Matchms

Overview

Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various formats, standardize metadata, filter peaks, calculate spectral similarities, and build reproducible analytical workflows.

When to Use This Skill

Use this skill when the user wants to:

• Load, clean, and harmonize MS/MS spectra (MGF, MSP, mzML, mzXML, JSON, USI) and their metadata
• Score spectral similarity (cosine, modified cosine, neutral-loss cosine) between queries and a reference library
• Annotate unknown metabolites by library matching, or derive InChI/InChIKey/fingerprints from spectrum metadata
• Build reproducible preprocessing pipelines (SpectrumProcessor) for metabolomics spectra

Does NOT Trigger