maxquant-processor

# 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)