Cell pellets were lysed directly (8 M urea, 100 mM ammonium bicarbonate (ABC), 150 mM NaCl, protease inhibitor (mini-cOmplete, Roche) and phosphatase inhibitors (phosSTOP, Roche), and protein digestion and phosphopeptide enrichment was performed as described above for SARS-CoV-2 infected Vero E6 cells.