Protein fractionation for proteomics using the SAINOME-plate

SUMMARY The SAINOME-plate consists of a 384-well plate and a cover that contains a cutter, which can cut a polyacryl-amide gel into approximately 4.5-mm square pieces following electrophoresis. In this study, we applied SDS-PAGE and the SAINOME-plate to fractionation of protein mixtures from cell extracts or serum for proteomic approaches. Compared with gel-fractionation using a cutter or a scalpel, SAINOME-plate gel-fractionation is simpler and higher-throughput. In terms of reproducibility of proteomic profiling, SAINOME-plate gel-fractionation was comparable to scalpel gel-fractionation. Additionally, human keratin contamination was lower with the SAINOME-plate than with a scalpel. In serum protein fractionation, the number of proteins identified increased approximately 2-fold and 3.7-fold relative to non-fractionation when the gel was divided into 8 and 96 fractions, respectively. The results demonstrate that the SAINOME-plate gel-fractionation will be a useful method in mass spectrometry-based proteomics.