Analysis of the Drosophila melanogaster proteome dynamics during the embryo early development by a combination of label‐free proteomics approaches
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Fabre, B., Korona, D., Groen, A., Vowinckel, J., Gatto, L., Deery, M., Ralser, M., et al. (2016). Analysis of the Drosophila melanogaster proteome dynamics during the embryo early development by a combination of label‐free proteomics approaches. Proteomics https://doi.org/10.1002/pmic.201500482
During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In the case of the well studied model Drosophila melanogaster, transcriptomic studies, most notably from the modENCODE project, have described in detail changes in gene expression at the mRNA level across development. Although such data are clearly very useful for understand how the genome is regulated during embryogenesis, it is important to understand how changes in gene expression are reflected at the level of the proteome. In this study, we describe a combination of two quantitative label‐free approaches, SWATH and Data Dependent Acquisition, to monitor changes in protein expression across a timecourse of Drosophila melanogaster embryonic development. We demonstrate that both approaches provide robust and reproducible methods for the analysis of proteome changes. In a preliminary analysis of Drosophila embryogenesis, we identified several pathways, including the heat‐shock response, nuclear protein import and energy production, that are regulated during embryo development. In some cases changes in protein expression mirrored transcript levels across development, whereas other proteins showed signatures of post‐ transcriptional regulation. Taken together, our pilot study provides a solid platform for a more detailed exploration of the embryonic proteome.
early embryo development, label-free quantification, mass-spectrometry, SWATH
Funding: B.F, D.K and L.G are funded by BBSRC (Ref: BB/L002817/1). MR and JV acknowledge funding by the Wellcome Trust (RG 093735/Z/10/Z) the ERC (Starting grant 260809), M.R. is a Wellcome Trust Research Career Development and Wellcome-Beit Prize fellow.
Wellcome Trust (093735/Z/10/Z)
European Research Council (260809)
BBSRC (via University of Manchester) (R116574-LLM)
Biotechnology and Biological Sciences Research Council (BB/L002817/1)
External DOI: https://doi.org/10.1002/pmic.201500482
This record's URL: https://www.repository.cam.ac.uk/handle/1810/254943