PyOpenMS — Mass Spectrometry Analysis

Overview

PyOpenMS provides Python bindings to the OpenMS C++ library for computational mass spectrometry. It supports proteomics and metabolomics data processing including file I/O for 10+ MS formats, signal processing, feature detection, peptide/protein identification, and quantitative analysis across samples.

When to Use

• Processing raw LC-MS/MS data (mzML, mzXML) for proteomics or metabolomics
• Detecting chromatographic features and linking them across multiple samples
• Identifying peptides and proteins from MS/MS search engine results with FDR control
• Running untargeted metabolomics workflows (peak picking → feature detection → alignment → annotation)
• Converting between mass spectrometry file formats (mzML, mzXML, featureXML, idXML)
• Smoothing, filtering, and centroiding raw spectral data
• For simple spectral library matching and metabolite identification, use matchms instead
• For protein sequence analysis (not mass spec), use biopython instead

Prerequisites