matchms

What problem does it solve?

Mass spectrometry workflows often require robust, reproducible processing, comparison, and identification of spectra across libraries. Matchms provides a Python toolkit to import, standardize, filter, and compare spectra, enabling reliable compound identification from spectral data.

Core Features & Use Cases

• Importing and exporting spectra in multiple formats (mgf, mzML, json)
• Spectrum filtering, metadata harmonization, and quality control
• Calculating spectral similarities (CosineGreedy, ModifiedCosine, NeutralLossesCosine) and matching against libraries
• Building reproducible processing pipelines and deriving chemical information from spectra

Quick Start

Process a small example dataset by loading spectra, applying default filters, and computing cosine similarity against a reference spectrum.