To study the functional effects of SARS-CoV-2 infection and possible differences between the VOCs, we quantified the differences in the total and phosphorylated proteomes (phosphoproteomes) at different time points of infection (1 hpi, 8 hpi, 16 hpi, 36 hpi) in VeroE6-TMPRSS2-H10 cells using a Data-Independent Acquisition combined with Parallel Accumulation Serial Fragmentation (DIA-PASEF) quantitative proteomics analysis pipeline (Fig. 1b). Here, TMPRSS2 is linked to infection.