Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Metabolite annotation and identification

MIST

Predict molecular fingerprints from tandem mass spectra and retrieve candidate structures.

LC-MSPython packageCommand lineSource available with restrictions
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Overview

Metabolite Inference with Spectrum Transformers encodes chemical formula information associated with fragments. Fingerprint and contrastive models support database-based structure ranking.

What can this tool do?

Structure-database searchingSubstructure prediction

Common uses

  • Generate fingerprint predictions for query spectra.
  • Benchmark candidate retrieval with supplied research workflows.

Scientific fit

Primary function

Metabolite annotation and identification

Data compatibility

Inputs

Mass spectra

Outputs

Compound list or annotations, Statistical results

Input formats

Other, Peak lists and metadata in the quickstart layout

Output formats

Other, Fingerprint predictions and retrieval results

Scope and considerations

Designed for

  • Generate fingerprint predictions for query spectra.

Not designed for

  • Finding an absent database structure through retrieval alone.

Important requirements

  • Python, compatible model weights, spectral preprocessing and candidate data in the documented layout.

Considerations

  • The repository notes changes from the published implementation and proprietary data in some benchmarks; pin the code and evaluation set.

Access and documentation

Primary access

Research code and pretrained models are public; check code and dataset licenses separately.

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. Goldman, Wohlwend, Stražar, et al. Annotating metabolite mass spectra with domain-inspired chemical formula transformers. Nature Machine Intelligence 5, 965-979 (2023). doi:10.1038/s42256-023-00708-3

Related tools

CSI:FingerIDComplementary to · A SIRIUS-integrated machine-learning method and webservice for predicting molecular fingerprints from MS/MS data and ranking candidate structures from molecular-structure databases.

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