We conducted proteomic and phosphoproteomic profiling of two widely used Parkinson’s disease (PD) mouse models: the neurotoxin-based MPTP model and the α-synuclein preformed fibril (PFF) inoculation model. Tissues from substantia nigra and cerebellum were collected for multi-omics analysis to uncover region-specific protein expression and phosphorylation changes associated with PD pathogenesis.