PXD017994

PXD017994 is an original dataset announced via ProteomeXchange.

Title	Plasma-derived EV Phosphoproteomics through Chemical Affinity Purification
Description	Invasive nature and pain caused to patients inhibit the routine use of tissue biopsy-based procedures for cancer diagnosis and surveillance. The analysis of extracellular vesicles (EVs) from biofluids have recently gained significant traction in the liquid biopsy field. EVs offer an essential “snapshot” of their precursor cells in real time and contain information-rich collection of nucleic acids, proteins, lipids, etc. The analysis of protein phosphorylation, as a direct marker of cellular signaling and disease progression, could be an important stepstone to successful liquid biopsy applications. Here, we introduce a rapid EV isolation method based on chemical affinity called EVtrap (Extracellular Vesicles Total Recovery and Purification) for EV phosphoproteomics analysis of human plasma. Incorporating EVtrap with high performance mass spectrometry (MS), we were able to identify over 16,000 unique peptides representing 2,238 unique EV proteins from just 5 μL plasma sample, including most known EV markers, with substantially higher recovery levels compared to ultracentrifugation. Most importantly, more than 5,500 unique phosphopeptides representing almost 1,600 phosphoproteins in EVs were identified using only 1 mL of plasma. Finally, we carried out quantitative EV phosphoproteomics analysis of plasma samples from patients diagnosed with chronic kidney disease or kidney cancer (RCC), identifying dozens of phosphoproteins capable of distinguishing disease states from healthy controls. The study demonstrates the potential feasibility of our robust analytical pipeline for cancer signaling monitoring by tracking plasma EV phosphorylation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:07:15.802.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anton Iliuk
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-11 06:00:59	ID requested
1	2020-06-15 05:05:37	announced
⏵ 2	2024-10-22 05:07:20	announced	2024-10-22: Updated project metadata.

Iliuk A, Wu X, Li L, Sun J, Hadisurya M, Boris RS, Tao WA, Plasma-Derived Extracellular Vesicle Phosphoproteomics through Chemical Affinity Purification. J Proteome Res, 19(7):2563-2574(2020) [pubmed]

10.1021/acs.jproteome.0c00151;

submitter keyword: exosomes, kidney cancer, phosphoproteomics,EVtrap

Andy Tao
contact affiliation	Purdue University
contact email	watao@purdue.edu
lab head
Anton Iliuk
contact affiliation	Purdue University
contact email	ailiuk@purdue.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017994
     1. Label: PRIDE project
     2. Name: Plasma-derived EV Phosphoproteomics through Chemical Affinity Purification