> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# matchms — AI agent skill for life sciences

> Process, clean, compare, and search tandem mass spectra with matchms.

# `matchms`

> Process, clean, compare, and search 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.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** Apache-2.0 · **Version:** 2.1

## Install

```bash theme={null}
npx research-agent-skills install matchms
npx skills add KalarisLabs/research-agent-skills --skill matchms
```

## When to use it

Process, clean, compare, and search 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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/matchms/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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