Current Approaches on Viral Infection: Proteomics and Functional Validations

Zheng, Jie; Tan, Boon Huan; Sugrue, Richard; Tang, Kai

In recent decades, the field of virology is rapidly expanding with the advances of high throughput genome sequencing and proteome screening technologies. To date, the numbers of complete viral genomes and proteomes that cover 118 taxonomy groups have reached to 2853 and 1932 in the NCBI and Uniprot databases, respectively 1,2 . As these databases expand, the 1 http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&opt= Virus 2 http://www.uniprot.org/taxonomy/?query=virus+AND+reviewed% 3ayes&offset=250 daunting challenge still lies in illustrative delineation of sophisticated pathogen-host interactions or virus-hijacked signaling pathways. Advancements in mass spectrometry (MS) based proteomics have tremendously facilitated the investigations of viral proteomes as well as host responses associated with viral infections. Several popular MS based approaches have been applied to study viruses and their hosts ( Table 1) . These include 2D gel, tandem affinity purification (TAP), co-immunoprecipitation (Co-IP), and quantitative stable isotope labeling strategies, such as isotope coded affinity tag (ICAT), isobaric tag for relative and absolute quantitation (iTRAQ), and stable isotope labeling of amino acids in cell culture (SILAC) . Others developed novel approaches such as HLA peptidome scanning chips to study host responses upon virus infection (Zheng et al., 2011) . These MS based proteomic approaches are capable to explore from individual binding partners to quantitatively altered proteomes upon virus infections. Moreover, two other MS based approaches developed to study protein-protein interactions (PPIs) and protein conformational changes have also contributed to virology studies. These are chemical cross-linking and hydrogen/deuterium exchange (HDX) based MS methodologies.