pyOpenMS

Overview

pyOpenMS is an open-source Python library for mass spectrometry data analysis in proteomics and metabolomics. Process LC-MS/MS data, perform peptide identification, detect and quantify features, and integrate with common proteomics tools (Comet, Mascot, MSGF+, Percolator, MSstats) using Python bindings to the OpenMS C++ library.

When to Use This Skill

This skill should be used when:

• Processing mass spectrometry data (mzML, mzXML files)
• Performing peak picking and feature detection in LC-MS data
• Conducting peptide and protein identification workflows
• Quantifying metabolites or proteins
• Integrating proteomics or metabolomics tools into Python pipelines
• Working with OpenMS tools and file formats

Core Capabilities

1. File I/O and Data Import/Export