Protein identification and quantification from each subcellular fraction and secretome was done using 4plex iTRAQ (isobaric tag for relative and absolute quantitation) labeling combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis (Fig. 1A) . A total of eight iTRAQ sample sets were analysed, including two biological replicates of mitochondrial, cytoplasmic and nuclear cell fractions as well as secretomes. Additionally, each iTRAQ sample set was analysed twice with LC-MS/MS to improve the quality of protein identifications and quantifications. Based on the LC-MS/MS data we identified 1999, 1423, 1230 and 627 proteins from the mitochondrial, cytoplasmic and nuclear cell fractions and secretome, respectively, with false discovery rates (FDR) of the sample sets varying from 0.5 to 1.6%. More than one thousand proteins were identified from more than one cell fractions and altogether we identified 3477 distinct proteins. From the identified proteins, we reliably quantified 2466 proteins, and of these proteins 1321 were differentially expressed in the intracellular fractions (fold difference $1.5 or #0.67) and 544 in the secretome (fold difference $3) as a result of infection ( Fig. 1C , Tables S1 and S2). To confirm iTRAQ quantification results, Western blot analyses were performed for a selected set of proteins ( Fig. S1A-D) .