PXD003930

PXD003930 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of distinct regions of human carotid atherosclerotic plaques
Description	Protein profiles were determined from different distinct regions of human atherosclerotic plaques, including: internal control, fatty streak, plaque shoulder, plaque centre, and fibrous cap. Protein extracts from all 5 regions, from 3 men and 3 women, were separated by two-dimensional gel electrophoresis (in total 30 2-DE gels). Stained gels were matched by protein spot distribution, and a protein mapping was performed to identify as many protein spots as possible, by MALDI-TOF MS / peptide mass fingerprinting (Voyager DE Pro; Applied Biosystems). This resulted in the identification of 97 protein spots, corresponding to 52 unique protein by accession number. To expand on this nLC-MS/MS (Easy-nLC / LTQ Orbitrap Velos Pro; Thermo Fisher Scientific) experiments were run on additional carotid plaque samples from 10 men and 10 women, using three of the predefined regions; internal control, fatty streak, plaque core. MS/MS analysis resulted in the identification of over 1000 proteins. Human carotid atherosclerotic plaques (n = 26) were obtained from the Linköping Carotid Study, and all methods/protocols described herein have been approved by the local ethics committee (Linköping University Hospital, Linköping, Sweden). Written informed consent was also obtained from all patients.
HostingRepository	PRIDE
AnnounceDate	2019-01-03
AnnouncementXML	Submission_2019-01-03_02:26:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liam Ward
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Voyager-DE PRO

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-08 07:30:50	ID requested
1	2016-05-24 00:26:52	announced
⏵ 2	2019-01-03 02:26:51	announced	Updated publication reference for PubMed record(s): 27198765, 30594242.

Ward LJ, Olausson P, Li W, Yuan XM, Proteomics and multivariate modelling reveal sex-specific alterations in distinct regions of human carotid atheroma. Biol Sex Differ, 9(1):54(2018) [pubmed]

Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, Distinctive proteomic profiles among different regions of human carotid plaques in men and women. Sci Rep, 6():26231(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, carotid artery, atherosclerosis, MS/MS, peptide mass fingerprinting

Xi-Ming Yuan
contact affiliation	Occupational and Environmental Medicine Center, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
contact email	ximing.yuan@liu.se
lab head
Liam Ward
contact affiliation	Linköping University
contact email	liam.ward@liu.se
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/2016/05/PXD003930

PRIDE project URI

• PRIDE
  1. PXD003930
     1. Label: PRIDE project
     2. Name: Proteomic analysis of distinct regions of human carotid atherosclerotic plaques