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.
npx skills add K-Dense-AI/scientific-agent-skills --skill matchms --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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: ```bash uv pip install "matchms==0.33.1" ``` Verify the runtime: ```bash uv run python -c "import matchms; print(matchms.__version__)" ```
- Purpose and Scope
- Install the Verified Release
- Operating Workflow
- Current API Guardrails
- Quick Start: Clean and Search a Library
- Pair Scoring
- Choose a Similarity Method
- Large Comparisons
- Bundled Library-Search CLI
- Spectrum Objects and Visualization
- References
- Non-Negotiable Checks
uv pip install "matchms==0.33.1" uv run python -c "import matchms; print(matchms.__version__)" uv run python scripts/library_search.py \ queries.mgf library.msp hits.csv \
What does the matchms skill do?
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.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill matchms --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.