matchms
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
npx skills add LeonChaoX/qinyan-academic-skills --skill matchms --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 compreh
- 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
- 6. Metadata Management
- Common Workflows
- Installation
- Reference Documentation
uv pip install matchms uv pip install matchms[chemistry]
What does the matchms skill do?
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill matchms --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.