PXD039504-1

PXD039504 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Data-independent acquisition phosphoproteomics of urinary extracellular vesicles enables renal cell carcinoma grade differentiation
Description	Translating the research capability and knowledge in cancer signaling into clinical settings has been slow and ineffective. Recently, extracellular vesicles (EVs) have emerged as a promising source for developing disease phosphoprotein markers to monitor disease status. This study focuses on the development of a robust data-independent acquisition (DIA) using mass spectrometry to profile urinary EV phosphoproteomics for renal cell cancer (RCC) grades differentiation. We examined gas-phase fractionated (GPF) library, direct DIA (library-free), forbidden zones, and several different windowing schemes. After the development of a DIA mass spectrometry method for EV phosphoproteomics, we applied the strategy to identify and quantify urinary EV phosphoproteomes from 57 individuals representing low-grade clear cell RCC, high-grade clear cell RCC, chronic kidney disease (CKD), and healthy control (HC) individuals. Urinary EVs were efficiently isolated by functional magnetic beads, and EV phosphopeptides were subsequently enriched by PolyMAC. We quantified 2,584 unique phosphosites and observed that multiple prominent cancer-related pathways, such as ErbB signaling, renal cell carcinoma, and regulation of actin cytoskeleton, were only upregulated in high-grade clear cell RCC. These results show that EV phosphoproteome analysis utilizing our optimized procedure of EV isolation, phosphopeptide enrichment, and DIA method provides a powerful tool for future clinical applications.
HostingRepository	MassIVE
AnnounceDate	2023-03-25
AnnouncementXML	Submission_2023-03-25_08:11:27.688.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marco Hadisurya
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Phospho
Instrument	Q Exactive HF-X

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-16 19:49:49	ID requested
⏵ 1	2023-03-25 08:11:28	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Renal cell carcinoma, Extracellular vesicles, Phosphorylation, Cancer Grades

submitter keyword: Renal cell carcinoma, Extracellular vesicles, Phosphorylation, Cancer Grades

Contact List

W. Andy Tao
contact affiliation	Purdue University
contact email	taow@purdue.edu
lab head
Marco Hadisurya
contact affiliation	Purdue University
contact email	mhadisur@purdue.edu
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive.ucsd.edu/MSV000091069/