The total cellular proteins from each biological replicate were equally divided into three aliquots, which were used as three independent technical replicates for the LC-MS/MS runs. For tryptic digestion and iTRAQ labeling, an aliquot of each protein sample containing ∼100 μg of total cellular proteins was adjusted to a 100-μL final volume using the RIPA lysis buffer. A final concentration of 10 mM of tris (2-carboxyethyl) phosphine (TCEP) was added to each protein sample, which was then incubated at 37 °C for 1 h. Afterward, iodoacetamide was added at a final concentration of 40 mM, and the protein solution was incubated for 40 min at room temperature shielded from light. Subsequently, prechilled acetone was added to the protein solution in a ratio of 6:1 and precipitated at −20 °C for 4 h. After centrifugation (10 000g, 4 °C) for 20 min, the precipitate was dissolved with 100 μL of 100 mM triethylammonium bicarbonate (TEAB). The processed protein samples were digested with 2 μg/μL of trypsin overnight at 37 °C. Following tryptic digestion, the generated peptides were dried by vacuum centrifugation, and redissolved with 20 μL of 0.5 M TEAB. The prepared peptides were then labeled with an iTRAQ reagents-8 plex kit (AB Sciex, Foster City, CA, USA) as per the manufacturer’s protocol. Briefly, the three independent biological replicates of mock-infected cellular samples were each labeled with iTRAQ-113, iTRAQ-114, and iTRAQ-115; the three independent biological replicates of PDCoV-infected samples were each labeled with iTRAQ-116, iTRAQ-119, and iTRAQ-121. All the labeled samples of each group were mixed with an equal amount, and then fractionated using an ACQUITY ultra performance liquid chromatography (UPLC) system (Waters Corp., Milford, MA, USA) combined with an ACQUITY UPLC BEH C18 column (300 Å, 1.7 μm, 2.1 mm × 150 mm). Finally, a total of 10 fractions of each group were collected. After merging two fractions of each group into one, the pooled 10 fractions were dried by using a rotary vacuum concentrator.