matchms (Claude Skill)

Spectral similarity and compound identification for metabolomics.

   
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 (Apache-2.0)
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/matchms-spectral-matching 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 matchms 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/matchms ~/.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

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.

Primary use cases: comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries.

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: Apache-2.0. The skill name to enable after install is matchms.

Sources

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