Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Reference data and database search

plantMASST

A domain-specific GNPS search and exploration resource for contextualizing query MS/MS spectra across taxonomically defined plant metabolomics datasets.

LC-MSUntargeted metabolomicsMetabolite profilingWeb applicationPython package
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Overview

plantMASST searches query tandem mass spectra against a public collection of taxonomically curated plant extracts and displays matches within plant taxonomy. Its current Explorer interface can also browse the indexed plant collection without a query spectrum, inspect files for individual taxa, and launch selected public files into GNPS2 molecular-networking workflows. The resource is community-driven and uses harmonized taxonomy and repository metadata.

What can this tool do?

Repository-scale spectral searchMetadata-based contextualizationSpectral-library matchingInteractive dashboard

Common uses

  • Search an MS/MS spectrum across taxonomically defined plant extracts.
  • Explore which plant taxa and public files are represented in the current reference collection.
  • Launch selected public plant files into GNPS2 molecular-networking analysis.
  • Browse the Explorer collection and select plant data for subsequent GNPS analysis.

Scientific fit

Primary function

Reference data and database search

Other functions

Spectral processing and comparison, Data management and sharing

Analysis types

Untargeted metabolomics, Metabolite profiling

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

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

  • Chemotaxonomic contextualization of known and unknown plant-associated MS/MS spectra.

Not designed for

  • Establishing taxon-specific biosynthesis or absence across unmeasured plant species.

Important requirements

  • A query spectrum/USI for search mode, or no query for the Explorer view.

Considerations

  • The associated methodological publication is currently a preprint; the live resource continues to evolve as community plant data are deposited.
  • Taxonomic and spectral coverage is not uniform across plant diversity.
  • Keep the query and selected taxonomy context; investigate the original plant extracts before interpreting a chemotaxonomic pattern.

Access and documentation

Primary accessDocumentationSource 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 Gomes PWP, Mannochio-Russo H, Schmid R, et al. plantMASST - Community-driven chemotaxonomic digitization of plants. bioRxiv (2024). Preprint; not peer reviewed. doi:10.1101/2024.05.13.593988

Related tools

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