pyopenms
Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
- Version
- 3.0
- License
- 3 clause BSD license
- Compatibility
- Requires CPython 3.11+ and pyOpenMS 3.6.0; pandas and NumPy for tables, Matplotlib for plots. Wheels support macOS 15+ arm64, Linux glibc 2.34+ x86-64/arm64, and Windows x86-64. Search-engine executables are separate.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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Files
- skills/pyopenms/SKILL.md
- skills/pyopenms/SKILL_CN.md
- skills/pyopenms/references/data_structures.md
- skills/pyopenms/references/feature_detection.md
- skills/pyopenms/references/file_io.md
- skills/pyopenms/references/identification.md
- skills/pyopenms/references/metabolomics.md
- skills/pyopenms/references/signal_processing.md
- skills/pyopenms/scripts/_common.py
- skills/pyopenms/scripts/accurate_mass_search.py
- skills/pyopenms/scripts/align_link_quantify.py
- skills/pyopenms/scripts/consensus_to_matrix.py
- skills/pyopenms/scripts/convert_format.py
- skills/pyopenms/scripts/detect_adducts.py
- skills/pyopenms/scripts/detect_features_centroided.py
- skills/pyopenms/scripts/detect_features_metabo.py
- skills/pyopenms/scripts/digest_protein.py
- skills/pyopenms/scripts/export_gnps_sirius.py
- skills/pyopenms/scripts/extract_chromatograms.py
- skills/pyopenms/scripts/inspect_ms_data.py
- skills/pyopenms/scripts/mass_calculator.py
- skills/pyopenms/scripts/plot_ms_data.py
- skills/pyopenms/scripts/process_identifications.py
- skills/pyopenms/scripts/process_spectra.py
- skills/pyopenms/scripts/theoretical_spectrum.py
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