Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

microbiomeMASST

A GNPS-associated metadata-network search resource for mapping query metabolites and MS/MS spectra across microbiome metabolomics studies, sample contexts, hosts, and microbial metadata.

LC-MSUntargeted metabolomicsMetabolite profilingMulti-omicsWeb application
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Overview

microbiomeMASST extends domain-specific repository searching from curated monocultures to a harmonized network of microbiome metabolomics datasets and metadata. It is designed to reveal where molecules occur across host-associated and microbial study contexts and to make large public microbiome metabolomics collections searchable through spectrum-to-metadata relationships. The scientific description is currently available as a 2026 preprint.

What can this tool do?

Repository-scale spectral searchMetadata-based contextualizationNetwork visualization

Common uses

  • Map query spectra across harmonized microbiome metabolomics datasets and metadata contexts.
  • Explore host, sample, microbial, and experimental contexts associated with matching spectra.
  • Generate hypotheses about metabolite distributions across microbiome studies using public data.
  • Follow spectrum-to-metadata associations to source studies for focused reanalysis.

Scientific fit

Primary function

Reference data and database search

Other functions

Data management and sharing, Spectral processing and comparison

Analysis types

Untargeted metabolomics, Metabolite profiling, Multi-omics

MS level

MS/MS

Acquisition

Data-dependent acquisition (DDA), General or unspecified acquisition

Ion mobility

Ion mobility not required

Data compatibility

Inputs

Mass spectra

Outputs

Mass spectra, Sample metadata, Human-readable report

Input formats

MGF, Universal Spectrum Identifier (USI) or peak list

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Repository-scale contextualization of metabolites across microbiome metabolomics metadata networks.

Not designed for

  • Inferring causation or identifying a microbial producer from cross-study metadata associations alone.

Important requirements

  • Query MS/MS information and public-data metadata indexed by the current resource.

Considerations

  • The primary scientific description is a preprint and the underlying metadata network is actively evolving.
  • Associations from public-data co-occurrence are hypothesis-generating and can reflect sampling, deposition, or study-design biases.
  • Check study membership and available controls because repeated samples and heterogeneous studies are not independent biological replications.

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. Preprint · not peer reviewed Charron-Lamoureux V, Xing S, Patan A, et al. A searchable metadata network graph for microbiome metabolomics. bioRxiv (2026). Preprint; not peer reviewed. doi:10.64898/2026.02.04.703849

Related tools

microbeMASSTComplementary to · A taxonomically informed GNPS search service that connects query MS/MS spectra to matching spectra from curated bacterial, fungal, and archaeal monoculture datasets.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.Pan-ReDUUses · A pan-repository metadata harmonization and search infrastructure for finding, contextualizing, downloading, and reanalyzing public metabolomics data across major 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

    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