matchms
Processes, cleans, compares, and searches tandem mass spectra with matchms
by k-dense-aiFree
Description
matchms is an agent skill for processing, cleaning, comparing and searching tandem mass spectra with the matchms Python package. Use it for mass spectrometry file input and output, harmonising metadata, filtering peaks, comparing spectra and searching libraries. Its scoring methods include cosine, modified cosine, neutral loss, approximate and entropy scores. It also builds structured score matrices, extracts top hits and creates spectral networks. It reads and writes MGF, MSP, mzML, mzXML, JSON, mzSpecLib and metabolomics USI workflows. Typical jobs are query-versus-reference library search, metadata cleaning with adduct and precursor handling, and peak filtering before comparison. The skill is clear about its scope. It is not a replacement for other tools in areas that matchms does not cover, and the skill lists those cases. It targets matchms 0.33.1, released on 8 June 2026 and verified again on 1 October 2026. Older tutorials use names that have since been removed, so the skill points to a migration reference for those. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Cleans and filters tandem mass spectra
- Cosine, modified cosine and entropy scoring
- Library search and top-hit extraction
- MGF, MSP, mzML, mzXML and JSON formats
- Targets matchms 0.33.1
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matchms FAQ
What does matchms do?
Imports, cleans, processes and compares tandem mass spectra, including library search.
Which scores are available?
Cosine, modified cosine, neutral-loss, approximate and entropy scoring.
Which file formats?
MGF, MSP, mzML, mzXML, JSON, mzSpecLib and metabolomics USI workflows.
Why do old tutorials fail?
The skill says older tutorials use names that were removed, and it points to a migration reference.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill matchms.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best matchms alternatives?
Popular alternatives to matchms include pyopenms, gget and anndata. See all matchms alternatives