PyOpenMS

Overview

PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use it to read/write MS file formats, process raw spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines.

This skill ships ready-to-run scripts in scripts/ covering the most common high-level workflows. Prefer running a script over writing new code—each is a parameterized CLI tool that handles loading, processing, and export. Drop into the Python API (and the references/) only when no script fits.

Installation

uv pip install pyopenms