The emergence of bacterial pathogen resistance to common antibiotics strongly supports the necessity to develop alternative mechanisms for combating drug-resistant forms of these infective organisms. Currently, few pharmaceutical companies have attempted to investigate the possibility of interrupting metabolic pathways other than those that are known to be involved in cell wall biosynthesis. Bacterial proteases have been showed to play an important role during infection and their inhibitors can retard the growth, proliferation and invasion of bacterial pathogens. To separate and identify these proteases, we have developed a specific, sensitive assay in SDS-polyacrylamide gels after 2D electrophoresis. This method allows simultaneous determination of protease cleavage specificity, molecular weight, isoelectric point, and if necessary, amino acid sequencing.