from kosmos509
Mass spectrometry data processing: import/export mzML/MGF/MSP, filter and normalize spectra, compute spectral similarity (cosine/modified cosine), and build rep
MatchMS provides a Python toolkit for loading, cleaning, filtering, and comparing mass spectra. It supports common MS formats (mzML, MGF, MSP), metadata harmonization, peak filtering and normalization, and several spectral similarity metrics for library matching and large-scale comparisons.
Use this skill when you need to preprocess mass-spectrometry datasets, run quality-control filters, match unknown spectra against reference libraries, or compute pairwise similarity scores for clustering and annotation. It's aimed at metabolomics and small-molecule MS analysis workflows.
Best used with Python-capable agents and environments (Codex/Claude Code/Copilot-style tools that can run Python snippets). The skill assumes access to Python runtime and common scientific libs (numpy).
Well-structured documentation skill for the matchms Python library covering mass spectrometry data import/export, filtering, spectral similarity, and pipeline construction. No bundled scripts — purely instructional with code examples. Clean SKILL.md with good progressive disclosure via references/ directory, though references are not actually bundled. Niche scientific domain with a real but small audience.
Clean instructional skill, no security concerns. Well-written but references/ directory is aspirational rather than bundled. Installation via 'uv pip install' without confirmation is minor security consideration.
