PXD056613

PXD056613 is an original dataset announced via ProteomeXchange.

Title	The proteome of circulating extracellular vesicles and their functional effect on platelets vary with the isolation method
Description	Extracellular vesicles (EVs) play a crucial role in cell-to-cell communication and serve as a source of biomarkers in several pathologies. In this study, we aimed to characterize plasma-derived EVs isolated by ultracentrifugation (UC) or size exclusion chromatography (SEC) to define the best method for proteomic and functional studies. EVs characterization included nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), detection of biomarkers by western blotting, and quantitative proteomic analysis. SEC-EVs samples had higher particle and protein concentration, particle-to-protein ratio, and smaller size compared to UC-EVs. A total of 171 proteins were identified through Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) analysis, with 11 increased in SEC-EVs and 5 in UC-EVs. The proteins increased in UC-EVs are complement proteins and immunoglobulins, while the proteins increased in SEC-EVs are apolipoproteins and proteins present in the extracellular space. Functional studies with EVs from activated platelets confirmed that EVs isolated by SEC exacerbate platelet aggregation, whereas there was no effect induced by UC-EVs. The latter suggests that EVs obtained by SEC seem more suitable for platelet-related functional studies compared to those obtained by UC. The results presented pave the way for future clinical orientated studies involving plasma-derived EVs.
HostingRepository	PRIDE
AnnounceDate	2025-02-14
AnnouncementXML	Submission_2025-02-14_01:14:19.307.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Susana Bravo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-08 05:52:57	ID requested
⏵ 1	2025-02-14 01:14:19	announced

Dataset with its publication pending

submitter keyword: platelets, ultracentrifugation,extracellular vesicles, size exclusion chromatography, proteomics.

Susana B Bravo López
contact affiliation	Instituto de Investigaciones Sanitarias de Santiago de Compostela
contact email	sbbravo@gmail.com
lab head
Susana Bravo
contact affiliation	FIDIS
contact email	sbbravo@gmail.com
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/2025/02/PXD056613

PRIDE project URI

• PRIDE
  1. PXD056613
     1. Label: PRIDE project
     2. Name: The proteome of circulating extracellular vesicles and their functional effect on platelets vary with the isolation method