Abstract
Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging because of highly abundant contractile proteins that interfere with detection of regulatory proteins. 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. We obtain absolute abundances for proteins expressed in a muscle cell line and skeletal muscle, which should serve as a valuable resource. 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.
Highlights
Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors*□S
We developed a streamlined workflow, consisting of cell line or tissue homogenization, filter-aided sample preparation (FASP) [23], followed by peptide separation into twelve fractions according to their isoelectric point as described [24]
A total of 8,309 proteins were identified in skeletal muscle, 9880 proteins in C2C12 myotubes, and 7,973 (78% of the total) proteins were identified in both systems
Summary
Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors*□S. We measured a very deep proteome of the C2C12 myotubes and transfer the peptide and protein identifications to a data set obtained under the same conditions from adult mouse skeletal muscle.
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