What file formats does matchms support within Claude Code?

Matchms supports a wide range of mass spectrometry formats including mzML, mzXML, MGF, MSP, and GNPS-compatible JSON files.

Is matchms suitable for large-scale library matching?

Absolutely. Matchms is designed to efficiently calculate similarity scores between large sets of query and reference spectra using optimized algorithms and reproducible pipelines.

Can I use matchms for chemical structure derivation?

Yes, it includes specialized filters to derive InChI and InChIKey from SMILES, add molecular fingerprints, and repair structural mismatches in metadata.

What spectral similarity metrics are available in this skill?

It provides several metrics including CosineGreedy, Modified Cosine (which accounts for precursor mass differences), NeutralLossesCosine, and FingerprintSimilarity.

Matchms Mass Spectrometry Analysis

Name: Matchms Mass Spectrometry Analysis
Author: jimmc414

byjimmc414

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324

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データサイエンスとML

Processes and analyzes mass spectrometry data using Python-based spectral similarity, metadata harmonization, and data filtering tools.

Matchms is a specialized capability for Claude Code designed for scientists and researchers working with mass spectrometry data. It provides a comprehensive suite of tools to import, filter, and analyze spectra from various formats like mzML, MGF, and MSP. The skill excels at metadata harmonization, peak normalization, and calculating complex spectral similarities such as Modified Cosine or Neutral Losses, enabling the creation of automated and reproducible metabolomics pipelines and autonomous chemical discovery workflows within the Claude environment.

主な機能

01Integrated visualization for spectrum plotting and library matching

02Extensible processing pipelines with 40+ built-in spectrum filters

03Automated metadata harmonization and chemical annotation (SMILES/InChI)

04324 GitHub stars

05Advanced spectral similarity metrics including Cosine and Modified Cosine

06Support for mzML, MGF, MSP, and JSON file formats

ユースケース

01Building automated metabolomics data processing and cleaning pipelines

02Identifying unknown compounds by matching query spectra against reference libraries

03Large-scale spectral clustering and network-based chemical analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos matchms

For use in Claude.ai and ChatGPT