Pyopenms

If you're doing proteomics or metabolomics work and need to process LC-MS/MS data, this is the Python interface to OpenMS, which is basically the standard toolkit for computational mass spectrometry. It handles all the usual file formats (mzML, mzXML, mzIdentML), does feature detection across samples, integrates with search engines like Comet and Mascot for peptide identification, and includes the signal processing algorithms you need for quantitative workflows. The API can feel a bit heavy since it's wrapping a large C++ library, but it's comprehensive and battle tested. Export to pandas DataFrames when you need to do custom analysis or ML work downstream.

Install to Claude Code

npx -y skills add k-dense-ai/scientific-agent-skills --skill pyopenms --agent claude-code