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Update SKILL.md files to add double quotation marks for all skills, ensuring clarity and consistency across all entries.

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Haoxuan "Orion" Li
2025-10-20 20:51:50 -07:00
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scientific-packages/matchms/SKILL.md
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---
name: matchms
description: Process and analyze mass spectrometry data using matchms, a Python library for spectral similarity calculations, metadata harmonization, and compound identification. Use this skill when: (1) Working with mass spectrometry data files (mzML, mzXML, MGF, MSP, JSON) - importing, exporting, or converting between formats; (2) Compound identification tasks - matching unknown spectra against reference libraries using cosine similarity, modified cosine, or neutral loss patterns; (3) Spectral data preprocessing - harmonizing metadata, normalizing intensities, filtering peaks by m/z or intensity, removing precursor peaks, or applying quality control filters; (4) Building reproducible workflows - creating standardized processing pipelines, batch processing multiple datasets, or implementing consistent analysis protocols; (5) Chemical structure analysis - deriving SMILES/InChI from spectra, adding molecular fingerprints, validating structural annotations, or comparing structural similarities; (6) Large-scale spectral comparisons - performing library-to-library comparisons, finding duplicate spectra, or clustering similar compounds; (7) Multi-metric scoring - combining spectral similarity with structural similarity or metadata matching for robust compound identification; (8) Quality control and validation - filtering low-quality spectra, validating precursor masses, ensuring metadata completeness, or generating identification reports. This skill is essential for metabolomics, proteomics, natural products research, environmental analysis, and any field requiring mass spectrometry data processing and compound identification.
description: "Process and analyze mass spectrometry data using matchms, a Python library for spectral similarity calculations, metadata harmonization, and compound identification. Use this skill when: (1) Working with mass spectrometry data files (mzML, mzXML, MGF, MSP, JSON) - importing, exporting, or converting between formats; (2) Compound identification tasks - matching unknown spectra against reference libraries using cosine similarity, modified cosine, or neutral loss patterns; (3) Spectral data preprocessing - harmonizing metadata, normalizing intensities, filtering peaks by m/z or intensity, removing precursor peaks, or applying quality control filters; (4) Building reproducible workflows - creating standardized processing pipelines, batch processing multiple datasets, or implementing consistent analysis protocols; (5) Chemical structure analysis - deriving SMILES/InChI from spectra, adding molecular fingerprints, validating structural annotations, or comparing structural similarities; (6) Large-scale spectral comparisons - performing library-to-library comparisons, finding duplicate spectra, or clustering similar compounds; (7) Multi-metric scoring - combining spectral similarity with structural similarity or metadata matching for robust compound identification; (8) Quality control and validation - filtering low-quality spectra, validating precursor masses, ensuring metadata completeness, or generating identification reports. This skill is essential for metabolomics, proteomics, natural products research, environmental analysis, and any field requiring mass spectrometry data processing and compound identification."
---
# Matchms