Individual skill
matchms
Processes, cleans, compares, and searches 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.
skills/matchms/SKILL.md
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- Last checked
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- MIT
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SKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesSKILL.mdcore · 12,821 bytesreferences/filtering.mddoc · 12,206 bytesreferences/importing_exporting.mddoc · 10,834 bytesreferences/migration.mddoc · 8,557 bytesreferences/similarity.mddoc · 14,080 bytesreferences/sources.mddoc · 9,854 bytesreferences/workflows.mddoc · 14,273 bytesscripts/library_search.pyruns · 21,090 bytes
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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,
verified again on 2026-10-01. Older tutorials can use removed names; see the
migration reference.
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