PXD059819

PXD059819 is an original dataset announced via ProteomeXchange.

Title	FAEVEr 96well for high-throughput EV proteomics
Description	Extracellular vesicles (EVs), nanoscale vesicles that are secreted by cells, are critical mediators for inter-cellular communication and play a crucial role in cancer development. As a result, EVs are regarded to have high potential value towards the clinic, both for diagnostic and therapeutic applications. Unfortunately, EVs reside in complex biofluids and their consistent isolation in adequate purities for bottom-up mass spectrometry has proven to be challenging, especially in high-throughput. Indeed, traditional isolation methods are often labor-intensive, not scalable and may vary in yield and purity. Here, we investigate the incorporation of the previously described filter-aided EV enrichment (FAEVEr) strategy in a streamlined 96well format for the isolation of EVs from conditioned medium, including the initial pre-clearing, the EV isolation and purification and even downstream sample preparation for proteomics. We evaluated our approach comparing the results with ultracentrifugation, still the most widely used method for EV enrichment, in terms of protein identifications, consistency, reproducibility and overall performance, including the invested time, resources and expertise. In addition, our results show that including relative high percentages of TWEEN-20, a mild detergent, positively affects the final purity of the EV proteome by removing the bulk of non-EV proteins (e.g. serum proteins) and significantly increasing the number of transmembrane protein identifications. Moreover, the FAEVEr 96well strategy improves the reproducibility with a consistent number of protein identifications and decreased number of missing values across the replicates. This reliability promotes the validity and comparability between experimental results, which is essential in both a clinical and research setting, where consistency is paramount.
HostingRepository	PRIDE
AnnounceDate	2025-07-10
AnnouncementXML	Submission_2025-07-10_08:01:39.610.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jarne Pauwels
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-15 06:23:55	ID requested
⏵ 1	2025-07-10 08:01:39	announced

10.1002/JEV2.70103;

submitter keyword: extracellular vesicles,TWEEN-20, 300 kDa MWCO filtration

Kris Gevaert
contact affiliation	1VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium 2Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
contact email	kris.gevaert@vib-ugent.be
lab head
Jarne Pauwels
contact affiliation	VIB-Ugent
contact email	jarne.pauwels@vib-ugent.be
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/2025/07/PXD059819

PRIDE project URI

• PRIDE
  1. PXD059819
     1. Label: PRIDE project
     2. Name: FAEVEr 96well for high-throughput EV proteomics