Insulin resistance in skeletal muscle is a hallmark feature of type 2 diabetes. An increasing number of enzymes and metabolic pathways have been implicated in the development of insulin resistance. However, the primary cellular cause of insulin resistance remains uncertain. Proteome analysis can quantitate a large number of proteins and their post-translational modifications simultaneously and is a powerful tool to study polygenic diseases like type 2 diabetes. Using this approach on human skeletal muscle biopsies, we have identified eight potential protein markers for type 2 diabetes in the fasting state. The observed changes in protein expression indicate increased cellular stress, e.g. up-regulation of two heat shock proteins, and perturbations in ATP (re)synthesis and mitochondrial metabolism, e.g. down-regulation of ATP synthase -subunit and creatine kinase B, in skeletal muscle of patients with type 2 diabetes. Phosphorylation appears to play a key, potentially coordinating role for most of the proteins identified in this study. In particular, we demonstrated that the catalytic -subunit of ATP synthase is phosphorylated in vivo and that the levels of a down-regulated ATP synthase -subunit phosphoisoform in diabetic muscle correlated inversely with fasting plasma glucose levels. These data suggest a role for phosphorylation of ATP synthase -subunit in the regulation of ATP synthesis and that alterations in the regulation of ATP synthesis and cellular stress proteins may contribute to the pathogenesis of type 2 diabetes.Insulin resistance in skeletal muscle, defined as reduced insulin-stimulated glucose disposal, is a characteristic feature of type 2 diabetes mellitus (T2DM) 1 and is believed to be largely accounted for by reduced non-oxidative glucose metabolism (1-3). Furthermore, insulin stimulation of glucose oxidation and suppression of lipid oxidation is significantly impaired in patients with T2DM (2, 3). Conversely, in the basal, fasting state increased glucose oxidation and reduced lipid oxidation is seen in skeletal muscle of insulin resistant subjects, whether caused by T2DM or obesity alone (4). These defects suggest an impaired capacity to switch between carbohydrate and fat as oxidative energy sources in insulin-resistant subjects. Together with reports of reduced oxidative enzyme activity and dysfunction of mitochondria in skeletal muscle of patients with T2DM (4 -6) and the fact that mitochondrial DNA defects cause T2DM through impairment of oxidative phosphorylation (7, 8), these abnormalities in fuel metabolism have led to the hypotheses that perturbations in skeletal muscle mitochondrial metabolism (6, 9, 10) and defects in the signaling pathways of AMP-activated protein kinase (AMPK) are implicated in the pathogenesis of T2DM (11). That rates of fuel oxidation and mitochondrial function can affect glucose uptake and glycogen synthesis has been reported earlier (12, 13). In addition, both chronic activation of AMPK and induced expression of the transcriptional co-activator of peroxisom...