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, a…
---
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 `references/`) only when no script fits.
## Installation
… load the full skill through Skill Me