PXD008441

PXD008441 is an original dataset announced via ProteomeXchange.

Title	Human Plasma Proteome with Three-dimensional Strategies by Highresolution Quadrupole Orbitrap Mass Spectrometry
Description	Five three-dimensional strategies combining HAP depletion (the 1st dimension) and protein fractionation (the 2nd dimension), followed by LC-MS/MS analysis (the 3rd dimension) were developed and compared for human plasma proteome profiling. Pros and cons of the five strategies are discussed for two issues: HAP depletion and complexity reduction. Strategies A and B used proteome equalization and tandem Seppro IgY14 immunodepletion, respectively, as the first dimension. Proteome equalization (strategy A) was biased toward the enrichment of basic and low-molecular weight proteins and had limited ability to enrich low-abundance proteins. By tandem removal of HAPs (strategy B), the efficiency of HAP depletion was significantly increased, whereas more off-target proteins were subtracted simultaneously. In the comparison of complexity reduction, strategy D involved a deglycosylation step before high-pH RPLC separation. However, the increase in sequence coverage did not increase the protein number as expected. Strategy E introduced SDS-PAGE separation of proteins, and the results showed oversampling of HAPs and identification of fewer proteins. Strategy C combined single Seppro IgY14 immunodepletion, high-pH RPLC fractionation and LC-MS/MS analysis. It generated the largest dataset, containing 1544 plasma protein groups and 258 newly identified proteins in a 30-h-machine-time analysis, making it the optimum three-dimensional strategy in our study. Further analysis of the integrated data from the five strategies showed identical distribution patterns in terms of sequence features and GO functional analysis with the 1929-plasma-protein dataset, further supporting the reliability of our plasma protein identifications. The characterization of 20 cytokines in the concentration range from sub-nanograms/milliliter to micrograms/milliliter demonstrated the sensitivity of the current strategies.
HostingRepository	iProX
AnnounceDate	2017-06-20
AnnouncementXML	Submission_2017-12-18_00:32:34.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cheng Chang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-13 19:38:55	ID requested
1	2017-12-13 19:39:06	announced
2	2017-12-14 22:41:00	announced	Update experiment information.
⏵ 3	2017-12-18 00:32:35	announced	Update experiment information.

Zhao Y, Chang C, Qin P, Cao Q, Tian F, Jiang J, Li X, Yu W, Zhu Y, He F, Ying W, Qian X, Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry. Anal Chim Acta, 904():65-75(2016) [pubmed]

submitter keyword: Plasma, Proteome profiling, IgY14 immunodepletion, Biomarker, Strategy A, Strategy B, Strategy C, Strategy D, Strategy E

Prof. Xiaohong Qian
contact affiliation	National Center for Protein Sciences (Beijing), Beijing Proteome Research Center.
contact email	qianxh1@163.com
lab head
Cheng Chang
contact affiliation	National Center for Protein Sciences (Beijing), Beijing Proteome Research Center.
contact email	1987ccpacer@163.com
dataset submitter

iProX dataset URI