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
Installs just this skill. Get the whole plugin for auto-invocation.
⚡ How it fires
How this skill gets triggered: by you, by Claude, or both.
Fires itselfClaude auto-loads it when your prompt matches the work.
You can call itInvoke it directly when you want it.
Slash command/pyopenms
👁️ Context preview
The summary Claude sees to decide when to auto-load this skill.
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
📊 Stats
Stars31,545
Forks3,146
LanguagePython
LicenseMIT
📦 Ships with scientific-agent-skills
</> SKILL.md
pyopenms.SKILL.md
---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
```bash
