pyOpenMS
Mass spectrometry pipelines for proteomics and metabolomics via OpenMS.
Install
Ships scriptsgh skill install K-Dense-AI/scientific-agent-skills pyopenms
Proteomics or metabolomics MS data: feature detection, quantification, peptide identification, or building an LC-MS/MS pipeline.
- Author
- K-Dense Inc.
- License
- BSD-3-Clause
Brings the OpenMS library into Python for LC-MS/MS work: reading mzML and mzXML, signal processing and centroiding, feature detection, retention-time alignment, consensus linking and label-free or isobaric quantification. Peptide and protein identification runs through FASTA re-indexing, FDR estimation and idXML export. Most common workflows ship as parameterized command-line scripts, and the guidance says to try one of those before writing new Python. Adduct grouping, accurate-mass annotation against HMDB and GNPS or SIRIUS export cover the metabolomics side.
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