Compare mass spectra against reference libraries using similarity metrics.
npx skills add https://github.com/mv-debug/kyco --skill matchms-mv-debug
Please help me install this Agent Skill. Skill: matchms Source: https://github.com/mv-debug/kyco/tree/main/.claude/skills/matchms Command: npx skills add https://github.com/mv-debug/kyco --skill matchms-mv-debug
MatchMS simplifies processing of mass spectrometry data, enabling robust spectral similarity analysis and reliable compound identification by comparing unknown spectra to curated libraries.
Install matchms and run a simple example to compute cosine similarity against a reference spectrum.
High-intent search queries and answers about installing and using this skill.
Spectral similarity scoring works by comparing experimental mass spectra against reference libraries using metrics like CosineGreedy, ModifiedCosine, and Fingerprint-based comparisons. MatchMS processes these spectra to derive robust similarity scores for reliable compound identification.
Yes, mzML and MGF files can be imported for metabolomics data processing. This Skill supports importing and exporting common MS data formats including mzML, MGF, MSP, and JSON, alongside spectrum processing and metadata harmonization.
Computing cosine similarity for LC-MS/MS spectra is best handled by using specific similarity metrics. This Skill supports CosineGreedy, ModifiedCosine, and NeutralLossesCosine algorithms to calculate robust spectral similarity scores for compound identification.
Yes, Python is required to run matchms for spectral similarity analysis. You need a Python environment with the matchms library installed to build reproducible processing pipelines and execute similarity computations.
To derive InChI and SMILES metadata for chemical annotation, use this Skill's spectrum processing and metadata harmonization features. It supports metadata derivation including InChI, SMILES, and fingerprints to annotate compounds during library matching workflows.
dailycafiMatch MS/MS spectra against reference libraries to identify compounds.
learningmatter-mitRetrieve PubChem compound identifiers and metadata via PUG-REST queries.
xjtulycParse molecular representations and compute descriptors, fingerprints, similarity, scaffolds, and substructure matches.
MAF2414Compute cosine and modified cosine similarity scores for mass spectra in metabolomics.
