PXD063043-1

PXD063043 is an original dataset announced via ProteomeXchange.

Title	High-throughput plasma/serum proteomics by coupling nanoparticle protein corona-based sample preparation and capillary zone electrophoresis-tandem mass spectrometry
Description	A high-throughput workflow for bottom-up proteomics (BUP) of human plasma using capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) and nanoparticle protein corona-assisted sample preparation is presented. The streamlined approach enabled the identification and quantification of hundreds of proteins from plasma/serum samples in 3.5 hours from sample to data. Nanoparticles with varied physiochemical properties studied in this work captured different pools of the plasma/serum proteome in the protein coronas, and the protein corona-based sample preparation approach enabled the measurement of low-abundance proteins compared to the approach without nanoparticles. Applying this high-throughput workflow to serum samples of a mouse NUT carcinoma (NC) cancer model allowed the determination of differentially expressed serum proteins between NC bearing mice and healthy controls. By comparing our quantitative proteomics data with published transcriptomics data, we revealed a handful of potential serum protein biomarkers of NC cancer (e.g., secreted phosphoprotein 1, Spp1). We expect this high-throughput workflow, with additional improvement in the speed of the mass spectrometer, will be useful for advancing the discovery of new protein biomarkers of diseases (e.g., cancer) using plasma/serum samples valuable for liquid biopsy applications.
HostingRepository	PRIDE
AnnounceDate	2025-08-04
AnnouncementXML	Submission_2025-08-03_16:26:19.540.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qianyi Wang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-16 16:16:44	ID requested
⏵ 1	2025-08-03 16:26:20	announced

10.1039/d5ay00721f;

Wang Q, Sadeghi SA, Fang F, Zheng D, Luo C, Gao G, Wang Q, Gu B, Sun L, High-throughput plasma/serum proteomics by coupling nanoparticle protein corona-based sample preparation and capillary zone electrophoresis-tandem mass spectrometry. Anal Methods, 17(31):6356-6365(2025) [pubmed]

submitter keyword: nanoparticle protein corona,bottom-up proteomics, high-throughput, CZE-MS/MS, biomarker

Liangliang Sun
contact affiliation	Department of Chemistry, Michigan State University, MI 48824, USA
contact email	lsun@chemistry.msu.edu
lab head
Qianyi Wang
contact affiliation	Michigan State University
contact email	wangqi55@msu.edu
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/2025/08/PXD063043

PRIDE project URI

• PRIDE
  1. PXD063043
     1. Label: PRIDE project
     2. Name: High-throughput plasma/serum proteomics by coupling nanoparticle protein corona-based sample preparation and capillary zone electrophoresis-tandem mass spectrometry