pyopenms
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
npx skills add LeonChaoX/qinyan-academic-skills --skill pyopenms --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.
# PyOpenMS ## Overview PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use for handling mass spectrometry file formats, processing spectral data, detecting features, identifying peptides/proteins, and performing quantitative analysis. ## Installation Install using uv: ```bash uv uv pip install pyopenms ``` Verify installation: ```python import pyopenms print(pyopenms.__version__) ``` ## Core Capabilities PyOpenMS organizes functionality into these domains: ### 1. File I/O and Data Formats Handle mass spectrometry file formats and convert between representations. **Supported formats**: mzML, mzXML, TraML, mzTab, FASTA, pepXML, protXML, mzIdentML, featureXML, consensusXML, idXML Basic file reading: ```python import pyopenms as ms # Read mzML file exp = ms.MSExperiment() ms.MzMLFile().load("data.mzML", exp) # Access spectra for spectrum in exp: mz, intensity = spectrum.get_peaks() print(f"Spectrum: {len(mz)} peaks") ``` **For detailed file handling**: See `references/file_io.md` ### 2. Signal Processing Process raw spectral data with smoothing, filtering, centroiding, and normalization.
- Overview
- Installation
- Core Capabilities
- 1. File I/O and Data Formats
- 2. Signal Processing
- 3. Feature Detection
- 4. Peptide and Protein Identification
- 5. Metabolomics Analysis
- Data Structures
- Common Workflows
- Quick Start: Load and Explore Data
- Parameter Management
- Export to Pandas
- Integration with Other Tools
uv uv pip install pyopenms
What does the pyopenms skill do?
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill pyopenms --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.