PXD000349

PXD000349 is an original dataset announced via ProteomeXchange.

Title	2D-DIGE global protein profiling of alcohol-dependent mouse brain
Description	Data analysis. Spot detection and matching were performed with a comparative cross analysis of all the gels using DeCyder software v.6.5 (GE Healthcare). 178 spots were selected based on 1.15-fold for protein ratio cut-off, allowing for the appearance of the spots in 23 out of 28 gels (69 out of 84 total images). Data from 95 spots were submitted. 93 spots were identified with high confidence. Spot picking and Trypsin digestion. The spots of interest were picked up by Ettan Spot Picker (GE Healthcare) based on the in-gel analysis and spot picking design by DeCyder software. The gel spots were washed a few times then digested in-gel with modified porcine trypsin protease (Promega, Fitchburg, WI). The digested tryptic peptides were desalted using a Zip-tip C18 (Millipore, Billerica, MA). Peptides were eluted from the Zip-tip with 0.5 uL of matrix solution (alpha-cyano-4-hydroxycinnamic acid, 5 mg/mL in 50% acetonitrile, 0.1% trifluoroacetic acid, 25mM ammonium bicarbonate) and spotted on a MALDI plate. Mass Spectrometry. MALDI-TOF MS and TOF/TOF tandem MS/MS were performed on AB SCIEX TOF/TOF 5800 System (AB SCIEX). MALDI-TOF mass spectra were acquired in reflectron positive ion mode, averaging 4000 laser shots per spectrum. TOF/TOF tandem MS fragmentation spectra were acquired for each sample, averaging 4000 laser shots per fragmentation spectrum on each of the 7-10 most abundant ions present in each sample (excluding trypsin autolytic peptides and other known background ions). Database search. Both the resulting peptide mass and the associated fragmentation spectra were submitted to GPS Explorer workstation equipped with MASCOT search engine (Matrix Science, Boston, MA) to search the Swiss-Prot database. Searches were performed without constraining protein molecular weight or isoelectric point, with variable carbamidomethylation of cysteine and oxidation of methionine residues, and with one missed cleavage also allowed in the search parameters. Candidates with either protein score C.I.% or Ion C.I.% greater than 95 were considered significant. When multiple IDs were significant for a given spot, the selection was made by evaluating apparent molecular weight, isoelectric point, the location of the spot in the gel, and the presence of strips of multiple protein isoforms in the adjacent spots.
HostingRepository	PRIDE
AnnounceDate	2017-08-01
AnnouncementXML	Submission_2017-08-01_08:17:23.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000349
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Giorgio Gorini
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	instrument model: AB SCIEX TOF/TOF™ 5800 System

Revision	Datetime	Status	ChangeLog Entry
0	2013-07-19 02:37:07	ID requested
1	2014-07-28 00:42:17	announced
⏵ 2	2017-08-01 08:17:24	announced	Updated project metadata.

Gorini G, Roberts AJ, Mayfield RD, Neurobiological signatures of alcohol dependence revealed by protein profiling. PLoS One, 8(12):e82656(2013) [pubmed]

submitter keyword: Mouse, Brain, Cortex, Midbrain, Alcohol Dependence, CIE, 2D-DIGE

Giorgio Gorini
contact affiliation	The University of Texas at Austin
contact email	gorini@utexas.edu
lab head
Giorgio Gorini
contact affiliation	The University of Texas at Austin
contact email	gorini@utexas.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/2014/07/PXD000349

PRIDE project URI

• PRIDE
  1. PXD000349
     1. Label: PRIDE project
     2. Name: 2D-DIGE global protein profiling of alcohol-dependent mouse brain