alterlab-matchms

# 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. ## Core Capabilities ### 1. Importing and Exporting Mass Spectrometry Data Load spectra from multiple file formats and export processed data: ```python from matchms.importing import load_from_mgf, load_from_mzml, load_from_msp, load_from_json from matchms.exporting import save_as_mgf, save_as_msp, save_as_json # Import spectra spectra = list(load_from_mgf("spectra.mgf")) spectra = list(load_from_mzml("data.mzML")) spectra = list(load_from_msp("library.msp")) # Export processed spectra save_as_mgf(spectra, "output.mgf") save_as_json(spectra, "output.json") ``` **Supported formats:** - mzML and mzXML (raw mass spectrometry formats) - MGF (Mascot Generic Format) - MSP (spectral library format) - JSON (GNPS-compatible) - metabolomics-USI references - Pickle (Python serialization) For detailed importing/exporting documentation, consult `references/importing_exporting.md`. ### 2. Spectrum Filtering and Processing Apply comprehensive filters to standardize metadata and refine peak data: ```python from matchms.filtering import default_filters, normalize_intensities from matchms.filtering import select_by_relative_intensity, require_minimum_number_of_peaks # Apply default metadata harmonization filters spectru...