In this comparative proteomic analysis, we focused on proteins in the nuclear fraction. As the nucleus is the epicenter of DNA uptake, transcription, capsid assembly and packaging. Three HEK-293 cell samples i) not transfected, ii) MOCK plasmid transfected, and iii) triple-transfected with rAAV2-production plasmids were harvested 24 h and 72 h after transfection. In total 3384 proteins in all samples were identified revealing regulated proteins due to transfection and rAAV production.