The liver is a complex and unique organ responsible for a breadth of functions crucial to sustaining life, especially for various metabolic processes in its mitochondria. Senescence-accelerated mouse prone/8 (SAMP8), a widely used aging model, exhibits an oxidative stress-induced aging phenotype and severe mitochondria-related liver pathology that are not seen in senescence-accelerated mouse resistant/1 (SAMR1). Here we used both two-dimensional electrophoresis-and ICAT-based mitochondrial proteomics analysis to view the liver mitochondrial protein alterations between SAMP8 and SAMR1. Compared with SAMR1, decreased expression and activity of mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase were detected in SAMP8 at 6 months old (SAMP8-6m). As the key enzyme of ketogenesis, 3-hydroxy-3-methylglutaryl-CoA synthase is well known to be transcriptionally regulated by peroxisome proliferator-activated receptor ␣, which was also expressed at lower levels in SAMP8-6m livers. In addition, down-regulation of two peroxisome proliferator-activated receptor ␣ target gene products (acyl-CoA oxidase and enoyl-CoA hydratase), elevation of triglyceride, and reduction of acetyl-CoA were observed, indicating abnormal fatty acid metabolism in SAMP8-6m livers. In addition eight proteins (NDUAA, NDUBA, NDUB7, NDUS1, NDUS3, NDUV1, ETFA, and UCRI) of mitochondrial complexes were down-regulated in SAMP8-6m, resulting in mitochondria-related liver dysfunction characterized by enhanced oxidative stress-induced molecular damage (lipid peroxide and oxidized protein) and depressed energy production (ATP). Glutamine synthetase and ornithine aminotransferase involved in glutamine synthesis were up-regulated in SAMP8 livers at both 1 and 6 months old that may be related to the accumulation of glutamate and glutamine. Our work provided useful clues to understanding the molecular mechanism underlying liver dysfunction in senescence-accelerated mouse. Molecular & Cellular Proteomics 7:1737-1747, 2008.The liver is regarded as the major organ for a number of physiological presses. As the main energy producers, liver mitochondria are considered to be the central integrators of intermediary metabolism including fatty acid oxidation, the Krebs cycle, oxidative phosphorylation, ketogenesis, and the urea cycle. Furthermore most of the liver disorders have been reported to have increased reactive oxygen species (ROS) 1 and decreased ATP as vital characteristics (1, 2), which are both generated through the mitochondrial respiratory chain.The senescence-accelerated mouse (SAM) model is an aging model obtained by continuous sister-brother breeding from original litters of AKR/J mice (3). SAM includes two strains, i.e. SAM prone (SAMP) and SAM resistant (SAMR). SAMP exhibit a shortened life span and early manifestation of various symptoms of senescence, whereas SAMR are senescence-resistant inbred strains (4). SAMP8, a substrain of SAMP, has become a major biogerontological resource in aging research with SAMR1 as control (5, 6).Recently Ye et al. (7) h...