pyopenms

name	pyopenms
description	Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
license	3 clause BSD license
allowed-tools	Read Write Edit Bash
compatibility	Requires Python 3.9+ and uv. Examples and scripts target pyOpenMS 3.5.0.
metadata	{"version":"2.0","skill-author":"K-Dense Inc."}

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 ) only when no script fits.