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Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label‐free proteomics approaches
Author(s) -
Fabre Bertrand,
Korona Dagmara,
Groen Arnoud,
Vowinckel Jakob,
Gatto Laurent,
Deery Michael J.,
Ralser Markus,
Russell Steven,
Lilley Kathryn S.
Publication year - 2016
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201500482
Subject(s) - drosophila melanogaster , proteome , biology , transcriptome , proteomics , embryogenesis , computational biology , gene expression , drosophila embryogenesis , melanogaster , microbiology and biotechnology , embryonic stem cell , gene , embryo , genetics
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.