Table 2: Advantages and limitations of the two major proteomics approaches.

2D-DIGE Shotgun Proteomics (MudPit) Advantage Moderate costs for necessary equipment (separation phase) Good protein separation Industrialized work processes Almost all protein types analyzable Limitation Gel-based variability Hydrophobic (membrane) proteins difficult to measure Difficult quantification of low abundance proteins in complex protein mixes High costs for equipment