Xing Xiaohua, Zhang Chengpu, Li Ning, Zhai Linhui, Zhu Yunping, Yang Xiaoming, Xu Ping
State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing, P. R. China; College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China.
Proteomics. 2014 Feb;14(2-3):286-90. doi: 10.1002/pmic.201300121. Epub 2014 Jan 6.
Drosophila melanogaster is one of the most widely used model organisms in life sciences. Mapping its proteome is of great significance for understanding the biological characteristics and tissue functions of this species. However, the comprehensive coverage of its proteome remains a challenge. Here, we describe a high-coverage analysis of whole fly through a 1D gel electrophoresis and LC-MS/MS approach. By combining the datasets of two types of SDS-PAGE and two kinds of tagmata, the high-coverage analysis resulted in the identification of 5262 genes, which correspond to 38.23% of the entire coding genes. Moreover, we found that the fly head and body have different molecular weight distributions of their proteomes when the proteins were resolved with SDS-PAGE and image analysis of the stained gel. This phenomenon was further confirmed by both label-free and isobaric tags for relative and absolute quantitation-based quantitative approaches. The consistent results of the two different quantitation methods also demonstrated the stability and accuracy of the LC-MS/MS platform. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD000454 and PXD000455 (http://proteomecentral.proteomexchange.org/dataset/PXD000454; (http://proteomecentral.proteomexchange.org/dataset/PXD000455).
黑腹果蝇是生命科学中使用最广泛的模式生物之一。绘制其蛋白质组图谱对于理解该物种的生物学特性和组织功能具有重要意义。然而，对其蛋白质组进行全面覆盖仍然是一项挑战。在此，我们描述了一种通过一维凝胶电泳和液相色谱-串联质谱法对全果蝇进行高覆盖分析的方法。通过结合两种类型的十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（SDS-PAGE）数据集和两种躯体部位的数据，高覆盖分析鉴定出了5262个基因，占整个编码基因的38.23%。此外，当用SDS-PAGE分离蛋白质并对染色凝胶进行图像分析时，我们发现果蝇头部和身体的蛋白质组具有不同的分子量分布。这种现象通过基于相对和绝对定量的无标记定量方法以及等压标签定量方法得到了进一步证实。两种不同定量方法的一致结果也证明了液相色谱-串联质谱平台的稳定性和准确性。质谱蛋白质组学数据已提交至蛋白质组交换库，标识符分别为PXD000454和PXD000455（http://proteomecentral.proteomexchange.org/dataset/PXD000454；http://proteomecentral.proteomexchange.org/dataset/PXD000455）。
