Fluorescent dual colour 2D-protein gel electrophoresis for rapid detectionof differences in protein pattern with standard image analysis software

The use of two different fluorescent dyes in two-dimensional (2D) polyacryl amide gel electrophoresis was recently described and termed difference gel electrophoresis (DIGE). Thereby differences between protein samples could b e accomplished by fluorescently tagging the samples with different dyes as weil as co-separation and visualisation in a single gel. We adapted this me thod to the ampholyte technique, using newly available fluorescent dyes and three common image software systems for analysis. Working with protein lys ates from tumour cell lines with defined added proteins we found that the t echnique is reproducible, sensitive and fast, because it circumvents the ne cessity of matching several 2D gels. This is mainly due to the fact that th e generated images from the two different fluorescent channels could be sup erimposed by standard image analysis, so that changes in the protein patter n could be easily detected either by a different colour or by comparing gre y values of corresponding spots. This method will be especially helpful in comparing proteins from normal and tumour tissue to highlight changes in ge nesis and progression in cancer.