Updated project metadata. Caco-2 cells were mock-infected or infected with SARS-CoV-2 patient isolates (in biological quintruplicates) for one hour, washed, and incubated for 24 hours before cell harvest. Extracted proteins were digested and split to 1) carry out whole-cell proteomics of a tandem mass tag (TMT) 10-plex samples using liquid chromatography synchronous precursor selection mass spectromety (LC-SPS-MS3), or 2) use Fe-NTA phosphopeptide enrichment (achieving 98% enrichment) for phospho proteome analyses of a TMT 10-plex analyzed by LC-MS2 First 5 channels = control Last 5 channels = infected