PXD023102

PXD023102 is an original dataset announced via ProteomeXchange.

Title	High-throughput, in-depth and absolute plasma proteome analysis with data-independent acquisition mass spectrometry for biomarker discovery and insight into molecular mechanism of myelodysplastic syndromes
Description	Mass spectrometry-based plasma proteomics has been approved to be a viable tool which can quantify hundreds of proteins in one single-LC-MS/MS experiment for biomarker discovery and gain insights of the disease mechanisms. Here we developed a new strategy exploiting data-independent acquisition (DIA) MS-based workflow for a high-throughput, in-depth and absolute quantification of plasma proteins without depleting high abundant protein in one single shot experiment. We tested spectral libraries, optimized LC instrumentation and DIA-MS experimental parameters, and developed absolute quantification algorithms. The strategy established here is applied to myelodysplastic syndromes (MDS) disease cohort as a pilot study. Total 769 proteins were absolutely quantified cross 22 clinical patient sample spanning over 6 orders of magnitude with quantification limit of 10-20 ng/ml, and 95 differentially expressed proteins were identified by adjusting p-value<0.05. A 10-protein combinations had excellent ability separating MDS to healthy (AUC=0.997). Functions of metabolomic vulnerabilities, acute inflammatory response, focal adhesion and microenvironment were revealed to be related to MDS.
HostingRepository	iProX
AnnounceDate	2020-12-12
AnnouncementXML	Submission_2020-12-13_18:10:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yue Zhou
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-13 18:09:03	ID requested
⏵ 1	2020-12-13 18:10:08	announced

Dataset with its publication pending

submitter keyword: Data-independent acquisition, plasma proteomics, quantitative proteomics, Orbitrap, myelodysplastic syndromes

Feng Guan
contact affiliation	JiangNan University, Northwest University
contact email	guanfeng@nwu.edu.cn
lab head
Yue Zhou
contact affiliation	JiangNan University
contact email	mrriyuekong@163.com
dataset submitter

iProX dataset URI