Individual skill
pyopenms
Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric 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.
plugins/KalarisLabs/research-agent-skills/skills/pyopenms/SKILL.md
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- Nov 4, 2026
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- Nov 6, 2026
- License
- Apache-2.0
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SKILL.mdcore · 10,111 bytesSKILL.mdcore · 10,111 bytesSKILL.mdcore · 10,111 bytesSKILL.mdcore · 10,111 bytesSKILL.mdcore · 10,111 bytesSKILL.mdcore · 10,111 bytesSKILL.mdcore · 10,111 bytesreferences/data_structures.mddoc · 12,556 bytesreferences/feature_detection.mddoc · 14,500 bytesreferences/file_io.mddoc · 8,783 bytesreferences/identification.mddoc · 12,579 bytesreferences/metabolomics.mddoc · 16,208 bytesreferences/signal_processing.mddoc · 10,308 bytesscripts/accurate_mass_search.pyruns · 4,518 bytesscripts/align_link_quantify.pyruns · 5,352 bytesscripts/consensus_to_matrix.pyruns · 2,775 bytesscripts/convert_format.pyruns · 3,293 bytesscripts/detect_adducts.pyruns · 3,683 bytesscripts/detect_features_centroided.pyruns · 3,027 bytesscripts/detect_features_metabo.pyruns · 4,169 bytesscripts/digest_protein.pyruns · 3,535 bytesscripts/export_gnps_sirius.pyruns · 3,359 bytesscripts/extract_chromatograms.pyruns · 3,810 bytesscripts/inspect_ms_data.pyruns · 5,980 bytesscripts/mass_calculator.pyruns · 3,481 bytesscripts/plot_ms_data.pyruns · 4,026 bytesscripts/process_identifications.pyruns · 4,464 bytesscripts/process_spectra.pyruns · 4,793 bytesscripts/theoretical_spectrum.pyruns · 2,935 bytes
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# PyOpenMS
## Overview
PyOpenMS provides Python bindings to the OpenMS library for computational mass
spectrometry, enabling analysis of proteomics and metabolomics data. Use it to
read/write MS file formats, process raw spectra, detect and quantify features,
identify peptides and proteins, and run end-to-end LC-MS/MS pipelines.
**This skill ships ready-to-run scripts in `scripts/`** covering the most common
high-level workflows. Prefer running a script over writing new code—each is a
parameterized CLI tool that handles loading, processing, and export. Drop into the
Python API (and the `references/`) only when no script fits.
