A method for global analysis of complex proteomes using sample prefractionation by solution isoelectrofocusing prior to two-dimensional electrophoresis

Two-dimensional electrophoresis is a critical technique for proteome resear ch, but currently available methods are not capable of resolving the >10,00 0 protein components in most eukaryotic proteomes. We have developed and de monstrated the utility of a novel solution isoelectrofocusing device and me thod that can reproducibly prefractionate cell extracts into well-defined p ools prior to 2D PAGE on a scale directly compatible with the high sensitiv ity of proteome studies. A prototype device was used to separate metabolica lly radiolabeled Escherichia coli extracts in method optimization and proof -of-principle experiments. Samples were loaded into separation chambers div ided by thin polyacrylamide gels containing immobilines at specific pH valu es and isoelectrically focused for several hours, which resulted in well-re solved fractions. Total recoveries in the fractionated samples were greater than 80% and most protein spots in the original sample were recovered afte r this prefractionation step. Nonideal behavior (precipitation/aggregation) , typically encountered when unfractionated samples at high protein loads w ere applied directly to either narrow- or broad-range IPG gels, was dramati cally reduced. Hence this approach allows increases in overall protein load s, resolution, and dynamic detection range compared with either alternative prefractionation methods or direct use of parallel narrow pH range gels wi thout sample prefractionation. The pH ranges and number of fractions can be readily adapted to the requirements of specific types of samples and proje cts. This method should allow quantitative comparisons of at least 10,000 p rotein components on a series of narrow pH range gels, and protein detectio n limits are estimated to be 1000 molecules per cell when mammalian proteom es are fractionated into five or more pools. (C) 2000 Academic Press.