Table 1.

A summary of proteomic techniques and their applications in virology.

Mass spectrometry based proteomic approaches	Main applications in virology	Relevant reference
Tandem affinity purification based MS approach	Protein–protein interactions	Jorba et al. (2008), Mayer et al. (2005), Mayer et al. (2007)
Co-immunoprecipitation based MS approach	Binding partners of target protein	Moresco et al. (2010), Noisakran et al. (2008)
HLA peptidome scanning chip based MS approach	Searching for disease related peptides or differently expressed proteins after virus infection	Herberts et al. (2003), Wahl et al. (2010)
Isotope coded affinity tag (ICAT)		Yan et al. (2004), Booy et al. (2005)
Isobaric tag for relative and absolute quantitation (iTRAQ) Stable isotope labeling of amino acids in cell culture (SILAC) Difference gel electrophoresis (DIGE)	Mapping differently expressed proteins in host proteome upon virus infection	Zhang et al. (2009), Chen et al. (2008) Dreger et al. (2009), Hammond et al. (2010) Pastorino et al. (2009), Sun et al. (2011a)
Cross-linking based MS approach	Investigating protein-nucleotides binding sites	Deval et al. (2007), Bhardwaj et al. (2008)
Hydrogen/deuterium exchange (HDX) based MS approach etc.	Conformational dynamics of host or viral proteins	Lisal et al. (2005), Monroe et al. (2010)