Robinson MM, Dasari S, Karakelides H, Bergen HR 3rd, Nair KS. Release of skeletal muscle peptide fragments identifies individual proteins degraded during insulin deprivation in type 1 diabetic humans and mice. Am J Physiol Endocrinol Metab 311: E628 -E637, 2016. First published July 19, 2016; doi:10.1152/ajpendo.00175.2016.-Insulin regulates skeletal muscle protein degradation, but the types of proteins being degraded in vivo remain to be determined due to methodological limitations. We present a method to assess the types of skeletal muscle proteins that are degraded by extracting their degradation products as low-molecular weight (LMW) peptides from muscle samples. High-resolution mass spectrometry was used to identify the original intact proteins that generated the LMW peptides, which we validated in rodents and then applied to humans. We deprived insulin from insulin-treated streptozotocin (STZ) diabetic mice for 6 and 96 h and for 8 h in type 1 diabetic humans (T1D) for comparison with insulin-treated conditions. Protein degradation was measured using activation of autophagy and proteasome pathways, stable isotope tracers, and LMW approaches. In mice, insulin deprivation activated proteasome pathways and autophagy in muscle homogenates and isolated mitochondria. Reproducibility analysis of LMW extracts revealed that ϳ80% of proteins were detected consistently. As expected, insulin deprivation increased whole body protein turnover in T1D. Individual protein degradation increased with insulin deprivation, including those involved in mitochondrial function, proteome homeostasis, nDNA support, and contractile/cytoskeleton. Individual mitochondrial proteins that generated more LMW fragment with insulin deprivation included ATP synthase subunit-␥ (ϩ0.5-fold, P ϭ 0.007) and cytochrome c oxidase subunit 6 (ϩ0.305-fold, P ϭ 0.03).In conclusion, identifying LMW peptide fragments offers an approach to determine the degradation of individual proteins. Insulin deprivation increases degradation of select proteins and provides insight into the regulatory role of insulin in maintaining proteome homeostasis, especially of mitochondria.peptidomics; isotope tracer; low molecular weight; method; autophagy THE ANTICATABOLIC EFFECT OF INSULIN was evident from early reports of humans with type 1 diabetes (T1D) showing dramatic atrophy of skeletal muscle without insulin and then restoration of muscle mass with insulin treatment (17). Skeletal muscle protein content represents the balance between protein synthesis and protein degradation. Previous studies demonstrated that skeletal muscle catabolism during insulin deprivation in T1D is due primarily to increased protein degradation, with little change to mixed muscle protein synthesis, representing the average of multiple protein pools (8,16,35). Separating specific muscle protein fractions revealed that insulin has a stimulatory effect on mitochondrial proteins when amino acids are provided (36,40). In contrast, the synthesis rates of contractile proteins, such as myosin heavy cha...