented metabolomics resources

    View change · Entry at this revision

Full GitHub history