Pyopenms

This is the Python interface to OpenMS, the computational mass spectrometry library that proteomics and metabolomics researchers actually use. It handles the full pipeline: reading mzML/mzXML files, signal processing, feature detection across LC-MS runs, and peptide identification workflows. The API wraps C++ underneath, so you get decent performance while staying in Python. Especially useful if you're dealing with quantitative proteomics where you need to align features across multiple samples or integrate results from search engines like Comet or Mascot. The parameter system takes some getting used to, but once you're past that, it beats writing custom parsers for every mass spec file format.