System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects

SUMMARY Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a part in the onset of the metabolic syndrome, its molecular basis and dependency on dietary and genotypic factors are poorly characterized. Here, we used a rich experimental design with two different mouse strains, dietary and metabolic perturbations to generate a compendium of quantitative proteome data, using three mass spectrometry strategies. The data recapitulates known properties of the metabolic system and indicate differential molecular adaptation of the two mouse strains to perturbations, contributing to a better understanding of the metabolic syndrome. We show that high-quality, high-throughput proteomic datasets provide an unbiased broad overview of complex systems upon perturbation. HIGHLIGHTS Rich experimental design with two mouse strains, dietary and metabolic perturbations Three mass spectrometry proteomic data collection strategies in one data compendium SWATH-MS data with systematic perturbation provide a broad unbiased view of the system The data reveals differential adaptation of molecular systems in two mouse strains