Quantitative Proteomics Study Of Tissue Specificity In Drosophila Melanogaster

Drosophila melanogaster is one of the most widely used model organism in biologicalscience, especially in the areas of genetics and development biology. Due to the wellannotated genome and numerous transgenic strains, D. melanogaster has laid the foundationfor life mystery and pathogenesis research. While the research of its proteome is stillremaining a challenge in the field, especially the comprehensive research due to thetechnology limitation.Here we describe a high-coverage analysis of whole fly through a one-dimensional gelelectrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS)approach. To reduce sample complexity, two kinds of fly tagmata heads and bodies weresequenced separately through two types of sodium dodecyl sulfate polyacrylamide gelelectrophoresis (SDS-PAGE), traditional SDS-PAGE and Tricine SDS-PAGE aimed at smallproteins. The high-coverage analysis resulted in the identification of5,262genes according to5,617proteins, which correspond to38.23%of the entire coding genes.Moreover, we found that the fly head and body have different molecular weightdistributions of their proteomes when the proteins were resolved with SDS-PAGE and imageanalysis of the stained gel. More proteins were concentrated on the lower part of the lane inthe body sample, whereas the proteins from the head were distributed more evenly within thewhole lane of the gel, suggesting that proteins with smaller molecular weights may beenriched in the body. This phenomenon was never reported in D. melanogaster and any otherspecies proteomics. To further validate this observation, the extracted ionchromatogram-based label-free quantitative approach was applied in silico to reconstitute theprotein distribution in gel, the results displayed an obvious preference for proteins with smallmolecular weights in the body, indicating good consistency between the virtual andexperimental images. To understand the different biological functions of the fly body andhead, Gene Ontology (GO) and Pathway analyses were performed on our datasets, proteinsup-expressed in body mainly take part in digestive system, cell metabolism and energymetabolism,which were very important for the maintenance of basic metabolism andbehavior patterns in D. melanogaster. While proteins up-expressed in head were all related tonervous system metabolism.This phenomenon was further confirmed by isobaric tags for relative and absolutequantitation-based quantitative approache. The consistent results of the two differentquantitation methods also demonstrated the stability and accuracy of the LC-MS/MSplatform. In addition, the large-scale proteomic analysis of D. melanogaster generated the largest dataset of D. melanogaster proteome so far, providing a physiological map of D.melanogaster with tissue specificity for life science study.