Method and Software Workflow for Integrating Paired CE-MS and LC-MS Bottom-up Proteomics Data from SDS-PAGE Pre-fractionated Samples

摘要

Because SDS-PAGE fractionation is orthogonal to both RPLC and CE separations, it can be combined with either RPLC-MS or CE-MS, or both for even larger proteome coverage. The scientific workflow presented here was designed to process data obtained in such experiments and produce simple and clear figures for a quick overview of the results. In our 24 + 24 datasets we found that RPLC-MS and CE-MS are complementary in peptide identification; based on hydrophobicity and molecular weight. The scientific workflow is general in purpose; it can be used for comparison of two sets of SDS-PAGE fractionated samples. This can be a comparison of two different samples analyzed by the same second dimension strategy, comparison of different protein extraction strategies, or even to investigate consistency between replicates.