pyopenms

Analyze mass spectrometry data with Python and OpenMS libraries.

Updated Dec 17, 2025

Search Tags:#metabolomics #mass spectrometry #Python #proteomics #OpenMS

Ready to run

npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill pyopenms-robotlearning123

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pyopenms
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/pyopenms
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill pyopenms-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires openms, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides Python bindings to OpenMS, enabling users to analyze mass spectrometry data for proteomics and metabolomics workflows.

Core Features & Use Cases

Mass Spectrometry Data Analysis: File handling, signal processing, feature detection, peptide and protein identification, metabolomics analysis.
Use Case: Imagine you have proteomics or metabolomics data in mzML format. Use this Skill to process the data, detect features, identify peptides, and perform quantification.

Quick Start

Use the pyopenms skill to load an mzML file 'my_data.mzML', perform feature detection, and save the results to 'features.featureXML'.

Frequently Asked Questions about pyopenms

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I analyze mass spectrometry data in Python for proteomics workflows?▼

You can analyze mass spectrometry data in Python by using pyopenms to handle mzML files, detect features, and identify peptides. It provides Python bindings to OpenMS for complete proteomics and metabolomics workflows.

What is metabolomics analysis with OpenMS and when do I need it?▼

Metabolomics analysis with OpenMS is the process of detecting and quantifying small molecules in mass spectrometry data. You need it when processing mzML files to extract biological insights from complex metabolite samples.

Do I need the OpenMS library installed to run pyopenms scripts?▼

Yes, you need the OpenMS library installed to run pyopenms scripts. This Skill requires the OpenMS dependency to provide its Python bindings for mass spectrometry data processing and analysis.

Can I perform signal processing and feature detection on mzML files using Python?▼

Yes, you can perform signal processing and feature detection on mzML files using Python. This Skill enables you to load mzML data, process signals, detect features, and save the results to featureXML files.

Is Python with OpenMS the best way to handle peptide and protein identification?▼

Python with OpenMS is a strong choice for peptide and protein identification because it provides programmatic bindings for mass spectrometry workflows. It allows you to script file handling, signal processing, and identification tasks efficiently.