matchms - Mass Spectrometry Data Processing Library
Process mass spectrometry data with spectral similarity and metadata harmonization
Tags
Updated: 2026-03-22Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Import spectra from files
- Export spectra to files
- Filter spectrum metadata
- Normalize peak intensities
- Select peaks by intensity
- Calculate cosine similarity
- Calculate modified cosine similarity
- Build processing pipelines
- Harmonize metadata keys
- Derive InChI from SMILES
- Add molecular fingerprints
- Plot spectrum
- Compare two spectra
Inputs
- mzML files
- mzXML files
- MGF files
- MSP files
- JSON files
- Spectral library
- Query spectra
- Reference spectra
- SMILES strings
- Pickle files
Outputs
- Processed spectra files
- Similarity scores
- Filtered spectra
- Spectrum plots
- Harmonized metadata
- InChI strings
- InChIKey strings
- Molecular fingerprints
Requirements
- Python environment
- matchms library
- Optional chemistry dependencies