PXD003720

PXD003720 is an original dataset announced via ProteomeXchange.

Title	Analysis of LDL-associated proteins using the method of digitized native protein mapping
Description	The method of digitized native protein mapping, combining nondenaturing micro 2DE, grid gel-cutting and quantitative LC-MS/MS (in data-independent acquisition mode, or MSE), was improved by using a new MS/MS mode, ion mobility separation enhanced-MSE (HDMSE) and applied to analyze the area of human plasma low-density lipoproteins (LDL). An 18 mm * 4.8 mm rectangular area which included LDL on a nondenaturing micro 2D gel of human plasma was grid-cut into 72 square gel pieces and subjected to quantitative LC-MS/MS. Compared with MSE, HDMSE showed significantly higher performance, by assigning 50% more proteins and detecting each protein in more squares. Totally 253 proteins were assigned with LC-HDMSE and the quantity distribution of each was reconstructed as a native protein map. The maps showed Apo B-100 was the most abundant protein in the grid-cut area, concentrated at pI 5.4-6.1 and apparent mass ca. 1000 kDa, which corresponded to four gel pieces, squares 39-42. An Excel macro was prepared to search protein maps which show protein quantity peaks localized within the concentrated region of Apo B-100 (squares 39-42). Twenty-two proteins out of the 252 matched this criteria, in which nineteen proteins have been reported to be associated with LDL. This method require only several microliters of a plasma sample and the principle of the protein separation is totally different from ultracentrifugation. The results obtained by this method would provide new insights on the structure and function of LDL.
HostingRepository	PRIDE
AnnounceDate	2016-05-17
AnnouncementXML	Submission_2016-05-17_09:44:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ya Jin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-01 02:29:43	ID requested
⏵ 1	2016-05-17 09:44:48	announced

Jin Y, Chen J, Wang A, Zhang J, Chen S, Manabe T, Tan W, Analysis of low-density lipoprotein-associated proteins using the method of digitized native protein mapping. Electrophoresis, 37(14):2063-74(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Digitized native protein mapping, nondenaturing micro 2DE, grid gel-cutting, quantitative LC-HDMSE, protein-protein interactions, human plasma low-density lipoprotein

Ya Jin
contact affiliation	School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, P. R. China
contact email	ya.jin@ymail.com
lab head
Ya Jin
contact affiliation	School of Bioscience and Biotechnology, South China University of Technology
contact email	ya.jin@ymail.com
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/PXD003720

PRIDE project URI

• PRIDE
  1. PXD003720
     1. Label: PRIDE project
     2. Name: Analysis of LDL-associated proteins using the method of digitized native protein mapping