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Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors.

Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M - Mol. Cell Proteomics (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;

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2D annotation distribution. Scatter plot of normalized annotation changes between skeletal muscle and C2C12 myotubes. Calculation of significance is detailed under “Experimental Procedures.” The annotations analyzed were: KEGG (purple), GOMF (green), GOCC (blue), and GOBP (red).
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Figure 4: 2D annotation distribution. Scatter plot of normalized annotation changes between skeletal muscle and C2C12 myotubes. Calculation of significance is detailed under “Experimental Procedures.” The annotations analyzed were: KEGG (purple), GOMF (green), GOCC (blue), and GOBP (red).

Mentions: Comparative analysis of two closely related systems highlights their significant differences but not their commonalities. Therefore, we next employed 2D annotation enrichment, which calculates enrichments in each of the systems compared with a background proteome, in this case the mouse proteome (29), and thereby reveals protein categories with significant regulation in the combined space of skeletal muscle and C2C12 myotubes proteome (Fig. 4). Together the differential protein quantification, the cluster analysis, and the 2D analysis allow us to probe functional differences between two different biological systems as reflected in their proteomes.


Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors.

Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M - Mol. Cell Proteomics (2015)

2D annotation distribution. Scatter plot of normalized annotation changes between skeletal muscle and C2C12 myotubes. Calculation of significance is detailed under “Experimental Procedures.” The annotations analyzed were: KEGG (purple), GOMF (green), GOCC (blue), and GOBP (red).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4390264&req=5

Figure 4: 2D annotation distribution. Scatter plot of normalized annotation changes between skeletal muscle and C2C12 myotubes. Calculation of significance is detailed under “Experimental Procedures.” The annotations analyzed were: KEGG (purple), GOMF (green), GOCC (blue), and GOBP (red).
Mentions: Comparative analysis of two closely related systems highlights their significant differences but not their commonalities. Therefore, we next employed 2D annotation enrichment, which calculates enrichments in each of the systems compared with a background proteome, in this case the mouse proteome (29), and thereby reveals protein categories with significant regulation in the combined space of skeletal muscle and C2C12 myotubes proteome (Fig. 4). Together the differential protein quantification, the cluster analysis, and the 2D analysis allow us to probe functional differences between two different biological systems as reflected in their proteomes.

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.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany;

Show MeSH