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maxquant-processor

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MaxQuant mass spectrometry skill for protein identification and quantification

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How to use this skill

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  2. Copy the prompt below and paste it into your agent.
  3. Review the proposed files and risks before you approve installation.
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I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/bioinformatics/skills/maxquant-processor/SKILL.md

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Copying this prompt does not install or run the skill. Review third-party files before use. Codex skill guide

MaxQuant Processor Skill

Purpose

Provide MaxQuant mass spectrometry analysis for protein identification and quantification.

Capabilities

  • Andromeda search engine execution
  • Label-free quantification (LFQ)
  • TMT/iTRAQ labeled quantification
  • Match between runs
  • FDR control and filtering
  • PTM site localization

Usage Guidelines

  • Configure search parameters for experiment type
  • Select appropriate quantification method
  • Enable match between runs for improved quantification
  • Apply FDR filtering at protein and peptide level
  • Localize PTM sites accurately
  • Document database and parameter versions

Dependencies

  • MaxQuant
  • MSFragger
  • Proteome Discoverer

Process Integration

  • Mass Spectrometry Proteomics Pipeline (ms-proteomics-pipeline)
  • Multi-Omics Data Integration (multi-omics-integration)