PXD049342

PXD049342 is an original dataset announced via ProteomeXchange.

Title	Comparison of three methods for isolating human plasma EVs by LC-MSMS
Description	The lack of standardized protocols for isolating extracellular vesicles (EVs), particularly from biobank-stored plasma, poses a substantial limitation for the study of biomarkers. Combining current isolation methods could enhance the specificity and purity of EVs isolation for their further use in diagnosis and personalized medicine. In this study, plasma samples from healthy individuals were subjected to extracellular vesicle isolation using ultracentrifugation (UC), size exclusion chromatography (SEC), and a combined approach of SEC and UC (SEC+UC). Characterization of the isolated EVs with NTA and TEM indicated that all isolation methods successfully isolated EVs, being not altered due to the long-term storage. Also, the western blot analysis confirmed the presence of exosome markers in all isolates but showed a higher expression of albumin in EVs-UC, suggesting potential plasma protein contamination. Proteomic analysis of samples from different isolation methods identified 542 proteins, with SEC+UC yielding the most complex proteome at 364 proteins. GO analysis of cellular component revealed differences in terms related to EVs and plasma, where SEC+UC proteins had the highest proportion of exosomal proteins. As a result of further study of the unique proteins detected in each isolation method, it was revealed that the SEC+UC method detected 181 unique proteins, demonstrating its superiority in the detection of low plasma concentration proteins. These findings support the robustness of the SEC+UC approach for EV isolation and proteomic studies due to its high efficiency and purity in isolating EVs. This study emphasizes the efficacy of the SEC+UC approach in obtaining highly pure and diverse EV populations suitable for comprehensive proteomic analysis with application to the discovery of biomarkers from biobank-stored plasma.
HostingRepository	PRIDE
AnnounceDate	2024-07-03
AnnouncementXML	Submission_2024-07-03_02:01:13.555.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD049342
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ana Torres
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-12 11:26:54	ID requested
⏵ 1	2024-07-03 02:01:14	announced

10.1186/s12575-024-00243-4;

Torres A, Bernardo L, S, á, nchez C, Morato E, Solana JC, Carrillo E, Comparing the Proteomic Profiles of Extracellular Vesicles Isolated using Different Methods from Long-term Stored Plasma Samples. Biol Proced Online, 26(1):18(2024) [pubmed]

10.6019/PXD049342;

submitter keyword: Human, Plasma, Extracellular vesicles

Eugenia Carrillo
contact affiliation	National Center for Microbiology, Instituto de Salud Carlos III
contact email	ecarrillo@isciii.es
lab head
Ana Torres
contact affiliation	Centro Nacional de Microbiología, Instituto de Salud Carlos III
contact email	anamaria.torres@isciii.es
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD049342
     1. Label: PRIDE project
     2. Name: Comparison of three methods for isolating human plasma EVs by LC-MSMS