AI SummaryMatchms is a Python library for mass spectrometry data processing, enabling researchers to import spectra from multiple formats, standardize metadata, calculate spectral similarities, and perform metabolomics analysis within Claude Code environments.
Install
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Description
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
Overview
Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various formats, standardize metadata, filter peaks, calculate spectral similarities, and build reproducible analytical workflows.
1. Importing and Exporting Mass Spectrometry Data
Load spectra from multiple file formats and export processed data: `python from matchms.importing import load_from_mgf, load_from_mzml, load_from_msp, load_from_json from matchms.exporting import save_as_mgf, save_as_msp, save_as_json
Import spectra
spectra = list(load_from_mgf("spectra.mgf")) spectra = list(load_from_mzml("data.mzML")) spectra = list(load_from_msp("library.msp"))
Export processed spectra
save_as_mgf(spectra, "output.mgf") save_as_json(spectra, "output.json") ` Supported formats: • mzML and mzXML (raw mass spectrometry formats) • MGF (Mascot Generic Format) • MSP (spectral library format) • JSON (GNPS-compatible) • metabolomics-USI references • Pickle (Python serialization) For detailed importing/exporting documentation, consult references/importing_exporting.md.
Quality Score
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75/100
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