<<< Full experiment listing

PXD052726

PXD052726 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimization of ultracentrifugation-based method to enhance the purity and proteomic profiling depth of plasma-derived extracellular vesicles and particles
DescriptionCirculating extracellular vesicles and particles (EVPs) are being investigated as potential biomarkers for early cancer detection, prognosis, and disease monitoring. However, the suboptimal purity of EVPs isolated from peripheral blood plasma has posed a challenge of in-depth analysis of the EVP proteome. Here, we compared the effectiveness of different methods for isolating EVPs from healthy donor plasma, including ultracentrifugation (UC)-based protocols, phosphatidylserine-Tim4 interaction-based affinity capture (referred to as "PS"), and several commercial kits. Modified UC methods with an additional UC washing or size exclusion chromatography step substantially improved EVP purity and enabled the detection of additional proteins via proteomic mass spectrometry, including many plasma membrane and cytoplasmic proteins involved in vesicular regulation pathways. This improved performance was reproduced in cancer patient plasma specimens, resulting in the identification of a greater number of differentially expressed EVP proteins, thus expanding the range of potential biomarker candidates. However, PS and other commercial kits did not outperform UC-based methods in improving plasma EVP purity. PS yielded abundant contaminating proteins and a biased enrichment for specific EVP subsets, thus unsuitable for proteomic profiling of plasma EVPs. Therefore, we have optimized UC-based protocols for circulating EVP isolation, which enable further in-depth proteomic analysis for biomarker discovery.
HostingRepositoryPRIDE
AnnounceDate2024-08-11
AnnouncementXMLSubmission_2024-08-10_16:27:11.471.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterhenrik molina
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion Lumos; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-05-30 11:57:58ID requested
12024-08-10 16:27:12announced
Publication List
10.1002/jex2.167;
Wan Z, Gu J, Balaji U, Bojmar L, Molina H, Heissel S, Pagano AE, Peralta C, Shaashua L, Ismailgeci D, Narozniak HK, Song Y, Jarnagin WR, Kelsen DP, Bromberg J, Pascual V, Zhang H, Optimization of ultracentrifugation-based method to enhance the purity and proteomic profiling depth of plasma-derived extracellular vesicles and particles. J Extracell Biol, 3(7):e167(2024) [pubmed]
Keyword List
submitter keyword: Extracellular vesicles and particles (EVPs)
early cancer detection
biomarkers
proteomics
Contact List
Haiying Zhang
contact affiliationDepartment of Pediatrics, Weill Cornell Medicine, New York, NY, USA
contact emailhaz2005@med.cornell.edu
lab head
henrik molina
contact affiliationTHE ROCKEFELLER UNIVERSITY
contact emailhenrik.molina@gmail.com
dataset submitter
Full Dataset Link List
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/2024/08/PXD052726
PRIDE project URI
Repository Record List
[ + ]