Abstract
RP-93 Comprehensive proteome analysis can be very challenging due to complexity and range of protein concentrations.Techniques such as 2D LC, pI-based fractionation and gel electrophoresis are typically employed to increase separation efficiency as a strategy for obtaining more peptide MS/MS spectra and thus increasing the number of proteins identified.Having a standard sample of moderate complexity facilitates comparison of different protein identification workflows.For this work, a complex proteomics standard consisting of a soluble extract from Pyrococcus furiosu was employed to evaluate the effectiveness of different fractionation schemes for increasing protein identification.The fractionation schemes evaluated included protein fractionation by 1D SDS-PAGE and RPLC as well as peptide fractionation by OFFGEL electrophoresis.A comparison of the proteins identified as well as the total number of proteins and peptides will be done for measuring the effectiveness and relative orthogonality of the different workflows.