Agent-Skills.md

Agent Skills: MaxQuant Processor Skill

MaxQuant mass spectrometry skill for protein identification and quantification

bioinformaticsID: a5c-ai/babysitter/maxquant-processor

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/maxquant-processor

Skill Files

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/maxquant-processor/SKILL.md

Skill Metadata

Name
maxquant-processor
Description
MaxQuant mass spectrometry skill for protein identification and quantification

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)