We investigated the relative quantification of proteins in hippocampal cytosolic and nonsynaptic mitochondrial (NSM) fractions of rats exposed to chronic social isolation (CSIS), an animal model of depression, comparing CSIS-resilient with CSIS-sensitive or control rats, via a comparative subproteomic study. Our aim was to characterize the subproteome changes representing potential long-term changes in protein expression underlying the aforementioned conditions.