Two-dimensional SDS-PAGE fractionation of biological samples for biomarker discovery

Abstract

Two-dimensional electrophoresis is still a very valuable tool in proteomics, due to its reproducibility and its ability to analyze complete proteins. However, due to its sensitivity to dynamic range issues, its most suitable use in the frame of biomarker discovery is not on very complex fl uids such as plasma, but rather on more proximal, simpler fl uids such as CSF, urine, or secretome samples. Here, we describe the complete work fl ow for the analysis of such dilute samples by two-dimensional electrophoresis, starting from sample concentration, then the two-dimensional electrophoresis step per se, ending with the protein detection by fl uorescence.