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matchms

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Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows.

scientific-skills/Data Analysis/matchms/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

# Matchms Skill

## When to Use

- Use this skill when you need process, clean, and compare mass spectrometry (ms/ms) spectra with matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows in a reproducible workflow.
- Use this skill when a data analytics task needs a packaged method instead of ad-hoc freeform output.
- Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
- Use this skill when `scripts/similarity_pipeline.py` is the most direct path to complete the request.
- Use this skill when you need the `matchms` package behavior rather than a generic answer.

## Key Features

- Scope-focused workflow aligned to: Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows.
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