matchms-spectral-matching
Matchms — Spectral Matching & Metabolite Identification
Overview
Matchms is a Python library for mass spectrometry data processing focused on spectral similarity calculation and compound identification. It provides multi-format I/O, 50+ spectrum filters for metadata harmonization and peak processing, 8 similarity scoring functions, and a pipeline framework for reproducible analytical workflows.
When to Use
- Identifying unknown metabolites by matching MS/MS spectra against reference libraries
- Computing spectral similarity scores (cosine, modified cosine, fingerprint-based)
- Processing and standardizing mass spectral data from multiple formats (mzML, MGF, MSP, JSON)
- Building reproducible spectral processing pipelines for quality control
- Harmonizing metadata across spectral databases (compound names, SMILES, InChI, adducts)
- Large-scale spectral library comparisons and duplicate detection
- For full LC-MS/MS proteomics workflows (feature detection, protein ID), use pyopenms instead
- For chemical structure similarity without mass spectra, use rdkit fingerprint comparison
Prerequisites
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