Amino acid analysis of proteins separated by two-dimensional electrophoresis in maize: Isoform detection and function identification

The possibility of using experimentally determined amino acid composition to assess relatedness between 75 proteins separated by two-dimensional electrophoresis (2-DE) and to identify them was tested on maize. Two independent parameters, the relative Euclidean distance and the correlation coefficient between the amino acid compositions, were evaluated and used. Previous sequence information for 31 out of the 75 proteins made it possible to evaluate the method for the detection of isoforms and for identification. However, the extension of the interrogation beyond maize to all plant sequences raised the problem of false positives that could nevertheless be limited by replications and by using additional information. The efficiency of the method to assess relatedness between proteins should make amino acid composition analysis a valuable tool in large protein characterization programs based on 2-DE, by facilitating the transfer of information from one well-documented organ/tissue or genotype to another.