The data set consists of 32 S. aureus cytosolic samples that were collected by GFP supported cell sorting during infection in lung epithelial cells. The data include 8 time points (2.5 h, 6.5 h , 24 h, 48 h, 72 h, and 96 h post infection plus exponential and non-adherent control) that were collected out of four biological replicates. DIA data are provided. The respective spectral library was already published (Michalik et al., 2017, Sci Rep. doi: 10.1038/s41598-017-10059-w.