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name: maxquant-processor description: MaxQuant mass spectrometry skill for protein identification and quantification allowed-tools:

• Read
• Write
• Glob
• Grep
• Edit
• WebFetch
• WebSearch
• Bash metadata: version: "1.0" category: bioinformatics tags:
  • proteomics
  • mass-spectrometry
  • quantification
  • identification graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:statistical-analysis, skill-area:python-data-pipelines, skill-area:data-analysis] workflows: [workflow:experiment-design] roles: [role:research-scientist, role:lab-technician]

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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)