PXD000635

PXD000635 is an original dataset announced via ProteomeXchange.

Title	Multifactorial Comparative Proteomic Study of Cytochrome P450 2E1 Function in Chronic Alcohol Administration
Description	With the use of iTRAQ technique, a multifactorial comparative proteomic study can be performed. In this study, to obtain an overview of ethanol, CYP2E1 and gender effects on liver injury and gain more insight into the underlying molecular mechanism, mouse liver proteomes were quantitatively analyzed using iTRAQ under eight conditions including mice of different genders, wild type versus CYP2E1 knockout, and normal versus alcohol diet. A series of statistical and bioinformatic analyses were explored to simplify and clarify multifactorial comparative proteomic data. MALDI plates were analyzed with a TOF/TOF 5800 mass spectrometer (AB Sciex). The instrument was calibrated using the 4700 mass calibration standard. MS spectra between m/z 800 and 4,000 were acquired for every spot using 1,000 laser shots in reflector mode. The 20 most intense ion signals per spot having a S/N > 10 were selected as precursors for MS/MS acquisition using 2,000 laser shots. Peptide and protein identifications were performed with the ProteinPilot Software 4.5 (AB Sciex) using the Paragon algorithm. Combined data and spectra from all 24 OFFGEL fractions were searched against the UniProt mouse database (release-2010_11). The following search parameters were selected: iTRAQ 8-plex peptide label, cysteine alkylation, trypsin specificity, ID focus on biological modifications, and processing including quantitation and thorough ID. A protein with a confidence threshold of 95% (unused confidence threshold ProtScore>1.3) was reported and the corresponding False Discovery Rate (FDR) was less than 1%. In protein grouping, competitor threshold was set as 2.00 in ProtScore.
HostingRepository	PRIDE
AnnounceDate	2014-07-25
AnnouncementXML	Submission_2014-07-25_01:50:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rong Wang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	deamidated residue; monohydroxylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; acetylated residue; phosphorylated residue
Instrument	4800 Proteomics Analyzer

Revision	Datetime	Status	ChangeLog Entry
0	2013-12-11 07:54:29	ID requested
1	2014-04-11 07:09:54	announced
⏵ 2	2014-07-25 01:50:11	announced	Updated project metadata.

Wang Y, Kou Y, Wang X, Cederbaum A, Wang R, Multifactorial comparative proteomic study of cytochrome P450 2E1 function in chronic alcohol administration. PLoS One, 9(3):e92504(2014) [pubmed]

submitter keyword: CYP2E1, alcohol metabolism, multifactorial comparative proteome, liver, iTRAQ

Rong Wang
contact affiliation	Genetics and Genomic Sciences
contact email	rong.wang@mssm.edu
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/2014/04/PXD000635

PRIDE project URI

• PRIDE
  1. PXD000635
     1. Label: PRIDE project
     2. Name: Multifactorial Comparative Proteomic Study of Cytochrome P450 2E1 Function in Chronic Alcohol Administration