matchms

SUMMARY

What it does

This skill provides procedural guidance for using the matchms Python package (version 0.33.1) to process, clean, compare, and search tandem mass spectra. It covers file I/O for formats like MGF, MSP, mzML, mzXML, JSON, mzSpecLib, and metabolomics-USI; metadata harmonization; peak filtering; spectral similarity scoring (cosine, modified cosine, neutral loss, etc.); library matching; score matrices; and molecular-similarity networks. The skill includes code examples, API guardrails for matchms 0.33.1, and references to detailed documentation. It explicitly states that matchms is not for LC-MS feature detection or proteomics pipelines, recommending pyopenms for those tasks. The skill is part of the Scientific Agent Skills library by K-Dense and is licensed under Apache-2.0.