The recent introduction of two-dimensional fluorescent difference gel electrophoresis has enabled the large screening of differential protein expression levels with higher confidence and greater sensitivity than using the classical two-dimensional electrophoresis approach. With this technology, multiple protein samples can be labeled with up to three fluorescent dyes. These labeled protein samples are mixed and applied on the same two-dimensional electrophoresis gel, subsequently scanned, and analyzed by specialized software. The possibility to run two or more protein samples on a single gel as well as the introduction of an internal standard on each gel drastically reduces the gel-to-gel variability and results in higher levels of certainty with regard to the differential character of the expressed proteins.