Process MS/MS spectra with filtering, similarity scoring, and metadata harmonization pipelines.
npx skills add https://github.com/jackspace/ClaudeSkillz --skill matchms
Please help me install this Agent Skill. Skill: matchms Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-pkg-matchms Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill matchms
Matchms provides a pipeline for importing, filtering, and comparing MS/MS spectra in metabolomics workflows.
Import a small set of spectra, apply default filters, and compute similarity to a library.
High-intent search queries and answers about installing and using this skill.
Mass spectrometry standardization involves normalizing peak intensities, filtering noise, and harmonizing metadata across spectra. Matchms automates this preprocessing and computes spectral similarity using cosine and alternative metrics to identify compounds against reference libraries in metabolomics workflows.
Matchms supports import and export of mzML, mzXML, MGF, MSP, and JSON formats, enabling seamless integration with diverse mass spectrometry platforms and metabolomics pipelines while maintaining data integrity across conversions.
Use the SpectrumProcessor to chain filtering, normalization, and similarity-scoring steps into repeatable workflows. This ensures consistent QC and compound identification across large MS datasets without manual reconfiguration.
Yes. Matchms calculates cosine and modified cosine similarity scores between experimental spectra and reference libraries, enabling compound identification and annotation in untargeted metabolomics and MS data analysis.
Matchms filters peaks by intensity threshold, normalizes peak heights, removes low-quality spectra, and harmonizes metadata fields. These QC steps improve similarity matching accuracy and reduce false identifications in mass spectrometry workflows.
Matchms has no mandatory external dependencies listed. It provides built-in Spectrum objects, metadata handling, and similarity metrics, making it self-contained for importing, filtering, and comparing MS/MS spectra in metabolomics workflows.
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LeonChaoXMatch unknown MS/MS spectra against reference libraries using similarity scoring.
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