matchms

Topics in the source

• Matchms
• Overview
• Core Capabilities
• 1. Importing and Exporting Mass Spectrometry Data
• 2. Spectrum Filtering and Processing
• 3. Calculating Spectral Similarities
• 4. Building Processing Pipelines
• 5. Working with Spectrum Objects

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. Load spectra from multiple file formats and export processed data: 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/importingexporting.md. Apply comprehensive filters to standardize metadata and refine peak data: Filter categories: Metadata processing: Harmonize compound names, derive chemical structures, standardize adducts, correct charges Peak filtering: Normalize intensities, select by m/z or intensity, remove precursor peaks Quality control: Require minimum peaks, validate precursor m/z, ensure metadata completeness Chemical annotation: Add fingerprints, derive InChI/SMILES, repair structural mismatches Matchms provides 40+ filters. For the complete filter reference, consult references/filtering.md. Compare spectra usi

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