PXD000230
PXD000230 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Membrane enriched proteome of transfected SW480 cells |
Description | This project used membrane-enriched proteomics to compare the membrane proteome of SW480 human colorectal cancer subclones that had been transfected with the full length coding sequence of the beta-6 integrin subunit under an overexpression promoter (SW480OE) against SW480 cells that had been transfected with an ‘empty’ mock vector (SW480M). Cell lysate samples were enriched for membrane proteins using a modified sodium carbonate stripping method before undergoing peptide immobilised pH gradient isoelectric focusing (IPG-IEF). Two IPG-IEF pH ranges were used to increase proteomic coverage: pH3-10 (broad range; BR) and pH3.5-4.5 (narrow range; NR). Each IPG-IEF strip was cut into 24 equal fractions and the peptides eluted. IPG-IEF of each pH range for both cell lines was performed in triplicate, resulting in four triplicate sets of 24 fractions. Data processing and bioinformatics: Spectra were identified against the *Homo sapiens* protein database (derived from Ensembl, Swiss-Prot and NCBI) using X!Tandem and the Global Proteome Machine (GPM) Tornado XE (build date 2010.12.01). GPM searches were set to tryptic peptides under GPM’s default fragment ion mass tolerance of 0.4Da and did not include semi-cleavage. Searches included single acid polymorphisms and default GPM residue modifications (oxidation,dioxidation, carbamidomethyl, deamidation, acetylation). |
HostingRepository | PRIDE |
AnnounceDate | 2013-05-30 |
AnnouncementXML | Submission_2013-05-30_03:44:45.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | David Cantor |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue; monohydroxylated residue; dihydroxylated residue; acetylated residue; deamidated residue |
Instrument | LTQ |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2013-04-26 05:35:22 | ID requested | |
1 | 2013-05-30 03:41:46 | announced | |
1 | 2014-07-25 01:05:44 | announced | |
⏵ 2 | 2013-05-30 03:44:45 | announced | Add reference |
Publication List
Cantor D, Slapetova I, Kan A, McQuade LR, Baker MS, 6 integrin alters the colorectal cancer cell proteome in favor of elevated proliferation and a switching in cellular adhesion that increases invasion. J Proteome Res, 12(6):2477-90(2013) [pubmed] |
Keyword List
submitter keyword: Membrane proteomics, LC-MS/MS, Integrin, SW480, Colorectal cancer |
Contact List
David Cantor | |
---|---|
contact affiliation | Chemistry and Biomolecular Sciences |
contact email | david.cantor@students.mq.edu.au |
Full Dataset Link List
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/2013/05/PXD000230 |