Viral proteomics: The emerging cutting-edge of virus research

Zhou, ShengTao; Liu, Rui; Zhao, Xia; Huang, CanHua; Wei, YuQuan

Compared with eukaryotic cell proteomes, virus proteomes are simple and highly conserved. However, relatively few virion proteomes have been characterized to date. Conventionally, determining the global protein composition of a specific virus particle involves pure virus preparation, detergent denaturation, electrophoretic separation, and identification of protein bands by immunoblotting or by se-quencing with Edman degradation [7] . In recent years, new approaches that utilize a combination of techniques have provided potent tools for virion research. Two-dimensional electrophoresis (2DE) coupled with identification of protein spots using mass spectrometry, also termed "the shotgun approach", has generated robust amounts of virus protein information. Another novel viral proteomics strategy is based on the analysis of differential enzymatic digestions of whole virions, or solubilized and deconvoluted virion proteins. The protein extracts thus obtained are fragmented into peptides that are further separated by 1D or multidimensional liquid chromatography (LC), and analyzed by MS. Both technologies require subsequent database search algorithms to define peptide fragmentation patterns and the corresponding proteins, and require specialized bioinformatics analysis. These techniques have been confirmed to be useful for the exploration of virion proteomes (Table 1 ).