Proteomics data generated after in-gel trypstic digestion of whole cell or extracellular vesicle proteins. Mass spetrometer used was a Thermo Scientific Quadrupole-orbitrap Qexactive coupled to a NanoLC reverse phase separation via electrospray ionisation. We used a proteomic approach to provide a complete protein characterization of S. aureus N315 and its derived EVs in RPMI supplemented with 10% LB.