CORRELATION OF ACIDIC AND BASIC CARRIER AMPHOLYTE AND IMMOBILIZED PH GRADIENT 2-DIMENSIONAL GEL-ELECTROPHORESIS PATTERNS BASED ON MASS-SPECTROMETRIC PROTEIN IDENTIFICATION

Separation of proteins on either carrier ampholyte-based or immobilize d pH gradient-based two-dimensional (2-D) gels gives rise to electroph oretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrom etry (MALDI-MS) to determine the identities of 335 protein spots in th ese two 2-D gel systems, including a substantial number of basic prote ins which had never been identified before. Proteins that were identif ied in both gel systems allowed us to crossreference the gel patterns. Vector analysis of these cross-references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel syste m can be used to predict its mobility in the other. Thus, as laborator ies adopt the immobilized pH gradient-based 2-D gel systems, the only reliable means of translating the data gained with the carrier ampholy te-based gel system is to positively identify the proteins in both 2-D systems.