Comprehensive proteomics and functional annotation of mouse brown adipose tissue.

Knowledge about the mouse brown adipose tissue (BAT) proteome can provide a deeper understanding of the function of mammalian BAT. Herein, a comprehensive analysis of interscapular BAT from C57BL/6J female mice was conducted by 2DLC and high-resolution mass spectrometry to construct a comprehensive proteome dataset of mouse BAT proteins. A total of 4949 nonredundant proteins were identified, and 4495 were quantified using the iBAQ method. According to the iBAQ values, the BAT proteome was divided into high-, middle- and low-abundance proteins. The functions of the high-abundance proteins were mainly related to glucose and fatty acid oxidation to produce heat for thermoregulation, while the functions of the middle- and low-abundance proteins were mainly related to protein synthesis and apoptosis, respectively. Additionally, 497 proteins were predicted to have signal peptides using SignalP4 software, and 75 were confirmed in previous studies. This study, for the first time, comprehensively profiled and functionally annotated the BAT proteome. This study will be helpful for future studies focused on biomarker identification and BAT molecular mechanisms.

Comprehensive map and functional annotation of the mouse white adipose tissue proteome.

White adipose tissue (WAT) plays a significant role in energy metabolism and the obesity epidemic. In this study, we sought to (1) profile the mouse WAT proteome with advanced 2DLC/MS/MS approach, (2) provide insight into WAT function based on protein functional annotation, and (3) predict potentially secreted proteins. A label-free 2DLC/MS/MS proteomic approach was used to identify the WAT proteome from female mouse WAT. A total of 6,039 proteins in WAT were identified, among which 5,160 were quantified (spanning a magnitude of 106) using an intensity-based absolute quantification algorithm, and 3,117 proteins were reported by proteomics technology for the first time in WAT. To comprehensively analyze the function of WAT, the proteins were divided into three quantiles based on abundance and we found that proteins of different abundance performed different functions. High-abundance proteins (the top 90%, 1,219 proteins) were involved in energy metabolism; middle-abundance proteins (90-99%, 2,273 proteins) were involved in the regulation of protein synthesis; and low-abundance proteins (99-100%, 1,668 proteins) were associated with lipid metabolism and WAT beiging. Furthermore, 800 proteins were predicted by SignalP4.0 to have signal peptides, 265 proteins had never been reported, and five have been reported as adipokines. The above results provide a large dataset of the normal mouse WAT proteome, which might be useful for WAT function research.