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pyopenms

Process LC-MS/MS data with peak picking and identification via pyOpenMS.

43|13|Updated Oct 10, 2025
Search Tags:#python#mass-spectrometry#proteomics#OpenMS#mzML
One-click install
npx skills add https://github.com/lifangda/claude-plugins --skill pyopenms-lifangda
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pyopenms
Source: https://github.com/lifangda/claude-plugins/tree/main/cli-tool/skills-library/scientific-computing/proteomics/pyopenms
Command: npx skills add https://github.com/lifangda/claude-plugins --skill pyopenms-lifangda

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

pyOpenMS provides Python bindings for the OpenMS framework, enabling efficient processing of LC-MS/MS data, peak picking, feature detection, and peptide/protein identification within Python pipelines.

Core Features & Use Cases

  • File I/O & data formats: mzML/mzXML, FASTA, mzTab, mzIdentML, TraML, pepXML/protXML
  • MS data structures: MSSpectrum, MSExperiment, MSChromatogram, and efficient peak access
  • Chemistry & peptide handling: handle molecular formulas, isotopes, peptide sequences, and modifications

Quick Start

Use pyOpenMS to load an mzML file, perform basic processing, and write results to an mzML or mzIdentML file.

Frequently Asked Questions about pyopenms

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

FAQPage Schema
How do I process mzML and mzXML LC-MS/MS data from proteomics experiments in Python?▼

pyOpenMS provides Python bindings to process mzML/mzXML LC-MS/MS data through peak picking, feature detection, and peptide identification. Load files using MSExperiment, apply OpenMS algorithms, and export results to mzIdentML or mzTab formats within Python pipelines.

Can I perform peptide and protein identification on mass spectrometry data using Python?▼

Yes, pyOpenMS integrates with external search tools like Comet, Mascot, MSGF+, and Percolator to identify peptides and proteins from LC-MS/MS data. Results are processed and quantified using MSstats, all within Python workflows.

What file formats does pyOpenMS support for mass spectrometry analysis?▼

pyOpenMS handles mzML, mzXML, FASTA, mzTab, mzIdentML, TraML, pepXML, and protXML formats. This broad format support enables seamless data import from instruments and export of processed results across proteomics pipelines.

How do I access and manipulate mass spectrometry data structures in Python?▼

pyOpenMS exposes core OpenMS data structures—MSExperiment, MSSpectrum, and MSChromatogram—with efficient peak access. These allow direct manipulation of spectra and chromatogram data within Python for custom analysis workflows.

Does pyOpenMS handle molecular formulas and peptide modifications?▼

Yes, pyOpenMS provides chemistry utilities to handle molecular formulas, isotopes, peptide sequences, and post-translational modifications, enabling precise mass calculations and peptide property analysis in Python.

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