Proteoform Identification in 2D Electrophoresis Maps by Using Isoelectric Point Prediction

The possibility of identifying specific protein proteoforms with post-translational modifications (PTM) by analyzing two-dimensional (2D) gel electrophoresis maps and using the prediction of the isoelectric point of proteins (pI) has been investigated. The pI values were predicted using the pIPredict 3 program, supporting a wide range of chemical and post-translational modifications. Eleven 11 proteins (albumin, alpha-1-microglobulin, annexin A2, apolipoprotein E, gastric triacylglycerol lipase, mitochondrial isocitrate dehydrogenase, clusterin, plasmin, prothrombin, endoplasmic reticulum chaperone, S-adenosylmethionine synthase type 1) identified on six 2D electrophoresis maps were used as examples. Various options for selecting hypotheses are considered. These take into consideration the following available information about a particular protein: possible modification sites, processing features, variability of the amino acid composition. The obtained results indicate that the use of predicting the pI value for proteins with hypothetical PTMs can form a set of hypotheses about specific proteoform occurrence on 2D electrophoresis maps.