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pyopenms — Claude Code skill: what it does, how to install

Processes mass spectrometry data for proteomics and metabolomics using pyOpenMS. It detects features, identifies peptides, and generates multi-sample quantification matrices.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill pyopenms -a claude-code
Open on GitHub

What pyopenms does

The skill provides parameterized CLI tools in scripts/ to handle mzML, mzXML, and idXML files without writing custom pipelines from scratch. These utilities centroid raw signals, extract ion chromatograms, group adducts, and assemble multi-sample quantitative tables. For small molecule library matching, the documentation recommends using matchms instead.

A working setup requires CPython 3.11 or higher, pyOpenMS 3.6.0, plus pandas, numpy, and matplotlib. Prebuilt wheels run on modern macOS arm64, Windows, and Linux. Standalone search engine binaries are not bundled: you must install them separately.

Filtering hits with --fdr calculates error rates strictly for peptide-spectrum matches. It does not validate protein-level identification thresholds. Keep this limitation in mind when exporting statistical reports.

What it helps with

  • detect metabolomic features and adducts in mzML files
  • build a multi-sample quantification matrix from consensus data
  • calculate theoretical fragment masses and isotope patterns
  • filter peptide identifications using targeted FDR thresholds

Example prompts for the agent

  • Inspect `sample.mzML` using `inspect_ms_data.py` and write the spectrum table to `spectra.csv`
  • Run `detect_features_metabo.py` on `sample.mzML` and output detected features to `features.csv`
  • Calculate theoretical masses for peptide `PEPTIDEM(Oxidation)K` with `mass_calculator.py`

How to install pyopenms

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill pyopenms -a claude-code

2Manually: put the files in place

~/.claude/skills/pyopenms/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/pyopenms/

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Questions about pyopenms

How to install pyopenms in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill pyopenms -a claude-code to install the skill. You also need a Python 3.11+ environment with pyopenms==3.6.0, pandas, numpy, and matplotlib installed.

What is the pyopenms skill used for?

It provides automated command-line workflows for computational mass spectrometry, covering feature detection, peptide identification, and LC-MS/MS data quantification.

Does the FDR script validate protein-level identifications?

No, the --fdr routine estimates error rates for peptide-spectrum matches and unique peptides, so protein inference requires a separate workflow.

See also

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