LAC ratios for the Benzoylpaeoniflorin proteins in the cytoplasmic and nuclear extracts showed a symmetrical distribution around the normalized median value of 1 for both sets of proteins suggesting that there was no bias in the experimental approach used. There were 3858 proteins reliably quantified in total in both the nuclear and cytoplasmic fractions, of which 1361 proteins were common. Typically, an alteration in protein amount between fold has been considered significant. In this analysis we used protein ratio cut-off values of 1.5 and 2 fold to select proteins for further bioinformatic analysis. The majority of both the cytoplasmic and nuclear proteins quantified remained relatively unchanged during DENV-2 infection with 94.5% and 90% of proteins in the cytoplasmic and nuclear fractions respectively showing a #1.5 fold change in amount. In the cytoplasmic fraction 12 and 28 proteins showed 2 or 1.5 fold increases and 57 and 183 proteins showed 2 or 1.5 fold decreases respectively in DENV-2 infected cells compared to mock infected cells. By comparison, in the nuclear fraction, 13 and 82 proteins showed 2 or 1.5 fold increases and 44 and 125 proteins showed 2 or 1.5 fold decreases respectively in DENV-2 infected cells compared to the fraction from mock infected cells. In previous studies that used 2D SDS-PAGE to analyze the proteome of DENV infected cells, between 350 and 800 protein spots were detected, of which between 1 and 40 proteins were found to be significantly altered in amount in response to infection and Gentiopicrin subsequently identified by LC-MS/MS. The use of 2D difference gel electrophoresis for the analysis of West Nile virus infected Vero cells extended the amount of protein spots detectable to,2000 and led to the reliable identification of 93 proteins that were significantly altered in amount. A recent study that analyzed changes in the proteome of HeLa cells in response to infection with Japanese encephalitis virus by high throughput SILAC-MS analysis resulted in the identification and quantification of 978 and 1009 proteins in nuclear and cytoplasmic fractions of which 158 were significantly altered in amount. By contrast the use of high throughput SILAC-MS based protein quantification in this study resulted in the efficient quantification and identification of more than 3000 cellular proteins that neither changed nor significantly altered in amount during virus infection and over 400 proteins that altered in amount by.1.5 fold. Similarly to the 2D SDS-PAGE proteomic studies, this study showed that DENV-2 infection results in a significant change in only a small subset of proteins. Although a number of the proteins that were found to be altered in amount during infection in this study were detected in other studies the majority of differentially regulated proteins detected in previous 2D SDS-PAGE based analyses of DENV infected cells were found to be unchanged in this analysis. This may reflect the different cell types, virus strains and time of infection analyzed in other studies, as previous proteomic studies have also observed both commonalities and differences in the alteration of proteins in different cell types at different times after infection. Analysis of the SILAC ratios of the proteins found in both the nuclear and cytoplasmic fractions showed that overall.