How does Modified Cosine similarity differ from standard Cosine?

Modified Cosine similarity accounts for differences in precursor m/z values, making it significantly more effective for identifying related chemical analogs.

Can I calculate chemical structure similarities?

Yes, Matchms can derive InChI and SMILES metadata to calculate molecular structure similarity using fingerprints like Morgan (requires the chemistry extension).

Is this skill suitable for large-scale spectral library matching?

Absolutely. It is designed to build efficient processing pipelines and score objects capable of handling high-throughput comparison of query spectra against extensive reference libraries.

What file formats does the Matchms skill support?

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

Matchms MS Analysis

Name: Matchms MS Analysis
Author: x-cmd

byx-cmd

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データサイエンスとML

Processes mass spectrometry data to calculate spectral similarities, harmonize metadata, and identify chemical compounds.

Matchms is an open-source Python library integration for Claude Code designed for sophisticated mass spectrometry data processing and analysis. It allows users to import spectra from various formats like mzML, MGF, and MSP, apply over 40 specialized metadata and peak filters, and execute high-performance similarity calculations such as Modified Cosine and Neutral Losses. This skill is essential for researchers and developers building reproducible metabolomics workflows, performing large-scale spectral library searches, and automating chemical data standardization.

主な機能

01Robust spectrum processing pipelines for peak filtering, normalization, and quality control

02Advanced similarity metrics including CosineGreedy, ModifiedCosine, and FingerprintSimilarity

03Integration for chemical annotation using SMILES, InChI, and molecular fingerprints

04Multi-format I/O support for mzML, MGF, MSP, and GNPS-compatible JSON

058 GitHub stars

06Comprehensive metadata harmonization for compound names, adducts, and chemical structures

ユースケース

01Automated metabolomics data processing and spectral library matching

02Standardizing and cleaning large-scale mass spectrometry datasets for research

03Identifying unknown chemical compounds through high-throughput similarity comparisons

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill matchms

For use in Claude.ai and ChatGPT

Download Skill