Individual skill
pyopenms-skill
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.
scientific-skills/Data Analysis/pyopenms-skill/SKILL.md
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- Last checked
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- Sep 17, 2026
- License
- MIT
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
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- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- engineering Derived category
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SKILL.mdcore · 3,414 bytesSKILL.mdcore · 3,414 bytesSKILL.mdcore · 3,414 bytesSKILL.mdcore · 3,414 bytespyopenms-skill_audit_result_v1.jsonasset · 12,462 bytesreferences/file_io.mddoc · 563 bytesreferences/signal_processing.mddoc · 642 bytesscripts/process_ms.pyruns · 1,564 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](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.