pyopenms-skill

name	pyopenms-skill
description	Comprehensive tool for computational mass spectrometry using PyOpenMS; use when you need to read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope features, or perform peptide identification in proteomics/metabolomics workflows.
license	MIT
author	AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

• Converting, validating, or batch-processing mass spectrometry files (e.g., mzML, mzXML, MGF) as part of a pipeline.
• Cleaning raw spectra before downstream analysis (smoothing, baseline correction, denoising, peak picking).
• Detecting and linking isotope patterns / features for proteomics or metabolomics feature tables.
• Running identification-oriented steps where peptide/protein identification integration is required.
• Building custom computational MS workflows in Python while leveraging OpenMS algorithms.

Key Features

• MS File I/O: Read/write common MS formats (mzML, mzXML, MGF).
• Signal Processing: Smoothing, baseline correction, filtering, and peak picking.
• Feature Detection: Isotope pattern detection and feature linking utilities.
• Identification Support: Hooks for peptide identification workflows via OpenMS-compatible components.