title: Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches.
abstract: 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.
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.|Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Fabre
authors.affiliation: Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Dagmara
authors.initials: D
authors.lastname: Korona
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.|Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Arnoud
authors.initials: A
authors.lastname: Groen
authors.affiliation: Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Jakob
authors.initials: J
authors.lastname: Vowinckel
authors.affiliation: Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.|Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK.
authors.forename: Laurent
authors.initials: L
authors.lastname: Gatto
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.|Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Deery
authors.affiliation: Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.|The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, UK.
authors.forename: Markus
authors.initials: M
authors.lastname: Ralser
authors.affiliation: Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Steven
authors.initials: S
authors.lastname: Russell
authors.affiliation: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.|Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.|Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
mesh_terms: D000818:Animals; D029721:Drosophila Proteins / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000378:metabolism*; D013058:Mass Spectrometry; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D049490:Systems Biology
chemical_list: D029721:Drosophila Proteins; D020543:Proteome
keywords: Early embryo development; Label-free quantification; Mass-spectrometry; SWATH; Systems biology