Chronic kidney disease (CKD) is the leading cause of mortality in aged cats. After injury, feline kidneys undergo extensive metabolic reprogramming, but a comprehensive evaluation is lacking. Integration of serum metabolome from early stages, late stages CKD and healthy control cats with renal cortex and medulla transcriptome and proteome can reveal spatiotemporal patterns of gene and protein expression changes. In this study, we conducted mass spectrometry (MS)-based proteomic analysis of kidney (cortex and medulla) tissues from cats with CKD and control cats, euthanized for humane reasons unrelated to the study.