Individual skill
matchms
Process, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.
plugins/KalarisLabs/research-agent-skills/skills/matchms/SKILL.md
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- Apache-2.0
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# Matchms
## Purpose and Scope
Matchms is a Python package for importing, cleaning, processing, and comparing
tandem mass spectra. This skill targets **matchms 0.33.1**, released 2026-06-08,
and corrects several breaking API changes that older tutorials do not reflect.
Use matchms for:
- MS/MS library search and query-versus-reference scoring
- Metadata harmonization, adduct/precursor handling, and peak filtering
- Cosine, modified-cosine, neutral-loss, approximate, and entropy scoring
- Structured score matrices, top-hit extraction, and spectral networks