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)