Membrane enriched proteome of transfected SW480 cells

ABSTRACT: 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).

INSTRUMENT(S): LTQ

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: David Cantor  

PROVIDER: PXD000230 | Pride | 2013-05-30

REPOSITORIES: Pride