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PXD039504

PXD039504 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleData-independent acquisition phosphoproteomics of urinary extracellular vesicles enables renal cell carcinoma grade differentiation
DescriptionTranslating 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.
HostingRepositoryMassIVE
AnnounceDate2023-03-25
AnnouncementXMLSubmission_2023-03-25_08:11:27.688.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMarco Hadisurya
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListPhospho
InstrumentQ Exactive HF-X
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-01-16 19:49:49ID requested
12023-03-25 08:11:28announced
Publication List
no publication
Keyword List
submitter keyword: Renal cell carcinoma, Extracellular vesicles, Phosphorylation, Cancer Grades
Contact List
W. Andy Tao
contact affiliationPurdue University
contact emailtaow@purdue.edu
lab head
Marco Hadisurya
contact affiliationPurdue University
contact emailmhadisur@purdue.edu
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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