Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Spectral processing and comparison

MS2LDA

Find recurring patterns of fragments and neutral losses across tandem mass spectra.

LC-MSPython packageWeb applicationSource available with restrictions
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Overview

MS2LDA represents recurring fragmentation patterns as Mass2Motifs, which can support substructure interpretation across a dataset. The project now provides MS2LDA 2.0 and an updated visualization interface.

What can this tool do?

Substructure prediction

Common uses

  • Discover shared fragmentation motifs.
  • Explore motif occurrences across molecular families.

Scientific fit

Primary function

Spectral processing and comparison

Data compatibility

Inputs

Mass spectra

Outputs

Human-readable report, Statistical results

Input formats

Other, MS/MS peak lists

Output formats

Other, Mass2Motifs, associations and visualizations

Scope and considerations

Designed for

  • Discover shared fragmentation motifs.

Not designed for

  • Treating every motif as a uniquely established substructure.

Important requirements

  • Processed MS/MS spectra and a workflow compatible with the current MS2LDA implementation.

Considerations

  • Motif interpretation depends on spectral coverage and annotation evidence; the official site flags retirement of its legacy interface.

Education

Learn this tool

External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.

GNPS - MS2LDADorrestein Lab · Video Workshop · Needs reviewNTMSS2022 Day3 S3 - MS2LDA and MolNetEnhancerFunctional Metabolomics Lab · Video Workshop · Needs reviewNTMSS2023 Day4 S5 - MS2LDAFunctional Metabolomics Lab · Video Workshop · Needs review

Browse all education resources →

Access and documentation

Primary access

Code and visualization services are public; consult the implementation license and hosted-service limits.

From tool to strategy

Strategies using MS2LDA

Shared-substructure discovery with Mass2MotifsMetabolite annotation · Proceedings of the National Academy of Sciences

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. van der Hooft JJ, Wandy J, Barrett MP, et al. Topic modeling for untargeted substructure exploration in metabolomics. Proc Natl Acad Sci U S A 113, 13738-13743 (2016). doi:10.1073/pnas.1608041113

Related tools

GNPSComplementary to · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.MolNetEnhancerComplementary to · Combine molecular networking, substructure motifs and chemical classifications into annotated networks.

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