Dataset Information

HEALTHY VERSUS ANEURYSMAL AORTA PROTEOMICS ANALYSIS

ABSTRACT: 0.5M NACL EXTRACTION REPLAY ANALYSIS

INSTRUMENT(S): LTQ Orbitrap, instrument model

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: ATHANASIOS DIDANGELOS

PROVIDER: PRD000416 | Pride | 2012-07-20

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_16940.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_16940.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_16940.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_16941.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_16941.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 252

Publications

Extracellular matrix composition and remodeling in human abdominal aortic aneurysms: a proteomics approach.

Didangelos Athanasios A Yin Xiaoke X Mandal Kaushik K Saje Angelika A Smith Alberto A Xu Qingbo Q Jahangiri Marjan M Mayr Manuel M

Molecular & cellular proteomics : MCP 20110518 8

Abdominal aortic aneurysms (AAA) are characterized by pathological remodeling of the aortic extracellular matrix (ECM). However, besides the well-characterized elastolysis and collagenolysis little is known about changes in other ECM proteins. Previous proteomics studies on AAA focused on cellular changes without emphasis on the ECM. In the present study, ECM proteins and their degradation products were selectively extracted from aneurysmal and control aortas using a solubility-based subfraction ...[more]

PMID: 21593211

Similar Datasets

Project description:Here, we established for the first time a proteomic analysis of B. methanolicus MGA3, and we used this approach to compare cells grown on methanol and mannitol at 50°C as well as cells grown on methanol at 37°C and 50°C. Bacillus methanolicus MGA3 is a facultative methylotroph of industrial relevance that is able to grow on methanol as its sole source of carbon and energy. The Gram-positive bacterium possesses a soluble NAD-dependent methanol dehydrogenase and assimilates formaldehyde via the ribulose monophosphate (RuMP) cycle. We used label-free quantitative proteomics to generate reference proteome data for this bacterium and compared the proteome of B. methanolicus MGA3 on two different carbon sources (methanol and mannitol) as well as two different growth temperatures (50°C and 37°C). From a total of approximately 1,200 different detected proteins, approximately 1,000 of these were used for quantification. While the levels of 213 proteins were significantly different at the two growth temperatures tested, the levels of 109 proteins changed significantly when cells were grown on different carbon sources. The carbon source strongly affected the expression of enzymes related to carbon metabolism, and in particular, both dissimilatory and assimilatory RuMP cycle enzyme levels were elevated during growth on methanol compared to mannitol. Our data also indicate that B. methanolicus has a functional TCA cycle that is differentially regulated on mannitol and methanol. Other proteins presumed to be involved in growth on methanol were constitutively expressed under the different growth conditions. Protein Identification: Raw data of gel slices with equal molecular weight were loaded together into the software package Progenesis LCMS Version. 4.1 (www.nonlinear.com), a software tool developed for label-free quantification of LC–MS data. Data was analyzed according to Progenesis LCMS analysis in Weisser et al., In brief, for data loading, the option "High Mass Accuracy Instrument" was selected. LC–MS data were normalized and aligned according to manufacturer’s specifications. In the aligning step manual seeding of "three to five" vectors along the retention time gradient was performed followed by automatic alignment. For the identification of peptide features in the corresponding mass spectrometry files, Mascot generic files (.mgf file format) are generated with Progenesis LCMS (using up to five tandem mass spectra for each feature with the top 200 fragment ion peaks ,charge deconvolution and de-isotopting activated). Mgf files were searched by Mascot 2.3 search engine against an amino acid database containing 20,399 entries including 3,418 MGA3 annotated proteins (downloaded from Uniprot on August 2013), 6,651 yeast proteins, 261 known mass spectrometry contaminants as forward entries and from all forward entries except the contaminats, a reverse decoy sequence. Parameters for precursor tolerance and fragment ion tolerance were set to ± 10 ppm and ± 0.6 Da, respectively. Mascot results were loaded into Scaffold v4.05, using the options for protein clustering and high mass accuracy PeptideProphet scoring.