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Metabolite annotation and identification

SMART

Rank molecular-formula candidates for spatial-metabolomics mass features.

Imaging mass spectrometrySpatial metabolomicsDesktop graphical interfaceCommand lineSource available with restrictions
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Overview

SMART uses a formula network and regression scoring to prioritize formula assignments from accurate mass and polarity.

What can this tool do?

Molecular-formula prediction

Common uses

  • Rank molecular-formula candidates for spatial-metabolomics mass features.

Scientific fit

Primary function

Metabolite annotation and identification

Analysis types

Spatial metabolomics

Data compatibility

Inputs

Feature or peak table

Outputs

Compound list or annotations

Input formats

Single m/z or table of m/z values, polarity and mass tolerance

Output formats

Ranked formula candidates and supporting database evidence

Scope and considerations

Designed for

  • SMART uses a formula network and regression scoring to prioritize formula assignments from accurate mass and polarity.

Not designed for

  • Unambiguous structure identification or raw imaging-data extraction.

Important requirements

  • Python and documented dependencies; matching SMART database and regression model files.
  • Release v0.1 provides smart_full.db and lr_with_sc.pkl; assets were listed but not downloaded or executed.

Considerations

  • Formula assignments remain hypotheses requiring additional evidence.
  • The README describes a larger raw database requiring author contact; do not equate it with the smaller release asset.

Access and documentation

Primary accessSource repository

Public source and release assets are available; no explicit software license was identified. Data availability differs between released assets and the larger raw database.

Evidence and review

Enveda intake checked against official documentation, license information and primary DOI/title/year on 2026-10-23. Editorial review only; no execution or independent benchmark.

Core publications

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

  1. SMART: An Approach for Accurate Formula Assignment in Spatially Resolved Metabolomics. Analytical Chemistry (2025). doi:10.1021/acs.analchem.4c06210

Related tools

BAMSimilar function · BAM generates and ranks structural candidates for suspect metabolites by applying biotransformation rules to known anchor structures.BUDDY / msbuddySimilar function · Generate and rank molecular formula annotations for small-molecule mass-spectrometry queries.CANOPUSSimilar function · A SIRIUS-integrated machine-learning method and webservice for predicting compound classes directly from high-resolution MS/MS data without requiring an exact database structure match.CFM-IDSimilar function · Predict tandem mass spectra, annotate fragments and rank candidate structures for small molecules.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-23 · First committed entry

    Add SMART VInSMoC and FNICM with verified scope and access notes

    View change · Entry at this revision

Full GitHub history