Indeed, the development of two-dimensional (2-D) electrophoresis technology has provided an important research tool for comparative proteomics. A number of other technologies for protein separation have also been investigated in the last few years, such as protein chips, liquid chromatography, and high-pressure liquid chromatography, to name just a few. However, 2-D gels are still considered the workhorse among research laboratories willing to accurately track changes in protein expression and to achieve differential proteomics. The unlimited possibilities of 2-D applications, such as finding targets for drug treatments or biomarkers for medical diagnostics and prognostics, have been a major incentive to the development of specialized software systems. Their major utilities are to accurately detect and quantify protein spots over the gels, to find corresponding proteins across gels, to highlight significant protein expression changes, and to statistically validate the variability found.