Drosophila melanogaster proteome dynamics during embryogenesis - 1
In this study we use a combination of proteomics Label-Free quantification methods to monitor protein expression changes over a time course of more than 20 hours of embryo development in Drosophila melanogaster.
Sample Processing Protocol
Embryos from Drosophila melanogaster iso-1 strain were lysed in Tris 50mM pH 7.5, 4% SDS, protease inhibitor (Complete, Roche). Trypsin in gel digestion was used as the sample preparation method in this study. Injection replicates of a embryo sample were performed on a Triple-TOF 6600 or a LTQ-Orbitrap Velos instruments in data dependent acquisition mode. A 1D gel SDS-PAGE fractionation follow by in gel digestion with trypsin of a embryo sample were performed and the peptides were injected a Triple-TOF 6600 in data dependent acquisition mode. A embryo developmental time course was realized over 22.5 hours and the embryos were lysed in Tris 50mM pH 7.5, 4% SDS, protease inhibitor (Complete, Roche) and a trypsin in gel digestion was performed. The peptides were injected a Triple-TOF 6600 in data dependent acquisition mode and SWATH mode or on a Q-Exactive with a PRM mode.
Data Processing Protocol
Data dependent acquisition were analysed with MaxQuant. The library for the SWATH analysis was generated using MaxQuant version 22.214.171.124 and Spectronaut version 7. PRM data were analysed using Skyline.
Bertrand Fabre, University of Cambridge
Kathryn Lilley, Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K. ( lab head )
Fabre B, Korona D, Groen A, Vowinckel J, Gatto L, Deery MJ, Ralser M, Russell S, Lilley KS. Analysis of the Drosophila melanogaster proteome dynamics during the embryo early development by a combination of label-free proteomics approaches. Proteomics. 2016 Mar 31 PubMed: 27029218