Quantification of differentially expressed active proteins after virus infection is essential for better analysis of results, particularly when examining enzymes. It is difficult to compare the altered serine hydrolases between healthy and infected samples by simply visualizing gel images or merely by mass spectrometry. To address this problem an advanced quantitative mass spectrometry-based method called ABPP-SILAC (stable isotope labeling with amino acid in cell culture) has been used to identify alterations in the levels of active enzyme targets (Everley et al., 2007) and in small molecule-binding proteins in cell lysates (Ong et al., 2009) . Comparative ABPP -SILAC can be used to quantify more accurately the intricate changes in host proteins caused by viral infection. Similarly, competitive ABPP-SILAC is valuable to identify inhibited enzymes during global screening of inhibitors.