MatchMS — Mass Spectrometry Processing

What it does

MatchMS provides a Python-centric toolkit for processing and comparing mass spectrometry spectra. It enables importing spectra from mzML/MGF/MSP formats, harmonizing metadata, applying peak filters and quality controls, calculating spectral similarity scores (cosine, modified cosine, fingerprint-based), and building reproducible processing pipelines for metabolomics workflows.

When to use it

Use this skill when working with mass spectrometry datasets that require cleaning, normalization, metadata harmonization, or when you need to compare unknown spectra against reference libraries. It's suitable for metabolomics research, library curation, and batch spectral matching tasks.

What's included

• Scripts: no top-level scripts in this SKILL.md, but the repo includes a references/ directory with detailed docs (has_references=true)
• References: importing/exporting, filtering, similarity metrics, and workflow examples in the references folder
• Instructions: code snippets demonstrating import/export, filter chains, spectrum object usage, and similarity computations with example pipelines.

Compatible agents

Works well with code-capable agents (Python execution or code generation) such as Codex, Claude Code, or Cursor that can generate or review data-processing scripts and pipelines.