To validate the obtained LC-MS/MS data, qPCR was performed to evaluate the transcription levels of two randomly selected DEPs, the downregulated ANAPC7 and the upregulated IFIT1. To this end, IPEC-J2 cells were mock-infected or infected with PDCoV at an MOI of 0.1. At 24 hpi, total cellular RNA was extracted from the cells and subjected to qPCR assays. As shown in Figure 2A, the level of mRNA encoding ANAPC7 and IFIT1 proteins was significantly downregulated and upregulated in PDCoV-infected cells, respectively, as compared to the mock-infected cells (p < 0.05). The qPCR results were in agreement with the MS data which were acquired by the iTRAQ approach (Figure 2B). For further confirmation of the proteomic data, the expression level of ANAPC7 and IFIT1 proteins in IPEC-J2 cells, which were infected exactly as the aforementioned conditions, was also tested by Western blot analysis. To track the progression of PDCoV infection, the mAb 1A3 that specifically recognizes PDCoV was utilized. As shown in Figure 2C, compared with the mock-infected IPEC-J2 cells, PDCoV significantly decreased the expression of ANAPC7 protein and its relative ratio to β-actin in the cells, whereas the expression of IFIT1 protein and its relative ratio to β-actin in the cells were significantly increased as a consequence of PDCoV infection. The original images of the entire PVDF membranes containing the target Western blots were included in Supplementary Figure S2. The Western blot results were also consistent with the MS data (Figure 2D). Taken together, these experimental results reveal that our quantitative proteomics data are quite reliable.