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Proteomics. 2016 Aug;16(15-16):2068-80. doi: 10.1002/pmic.201500482. Epub 2016 May 10.

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches.

Fabre B1,2,3, Korona D4,3, Groen A1,2,3, Vowinckel J2,3, Gatto L2,3,5, Deery MJ1,2,3, Ralser M2,3,6, Russell S4,3, Lilley KS1,2,3.

Author information

1
Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
2
Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK.
3
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
4
Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK.
5
Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK.
6
The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, UK.

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.

KEYWORDS:

Early embryo development; Label-free quantification; Mass-spectrometry; SWATH; Systems biology

PMID:
27029218
PMCID:
PMC5737838
DOI:
10.1002/pmic.201500482
[Indexed for MEDLINE]
Free PMC Article

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