Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill matchmsnpx skills add K-Dense-AI/scientific-agent-skills --skill matchms -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill matchms -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/matchmsgh skill install K-Dense-AI/scientific-agent-skills matchmsgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/K-Dense-AI__scientific-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/matchms ~/.claude/skills/matchms # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/matchms ~/.agents/skills/matchms # Codex, Cursor, Gemini CLI, Copilot, OpenCode