MAPDIA

MAPDIA performs statistical analysis of differential protein expression using fragment-level intensities from Data Independent Acquisition (DIA) mass spectrometry.

Key Features:

• Intensity Normalization: Provides total intensity sum normalization and local intensity sum normalization in retention time space to adjust fragment-level intensities across samples.
• Peptide/Fragment Selection: Identifies and retains peptides and fragments that preserve major quantitative trends while removing outlier observations across samples.
• Statistical Analysis: Implements hierarchical model-based statistical significance analysis for protein-level differential expression, supporting multi-group comparisons and control of false discovery rates using selected peptides and fragments.

Scientific Applications:

• Simulation Validation: Validated on comprehensive simulation datasets to assess detection of differentially expressed proteins.
• 14-3-3β Dynamic Interaction Network: Applied to DIA datasets characterizing the 14-3-3β interaction network and its dynamics.
• Prostate Cancer Glycoproteome: Applied to DIA datasets to analyze proteomic alterations in the prostate cancer glycoproteome.

Methodology:

The workflow comprises normalization of fragment-level intensities (total and local intensity sum in retention time space), peptide/fragment selection with outlier removal and trend preservation, and hierarchical model-based statistical significance analysis for multi-group protein-level differential expression with false discovery rate control.