PXD000455

PXD000455 is an original dataset announced via ProteomeXchange.

Title	Drosophila melanogaster proteome dataset with high coverage of the genome based on the LC-MS/MS platform
Description	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.
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:47:31.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000455
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Zhang Chengpu
SpeciesList	scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-09-09 14:47:57	ID requested
1	2013-12-02 08:42:21	announced
2	2014-03-04 07:37:16	announced	Updated publication reference for PubMed record(s): 24259522.
⏵ 3	2014-07-28 00:47:32	announced	Updated project metadata.

Xing X, Zhang C, Li N, Zhai L, Zhu Y, Yang X, Xu P, Qualitative and quantitative analysis of the adult Drosophila melanogaster proteome. Proteomics, 14(2-3):286-90(2014) [pubmed]

submitter keyword: proteome, high coverage, LC-MS/MS

Zhang Chengpu
contact affiliation	Beijing proteome research center
contact email	zhangchengpu0203@163.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2013/11/PXD000455

PRIDE project URI

• PRIDE
  1. PXD000455
     1. Label: PRIDE project
     2. Name: Drosophila melanogaster proteome dataset with high coverage of the genome based on the LC-MS/MS platform