Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

StructureMASST

A GNPS2 web application for structure- and substructure-centric searching across public metabolomics repositories using chemical names, SMILES, SMARTS, and matched reference spectra.

Multiple analytical platformsUntargeted metabolomicsMetabolite profilingExposomicsWeb application
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Overview

StructureMASST changes the starting point of repository-scale metabolomics search from one expert-selected MS/MS spectrum to a chemical structure or substructure. It retrieves relevant reference spectra, performs multi-spectrum MASST searches, and uses precomputed FASST Records with harmonized metadata to map molecules and structural families across public repositories, biological contexts, taxonomy, and environmental conditions. Searches can include exact structures, substructures, and modification-tolerant relationships.

What can this tool do?

Repository-scale spectral searchMetadata-based contextualizationStructure-database searchingSubstructure prediction

Common uses

  • Search public metabolomics data starting from a chemical name, SMILES, or SMARTS representation.
  • Map a structure or substructure across multiple reference spectra and public datasets rather than relying on one query spectrum.
  • Explore exact, substructure, and modification-tolerant distributions across harmonized biological and environmental metadata.
  • Map a chemical family to public datasets and examine the metadata of individual matches.

Scientific fit

Primary function

Reference data and database search

Other functions

Metabolite annotation and identification, Data management and sharing

Analysis types

Untargeted metabolomics, Metabolite profiling, Exposomics

MS level

MS/MS

Acquisition

Data-dependent acquisition (DDA), Targeted MS/MS, General or unspecified acquisition

Ion mobility

Ion mobility not required

Data compatibility

Inputs

Molecular structures

Outputs

Mass spectra, Sample metadata, Human-readable report

Input formats

SMILES or InChI

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Structure-centric and substructure-centric exploration of public MS/MS repositories.

Not designed for

  • Searching all theoretically possible structures without corresponding reference spectral evidence.

Important requirements

  • A chemical name or structure representation that can be mapped to reference spectra for repository searching.

Considerations

  • Mass-spectral matching generally does not resolve stereochemistry, and coverage is limited by available reference spectra and indexed public data.
  • StructureMASST uses computational spectral matches as evidence of occurrence; important findings should be validated with appropriate orthogonal evidence.
  • Inspect the reference spectra behind a structure query and distinguish exact-structure, substructure and analog matches.

Access and documentation

Primary accessSource repository

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.

Core publications

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

  1. El Abiead Y, Seo JI, Charron-Lamoureux V, et al. Structure-centric searching enables global mapping of the public metabolome. Nat Biotechnol (2026). doi:10.1038/s41587-026-03082-8

Related tools

MASSTComplementary to · 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.Pan-ReDUIntegrates with · A pan-repository metadata harmonization and search infrastructure for finding, contextualizing, downloading, and reanalyzing public metabolomics data across major repositories.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.FASSTUses · Accelerated indexed infrastructure for searching very large collections of tandem mass spectra, enabling current GNPS2 repository-scale search services to return results at billion-spectrum scale.

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 · Entry update

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision
  3. 2026-08-24 · First committed entry

    Complete GNPS SIRIUS and MZmine tool ecosystems

    View change · Entry at this revision

Full GitHub history