Analysis of protein patterns during differentiation using 2‐D electrophoresis and computer multidimensional classification

We describe the application of a general method of comparing and sorting the patterns of protein expression obtained from two‐dimensional (2‐D) electrophoresis of a mixture of proteins. The method involved the use of two multidimensional classification programs and was applied, first, to the comparison of the protein patterns expressed at different stages during nymphal differentiation of imaginal wing discs in the insect Pieris brassicae. Comparison of these stages was based on the similarity of protein expression. The technique used allowed processing of all the information visible on a gel and took into account the variations in most of the spots labeled. Two qualitatively different stages of protein expression were found during the nymphal stage, and fine variations not revealed by any other method were shown to exist in genetic programing. Next, the method was applied to sorting the different polypeptides expressed; this was also done on the basis of their similarity of expression. We were able to characterize three groups of related peptides with common regulation features and apparently common physicochemical characteristics. The complete map of the most highly correlated peptides, which may constitute subunits of the same protein, was constructed by the programs, thus permitting fast rational analysis of protein expression. The clinical applications of these classification techniques are discussed.