AlterLab MatchMS
Skill Verified ActiveSpectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.
To enable researchers to compare mass spectra, compute similarity scores, and identify unknown compounds from spectral libraries for metabolomics research.
Features
- Import and export mass spectrometry data
- Filter and process spectral data
- Calculate spectral similarities
- Build reproducible processing pipelines
- Manage metadata and chemical annotations
Use Cases
- Comparing mass spectra for identification
- Computing spectral similarity scores
- Identifying unknown compounds from spectral libraries
- Building metabolomics analysis workflows
Non-Goals
- Full LC-MS/MS proteomics pipelines
- Replacing pyopenms for complex proteomics workflows
Workflow
- Load spectra from various file formats (MGF, mzML, MSP, JSON, Pickle).
- Apply default and custom filters for metadata harmonization, peak processing, and quality control.
- Calculate spectral similarities using various metrics (CosineGreedy, ModifiedCosine, FingerprintSimilarity).
- Build and execute reproducible processing pipelines.
- Enrich spectra with chemical annotations and validate identifications.
Scope
- info:Tool surface sizeThe underlying library exposes numerous functions, but the skill itself integrates a focused subset, making the effective 'tool surface' manageable for the agent.
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsRuns the Vercel skills CLI (skills.sh) via npx — needs Node.js locally and at least one installed skills-compatible agent (Claude Code, Cursor, Codex, …). Assumes the repo follows the agentskills.io format.
Quality Score
VerifiedTrust Signals
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