MaxQuant

MaxQuant: Transforming Proteomics Data Analysis

MaxQuant has established itself as an essential tool in the proteomics research community, providing researchers with sophisticated algorithms and user-friendly interfaces for processing complex mass spectrometry data.

Core Functions

1. Data Processing Primary Features:

• Raw data analysis
• Peak detection
• Mass recalibration
• Peptide identification
• Protein quantification
• PTM analysis

2. Quantification Methods Support for:

• Label-free quantification
• SILAC
• TMT/iTRAQ
• Label-based methods
• Absolute quantification
• XIC-based quantification

Key Capabilities

1. Analysis Workflow Processing Steps:

• Raw file processing
• Feature detection
• Database searching
• Quantification
• Statistical analysis
• Result visualization

2. Advanced Features Specialized Tools:

• Match-between-runs
• PTM scoring
• De novo sequencing
• Ion mobility support
• Cross-linking analysis
• Machine learning integration

Research Applications

1. Discovery Proteomics

• Protein identification
• Expression analysis
• PTM mapping
• Interaction studies
• Biomarker discovery

2. Targeted Analysis

• Selected reaction monitoring
• Multiple reaction monitoring
• Parallel reaction monitoring
• Peptide quantification
• Protein validatio