pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
Target: Data analysis. Automatically collected · unverified.
Excerpt from the author’s documentation
Extracted from a fixed version of SKILL.md in its original language. This is the author’s documentation; installation, compatibility and runtime results have not been verified by this site.
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Topics in the source
- PyOpenMS
- Overview
- Installation
- Core Capabilities
- 1. File I/O and Data Formats
- 2. Signal Processing
- 3. Feature Detection
- 4. Peptide and Protein Identification
PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use for handling mass spectrometry file formats, processing spectral data, detecting features, identifying peptides/proteins, and performing quantitative analysis. Install using uv: Verify installation: PyOpenMS organizes functionality into these domains: Handle mass spectrometry file formats and convert between representations. Supported formats: mzML, mzXML, TraML, mzTab, FASTA, pepXML, protXML, mzIdentML, featureXML, consensusXML, idXML Basic file reading: For detailed file handling: See references/fileio.md Process raw spectral data with smoothing, filtering, centroiding, and normalization. Basic spectrum processing: For algorithm details: See references/signalprocessing.md Detect and link features across spectra and samples for quantitative analysis. For complete workflows: See references/featuredetection.md Integrate with search engines and process identification results. Supported engines: Comet, Mascot, MSGFPlus, XTandem, OMSSA, Myrimatch Basic identification workflow: For detailed workflows: See references/identification.md Per
This is an excerpt. Refer to the complete source and its current requirements.
- Source repository
- davila7/claude-code-templates
- Source file
- cli-tool/components/skills/scientific/pyopenms/SKILL.md
- Fixed revision
- 21be197f100a12b8d0dd9a211cc244c8179f84d3
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This record was collected automatically. Its documentation, suitability and runtime behavior have not been manually verified.
Author: davila7/claude-code-templates · original repository metadata. Documentation review: Not reviewed. Last source check: 2026-11-09T15:01:40.298Z.
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