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matchms
Maintainer K-Dense Inc. · Last updated April 1, 2026
Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various formats, standardi.
Original source
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/matchms
- Maintainer
- K-Dense Inc.
- License
- Apache-2.0 license
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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.
- spectra = list(load_from_mgf("spectra.mgf")) spectra = list(load_from_mzml("data.mzML")) spectra = list(load_from_msp("library.msp")).
Source Doc
Excerpt From SKILL.md
1. Importing and Exporting Mass Spectrometry Data
Load spectra from multiple file formats and export processed data:
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
## 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:
from matchms.filtering import default_filters, normalize_intensities
from matchms.filtering import select_by_relative_intensity, require_minimum_number_of_peaks
Use cases
- Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries.
- Use matchms in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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