pyOpenMS (Claude Skill)

Complete mass spectrometry analysis platform.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — part of the actively maintained K-Dense scientific-agent-skills collection
Pricing Free / OSS (3 clause BSD)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/proteomics-protein-engineering/pyopenms-mass-spectrometry into ~/.claude/skills/).
  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the pyopenms skill when prompted. Works across Claude Code, Cursor, and Codex via the Agent Skills spec (requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/pyopenms ~/.claude/skills/

    Project-scoped alternative: copy into .claude/skills/ instead of ~/.claude/skills/. The skill declares its own Python dependencies in its SKILL.md; install them (the K-Dense skills generally use uv / pip) when prompted on first use.

What it does

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.

Primary use cases: proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines.

Notes

Distributed as a SKILL.md (plus code examples) in the K-Dense collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: 3 clause BSD. The skill name to enable after install is pyopenms.

Sources

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