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
• MGF, MSP, mzML, mzXML, JSON, mzSpecLib, and metabolomics-USI workflows

Do not use matchms as a replacement for:

• LC-MS feature detection, chromatographic alignment, peptide identification, or protein quantification — use pyopenms
• Vendor raw-file conversion — convert to mzML/mzXML first
• A validated compound-identification protocol — similarity is evidence, not proof of identity

Install the Verified Release

Create or activate an environment, then install the release used by this skill:

uv pip install "matchms==0.33.1"

Verify the runtime:

uv run python -c "import matchms; print(matchms.__v…