In the present study, we used data-independent acquisition mass spectrometry (DIA-MS) to analyse the protein expression in Calu-3 cells infected with SARS-CoV and SARS-CoV-2 over the time-course of 24 hours. About 8400 proteins were identified, from which about 90% could be quantified across the experiment. This results in a deep and comprehensive proteome map, which reflects time-dependent protein expression changes during SARS-CoV and SARS-CoV-2 infections and provides deep insights into the virus-specific immunmodulation of human lung cells.