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