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)