- Differential In-Gel Electrophoresis is a method of comparing the relative abundace of proteins in two or more samples. Samples are labelled with fluorescent dyes, combined and separated by gel electrophoresis (usually in two dimensions - isoelectric point (pI) and mass). The same protein from different samples will co-migrate on the gel. The gel can then be scanned under exposure to the wavelength activating each fluorescent dye, recording the intensity of the fluorescence in each protein spot. This allows the relative abundance of a protein in the inital samples to be quantified. Usually, protein spots with differential abundance are exised from the gel for identification by Tandem-MS.