Analysis of the Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches Bertrand Fabre Dagmara Korona Arnoud Groen Jakob Vowinckel Laurent Gatto Mike J Deery Markus Ralser Steven Russell Kathryn S Lilley 10779/crick.12675893.v1 https://crick.figshare.com/articles/journal_contribution/Analysis_of_the_Drosophila_melanogaster_proteome_dynamics_during_embryonic_development_by_a_combination_of_label-free_proteomics_approaches/12675893 During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In 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 to 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 D. 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. 2020-07-27 10:53:08 Early embryo development Label-free quantification Mass-spectrometry SWATH Systems biology Animals Drosophila Proteins Drosophila melanogaster Mass Spectrometry Proteome Proteomics Systems Biology Ralser FC001134 Biochemistry & Molecular Biology 06 Biological Sciences 08 Information and Computing Sciences 11 Medical and Health Sciences