Drosophila melanogaster proteome dataset with high coverage of the genome based on the LC-MS/MS platform

ABSTRACT: Here we describe a high coverage dataset of whole fly through a one-dimensional gel electrophoresis LC-MS/MS approach. By combining the datasets of two kinds of SDS-PAGE and two kinds of tagmata, the high coverage analysis resulted in the identification of 5,262 genes, corresponding to 38.23% of the whole encoding genes. Sample info: 4-day adult male Canton-S Drosophila melanogaster was used in this study. To reduce sample complexity, fly heads and bodies (including reproductive system, genitalia and gonad) were sequenced separately. Protein extraction and analysis: Fly heads and bodies were isolated using prechilled size-exclusion sieves and distributed into 1.5-mL tubes separately. Approximately 120 ug of each sample were lysed in 200 ul lysis buffer containing 2% SDS, 10% glycine, 1% bromophenol blue, 10 mM DTT, and 0.01% protease inhibitor cocktail (Roche) and 0.5-mm glass beads by vortexing at the highest speed for 5 min. After boiling for 5min, 20 mM iodoacetamide was used to alkylate the proteins. Samples prepared as described above were separated by 1D SDS-PAGE, and the lanes were excised into fractions, followed by in-gel tryptic digestion. All prepared peptides were further analyzed on an LTQ-Orbitrap Velos hybrid mass spectrometer (Thermo Electron, San Jose, CA) coupled with UPLC (nano Acquity Ultra Performance LC, Waters). Protein search:The acquired MS/MS spectra were searched against the flybase database (http://flybase.org/, release 5.4, 24,043 entries) using Mascot (version 2.3, Matrix Science). The results were filtered by PepDistiller (v. 1.26) with a false discovery rate (FDR) lower than 1% at the peptide spectrum match level using the target-decoy strategy.

INSTRUMENT(S): LTQ Orbitrap, instrument model

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): B Cell, Whole Body

SUBMITTER: Zhang Chengpu Zhang Chengpu  

PROVIDER: PXD000455 | Pride | 2013-11-27

REPOSITORIES: Pride