Dataset Information

Comparison of cell-derived extracellular matrix isolated from LX-2 and HFF cells and analysed by LC-MS/MS

ABSTRACT: Not available

INSTRUMENT(S): 4000 Q TRAP

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatic Stellate Cell, Fibroblast

SUBMITTER: Jon Humphries

LAB HEAD: Jon Humphries

PROVIDER: PRD000680 | Pride | 2012-06-25

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_22483.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_22483.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_22483.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_22484.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_22484.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 18

Publications

Proteomic analysis of extracellular matrix from the hepatic stellate cell line LX-2 identifies CYR61 and Wnt-5a as novel constituents of fibrotic liver.

Rashid S Tamir ST Humphries Jonathan D JD Byron Adam A Dhar Ameet A Askari Janet A JA Selley Julian N JN Knight David D Goldin Robert D RD Thursz Mark M Humphries Martin J MJ

Journal of proteome research 20120628 8

Activation of hepatic stellate cells (HSCs) and subsequent uncontrolled accumulation of altered extracellular matrix (ECM) underpin liver fibrosis, a wound healing response to chronic injury, which can lead to organ failure and death. We sought to catalogue the components of fibrotic liver ECM to obtain insights into disease etiology and aid identification of new biomarkers. Cell-derived ECM was isolated from the HSC line LX-2, an in vitro model of liver fibrosis, and compared to ECM from human ...[more]

PMID: 22694338

Similar Datasets

Project description:A critical step during fertilization is the sperm acrosome reaction in which the acrosome releases its contents allowing the spermatozoa to penetrate the egg investments. The sperm acrosomal contents are composed of both soluble material and an insoluble material called the acrosomal matrix (AM). The AM is thought to provide a stable structure from which associated proteins are differentially released during fertilization. Mouse acrosomal matrices were isolated from 2 different populations of epididymal spermatozoa: AM_caput from caput epididymal spermatozoa (2 replicates) and AM_cauda from cauda epididymal spermatozoa (3 replicates). Proteins were separated by SDS-PAGE on a 15% polyacrylamide gel. After electrophoresis, proteins were stained with Coomassie blue. Gel lanes were cut into 8–9 slices and each slice placed into a 0.5 ml microcentrifuge tube. The gel pieces were washed to destain the gels. Reduction was performed with dithiothreitol solution. After reduction, the proteins were alkylated. The gel pieces were washed, dehydrated and air-dried. The digestion was proceed with trypsin and peptides extracted. The peptides obtained from in-gel digestion were analyzed by nano-flow nano-LC-MS/MS using an LTQ-XL ion trap mass spectrometer. To get the maximum number of publicly available sequences for analyses, the mouse sequences from Ensembl were merged with those from NCBI. The database was built using BioPerl modules. Specifically, from Ensembl two files were downloaded and merged including Mus_musculus.NCBIM37.64.pep.all.fa.gz (containing the superset of all translations resulting from Ensembl known or novel gene predictions) and Mus_musculus.NCBIM37.64.pep.abinitio.fa.gz (containing translations resulting from “ab initio” gene prediction algorithms such as SNAP and GENSCAN). From NCBI, the nonredundant (nr) file (on 11/2011) was downloaded and mouse sequences extracted (Taxonomy ID = 10090). This file was merged with the Ensembl sequences to create a file containing 356,881 sequences of which some were redundant. Duplicates were removed based on identical amino acid sequences to get 203,220 unique sequences used to build our blast database. Spectra obtained from the trypsin digestion products using the LTQ Orbitrap XL mass spectrometer were identified by the Proteome Discoverer (version 1.3) program, based on SEQUEST cluster as a search engine (University of Washington, licensed to Thermo Electron Corp., San Jose, CA) against our mouse database (203,220 nonredundant protein sequences). The search engine used the following parameters: precursor ion mass tolerance, 2.5 Da; fragment ion mass tolerance, 0.8 Da; fully tryptic enzyme specificity; two missed cleavages; dynamic modifications of cysteine carbamidomethylation and of methionine oxidation. The proportion of false positive assignations among the tentative peptide identifications, also called false discovery rate (FDR), has been estimated by using decoy databases constructed from the target database and was set at 1%.