It is known that influenza A virus infection triggers the production of IFN-a/b which is followed by the activation of IFN-inducible genes. Accordingly, a clear increase in the expression of several interferon-inducible proteins was seen in the cytoplasmic fraction of influenza A virus infected macrophages (Table S1 ). These proteins included three members of the interferon-inducible protein with tetratricopeptide repeat (IFIT) family, a group of proteins functioning as antiviral sensors that inhibit protein synthesis through translational arrest. Finally, the expression of several influenza A virus proteins such as hemagglutinin (HA), neuraminidase (NA) and nucleoprotein , cytoplasmic (C) and nuclear (N) fractions using mitochondrial, cytoplasmic and nuclear markers (voltage-dependent anion-selective channel protein 1 (VDAC1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and histone H1, respectively). C. Numbers of reliably quantified and differentially regulated proteins (fold difference $1,5 or #0,67 for intracellular fractions and $3 for secretome) in each subcellular fraction and secretome at different timepoints. D. Gene ontology-based classification of all the proteins identified from intracellular fractions. Mitochondrial, cytoplasmic, nuclear, lysosomal and endoplasmic reticulum (ER) annotations for the identified proteins are shown. doi:10.1371/journal.ppat.1001340.g001 (NP) was clearly increased in the cytoplasmic fraction of the infected cells (Table S1 ).