Characterization of the human skeletal muscle proteome by one-dimensional gel electrophoresis and HPLC-ESI-MS/MS

Abstract

Changes in protein abundance in skeletal muscle are central to a large number of metabolic and other disorders, including, and perhaps most commonly, insulin resistance. Proteomics analysis of human muscle is an important approach for gaining insight into the biochemical basis for normal and pathophysiological conditions. However, to date, the number of proteins identified by this approach has been limited, with 107 different proteins being the maximum reported so far. Using a combination of one-dimensional gel electrophoresis and high performance liquid chromatography electrospray ionization tandem mass spectrometry, we identified 954 different proteins in human vastus lateralis muscle obtained from three healthy, nonobese subjects. In addition to a large number of isoforms of contractile proteins, we detected all proteins involved in the major pathways of glucose and lipid metabolism in skeletal muscle. Mitochondrial proteins accounted for 22% of all proteins identified, including 55 subunits of the respiratory complexes I-V. Moreover, a number of enzymes involved in endocrine and metabolic signaling pathways as well as calcium homeostasis were identified. These results provide the most comprehensive characterization of the human skeletal muscle proteome to date. These data hold promise for future global assessment of quantitative changes in the muscle proteome of patients affected by disorders involving skeletal muscle.

Fig. 1. Molecular weight distribution and subcellular location of human skeletal muscle proteins

A, distribution of the 954 proteins identified in human vastus lateralis muscle (closed bars) compared with all proteins in the IPI human database (open bars) relative to their predicted molecular weight. B, distribution of the 954 identified proteins according to Gene Ontology (GO) annotation. In cases where an identified protein group contained more than one IPI ID, the average molecular weight was used.

Fig. 2. Proteomics coverage of major enzymes involved in glucose and lipid metabolism in human skeletal muscle

A, isoforms and/or subunits of enzymes involved in glycogen metabolism. Glycolysis (B), citric acid cycle (C), and fatty acid transport (D) into and oxidation in mitochondria. Proteins identified are shown in gray boxes, and the associated gene names, maximum observed number of unique peptides, and sequence coverage are presented in adjacent white boxes.