AI SummaryMatchms enables mass spectrometry data processing and spectral analysis for metabolomics research, supporting multiple file formats and similarity calculations. Researchers and bioinformaticians working with MS data benefit from standardized workflows and compound identification.
Install
Copy this and paste it into Claude Code, Cursor, or any AI assistant:
I want to install the "matchms" skill in my project. Please run this command in my terminal: # Install skill into the correct directory (5 files) mkdir -p .claude/skills/matchms && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/matchms/SKILL.md "https://raw.githubusercontent.com/jimmc414/Kosmos/master/kosmos-claude-scientific-skills/scientific-skills/matchms/SKILL.md" && mkdir -p .claude/skills/matchms/references && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/matchms/references/filtering.md "https://raw.githubusercontent.com/jimmc414/Kosmos/master/kosmos-claude-scientific-skills/scientific-skills/matchms/references/filtering.md" && mkdir -p .claude/skills/matchms/references && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/matchms/references/importing_exporting.md "https://raw.githubusercontent.com/jimmc414/Kosmos/master/kosmos-claude-scientific-skills/scientific-skills/matchms/references/importing_exporting.md" && mkdir -p .claude/skills/matchms/references && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/matchms/references/similarity.md "https://raw.githubusercontent.com/jimmc414/Kosmos/master/kosmos-claude-scientific-skills/scientific-skills/matchms/references/similarity.md" && mkdir -p .claude/skills/matchms/references && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/matchms/references/workflows.md "https://raw.githubusercontent.com/jimmc414/Kosmos/master/kosmos-claude-scientific-skills/scientific-skills/matchms/references/workflows.md" Then restart Claude Code (or reload the window in Cursor) so the skill is picked up.
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.
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