Columbia University, all rights reserved.
Quantitative Proteomics Center
Department of Biological Sciences
Such a gel can then be subjected to image analysis and protein spots are excised from the gel and processed. These proteins can be identified by a combination of mass spectrometry and database searching, and in many cases hundreds of proteins of interest are identified:
In difference gel electrophoresis (DIGE), two or more protein samples are labeled with different cyanine dyes and then separated by 2D gel electrophoresis. A laser fluorescence image is recorded which is composed of two sub-images; these overlap completely on a pixel-to-pixel basis. Differentially expressed proteins are easily detected in such an image, as in this example where the two sub-images are alternately flashed on the screen and the differentially expressed proteins appear in only one or the other sub-image:
In an enhanced version of this technique , the protein samples to be compared are labeled with different cyanine dyes and subsamples are also mixed with an internal standard in which all protein extracts in the experiment are pooled and labeled with a third dye.  The overall workflow for this technique is illustrated in this diagram:
This technology has been applied to basic, applied and clinical research supporting studies of cell and microbial cultures, animal, plant and human tissues (Lilley and Friedman, 2004; Marouga et al., 2005). Interest in this technique has steadily increased since it was first described by Minden’s group at Carnegie-Mellon (Unlu and Minden, 1995; Unlu et al., 1997). Also see examples of the application of this technique in our publications.

References
        
Lilley KS, Friedman DB (2004) All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Review of Proteomics 1:401-409.
        Marouga R, David S, Hawkins E (2005) The development of the DIGE system: 2D fluorescence difference gel analysis technology. Analytical and Bioanalytical Chemistry 382:669-678.
        Unlu M, Minden J (1995) DIFFERENCE GEL-ELECTROPHORESIS. Molecular Biology of the Cell 6:2596-2596.
        Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 18:2071-2077.
Here are some examples of studies that we have done with this technique: