Escherichia coli protein lysate was prepared using the 2-D Clean-Up Kit. As a direct result of employing 2-D Clean-Up Kit for sample preparation, increases in labeling efficiency and abundance of several proteins were observed when analyzed using Ettan™ DIGE. Two of these proteins were identified by tandem mass spectrometry and were shown to be isoforms of a membrane protein that is normally difficult to isolate using conventional 2-D gel electrophoresis.