title: Qualitative and quantitative analysis of the adult Drosophila melanogaster proteome.
abstract: 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).
authors.affiliation: 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.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Xing
authors.forename: Chengpu
authors.initials: C
authors.lastname: Zhang
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Linhui
authors.initials: L
authors.lastname: Zhai
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Yang
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
mesh_terms: D000818:Animals; D029721:Drosophila Proteins / Q000032:analysis*; D004331:Drosophila melanogaster / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D008297:Male; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D053719:Tandem Mass Spectrometry
chemical_list: D029721:Drosophila Proteins; D020543:Proteome
keywords: Animal proteomics; Drosophila melanogaster; High-coverage proteome; Label-free; Tandem mass spectrum; iTRAQ