PXD000455 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2014-03-04 |
AnnouncementXML | Submission_2014-03-04_07:37:16.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 |
Dataset History
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. |
Publication List
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] |
Keyword List
submitter keyword: proteome, high coverage, LC-MS/MS |
Contact List
Zhang Chengpu |
contact affiliation | Beijing proteome research center |
contact email | zhangchengpu0203@163.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD000455
- Label: PRIDE project
- Name: Drosophila melanogaster proteome dataset with high coverage of the genome based on the LC-MS/MS platform