PXD045192

PXD045192 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Hands-free Proteomic Profiling of Urinary Extracellular Vesicles with a High-throughput Automated Workflow
Description	Extracellular vesicles (EVs) have emerged as a promising source of disease biomarkers for non-invasive early-stage diagnoses, but a bottleneck in EV sample processing restricts their immense potential in clinical applications. Existing methods are limited by low EV yield and integrity, slow processing speeds, low sample capacity, and poor recovery efficiency. We aimed to address these issues with a high-throughput, automated workflow for EV isolation, EV lysis, protein extraction, and protein denaturation. The automation can process clinical urine samples in parallel, resulting in protein-covered beads ready for various analytical methods, including immunoassays, protein quantitation assays, and mass spectrometry. Compared to the standard manual lysis method for contamination levels, efficiency, and consistency of EV isolation, the automated protocol shows reproducible and robust proteomic quantitation with less than 10% median coefficient of variation. When we applied the method to clinical samples, we identified a total 3,793 unique proteins and 40,380 unique peptides, with 992 significantly upregulated proteins in kidney cancer patients versus healthy controls. These upregulated proteins were found to be involved in several important kidney cancer metabolic pathways also identified with a manual control. This hands-free workflow represents a practical EV extraction and profiling approach that can benefit both clinical and research applications, streamlining biomarker discovery, tumor monitoring, and early cancer diagnoses.
HostingRepository	jPOST
AnnounceDate	2023-10-20
AnnouncementXML	Submission_2023-10-20_14:24:08.006.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marco Hadisurya
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: cellular organisms; NCBI TaxID: 131567;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-07 05:57:04	ID requested
⏵ 1	2023-10-20 14:24:08	announced

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: kidney cancer, proteomics, urine, renal cell carcinoma, DIA, automation, TimsTOF, high-throughput, EVtrap, extracellular vesicles, exosomes

submitter keyword: kidney cancer, proteomics, urine, renal cell carcinoma, DIA, automation, TimsTOF, high-throughput, EVtrap, extracellular vesicles, exosomes

Contact List

W. Andy Tao
lab head
Marco Hadisurya
contact affiliation	Purdue University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST 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://ftp.jpostdb.org/JPST002311/