Proteomic analysis of skeletal muscle from the Hybryid Mouse Diversity Panel

To begin to understand how variations in the genome drive changes in the skeletal muscle proteome, we performed a proteomic analysis of Gastrocnemius muscle from 73 inbred mouse strains of the Hybrid Mouse Diversity Panel (HMDP) that were fed a chow diet and housed under identical environmental conditions (n=2-4; 162 mice). These data were integrated with genomic and various molecular/phenotypic data via systems genetic analysis which is a powerful forward genetics approach to identify potential new regulators of complex traits. Proteomics was performed with eighteen 10-plex tandem mass tags (TMT) experiments each consisting of 9 strains plus a pooled common internal reference. Peptides were analysed by 2D-liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS) resulting in the quantification of 5,350 proteins with 4,027 quantified in >50 mice and 2,069 proteins quantified in all 162 animals.