pyopenms-mass-spectrometry
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
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