pyopenms

SUMMARY

What it does

PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. The skill includes ready-to-run scripts for inspecting and converting MS data, processing spectra, detecting features, aligning and quantifying across samples, annotating adducts and accurate masses, processing identifications, performing chemistry calculations (mass, digestion, theoretical spectra), extracting chromatograms, and plotting MS data. It supports extensive file formats and algorithms. The skill requires Python 3.9+ and uv, and targets pyOpenMS 3.5.0. The source is a SKILL.md file from the K-Dense-AI/scientific-agent-skills repository, licensed under MIT (as declared in the submitted record).