matchms

Compare mass spectra and identify compounds from spectral libraries.

3|Updated Apr 17, 2026

Search Tags:#data analysis #metabolomics #mass spectrometry #spectral analysis #compound identification

Ready to run

npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill matchms-ramanebrahimi

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: matchms
Source: https://github.com/RamanEbrahimi/raman-marketplace/tree/main/plugins/agentic-research/skills/scientific-skills/matchms
Command: npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill matchms-ramanebrahimi

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires matchms, rdkit, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the process of spectral similarity and compound identification in metabolomics, enabling users to compare mass spectra, compute similarity scores, and identify unknown compounds from spectral libraries.

Core Features & Use Cases

Spectral Comparison: Compare mass spectra and compute similarity scores like cosine and modified cosine.
Compound Identification: Identify unknown compounds from spectral libraries.
Use Case: For a researcher trying to identify metabolites in a sample, this Skill can be used to compare the sample's mass spectrum against a library of known metabolites and provide potential matches.

Quick Start

Use the matchms skill to compare the mass spectrum of the sample 'sample.mgf' against the 'metabolite_library.mgf' library and get the top 10 matching compounds.

Frequently Asked Questions about matchms

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I identify unknown compounds from a mass spectrometry library?▼

Compound identification involves comparing your sample's mass spectrum against a known metabolite library to compute similarity scores and retrieve the top matching compounds.

How do I compare mass spectra to compute similarity scores for metabolomics?▼

You can compare mass spectra to compute spectral similarity scores for metabolomics by using functions like cosine and modified cosine to evaluate the match between unknown samples and library references.

What mass spectrometry import and export formats are supported for spectral analysis?▼

Spectral analysis supports various import and export formats for mass spectrometry data, allowing you to load sample files and metabolite libraries to perform compound identification and similarity comparisons.

Do I need rdkit to perform compound identification and spectral analysis?▼

Yes, you need rdkit installed alongside the core matchms library to handle the underlying chemistry processing required for spectral similarity and compound identification tasks.

What is the best way to find the top matching metabolites from a spectral library?▼

The best way to find top matching metabolites is to compare your sample's mass spectrum against a metabolite library file, computing similarity scores to rank and retrieve the closest matching compounds.