The ClpXP ATP-dependent unfoldase-protease complex plays important roles in maintaining protein homeostasis in the mitochondria. Pathogenic variants of CLPP have been identified in patients with Perrault syndrome type 3 (PRLTS3), a rare recessive mitochondrial disease characterized by sensorineural hearing loss, ovarian dysfunction, and neurological abnormalities. We performed proteomic analysis (DIA acquisition) of PRLTS3 patient-derived fibroblasts and in conjunction with other experiments, identified three novel substrates of ClpXP.