Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors.
Bottom Line: Using a state-of-the art MS workflow and a strategy to map identifications from the C2C12 cell line model to tissues, we identified a total of 10,218 proteins, including skeletal muscle specific transcription factors like myod1 and myogenin and circadian clock proteins.Quantitation of protein isoforms of glucose uptake signaling pathways and in glucose and lipid metabolic pathways provides a detailed metabolic map of the cell line compared with tissue.This revealed unexpectedly complex regulation of AMP-activated protein kinase and insulin signaling in muscle tissue at the level of enzyme isoforms.
Affiliation: From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;Show MeSH
Mentions: Absolute protein abundance (mass) was calculated as described before (30). Briefly, the mass spectrometric signal of an individual protein was divided by the sum of all proteins. Because the resulting values were small, we multiplied them by 1 million and expressed absolute abundance as part-per-million (ppm) (Figs. 5, 6, and supplemental Table I). In other words, the absolute protein abundance described here is the fractional signal of each protein in relation to the total protein signal and hence is expressed in ppm. Quantifiable proteins in the analysis of skeletal muscle and C2C12 myotubes were defined as those identified at least two times in each group. Error bars in Figures 5, 6, and supplemental Fig. S4 denote standard deviation of median. In Table SI, quantifiable proteins were defined as those identified at least two times in skeletal muscle. The absolute abundances that are provided were calculated for the list of the proteins identified after using “match between runs” (Table SI).
Affiliation: From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;