PXD029710

PXD029710 is an original dataset announced via ProteomeXchange.

Title	Nanodiamond Solid Phase Extraction and Triton X-114 Cloud Point Separation for Robust Fractionation and Shotgun Proteomics Analysis of Human Serum Proteome
Description	Human serum is one of the most attractive specimens in biomarker research. However, its overcomplicated properties have hindered the analysis of low-abundance proteins by conventional mass spectrometry techniques. This work proposes an innovative strategy for utilizing nanodiamonds (NDs) in combination with Triton X-114 protein extraction to fractionate the crude serum to six pH-tuned fractions, simplifying the overall proteome and facilitate protein profiling with high efficiency. A total of 663 pro-teins are identified and evenly distributed among the fractions along with 39 FDA-approved biomarkers – a remarkable increase from the 230 proteins found in unfractioned crude serum. In the low-abundance proteins section, 88 proteins with 7 FDA-approved biomarkers are detected – a marked increase from the 15 proteins observed in the untreated sample. Notably, fractions at pH11, derived from the aqueous phase of detergent separation, suggest potential applications in rapid and robust protein analysis. Notably, by outlining the excellent properties of the NDs for proteomic research, this work suggests a promising extraction protocol utilizing the great compatibility of NDs with streamlined serum proteomics, and identifies potential avenues for future developments. Finally, we believe that this proposed method to improve shotgun proteomics may be of interest to a specialized proteomics community.
HostingRepository	PRIDE
AnnounceDate	2022-02-14
AnnouncementXML	Submission_2022-02-14_01:33:26.834.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029710
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Le Nghia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-12 06:06:58	ID requested
⏵ 1	2022-02-14 01:33:27	announced

Khuong HL, Chen CH, Lin JL, Le TN, Pham TH, Le TBT, Nguyen XC, Phan VC, Chu HH, Hsiao WW, Nguyen TMP, Pham DM, Nanodiamond Solid-Phase Extraction and Triton X-114 Cloud Point Separation for Robust Fractionation and Shotgun Proteomics Analysis of the Human Serum Proteome. J Proteome Res, 21(1):67-76(2022) [pubmed]

submitter keyword: nanodiamond, solid phase extraction, triton X-114, proteomic analysis, cloud point separation, human serum, prote-ome, fractionation, LC-MS/MS

Minh Dinh Pham
contact affiliation	Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
contact email	minhphd@gmail.com
lab head
Le Nghia
contact affiliation	Department of Chemical Engineering, National Taiwan University of Science and Technology
contact email	letrongnghia720@gmail.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/2022/02/PXD029710

PRIDE project URI

• PRIDE
  1. PXD029710
     1. Label: PRIDE project
     2. Name: Nanodiamond Solid Phase Extraction and Triton X-114 Cloud Point Separation for Robust Fractionation and Shotgun Proteomics Analysis of Human Serum Proteome