Global Proteome Analysis Using High Throughput Top Down Proteomics

Abstract

Although the more widely used proteomic strategy has typically been peptide-based, unambiguous characterization of protein sequence and post-translational modifications (PTMs) can also be achieved through the analysis of intact proteins. In the past, however, the field of top down proteomics has not been achieved in a high throughput, comprehensive proteomic analysis. This was attributed to underdevelopment in separations, MS instrumentation and bioinformatics. Recently, our lab has made efforts in improving these three areas with goals of achieving high throughput Top Down proteomics with online detection and identification. We now show that using a multiplexed two-dimensional liquid electrophoretic platform coupled to LC-LTQ-FTMS affords the opportunity to achieve unprecedented proteome coverage using the Top Down methodology.