Using quantitative proteomics, we have globally profiled ubiquitination in SNpc tissue of a Parkinson's disease transgenic mouse model (A30P*A53 T α-synuclein, hm<sup>2</sup>α-SYN-39 mouse strain) at pre-symptomatic stage; Our datasets of 3,971 ubiquitination sites in 1,595 proteins provide valuable insight into pre-symptomatic Parkinson's disease.