PXD063334-1

PXD063334 is an original dataset announced via ProteomeXchange.

Title	Proteomic and lipidomic profiling of immune cell-derived subpopulations of extracellular vesicles
Description	Introduction: Extracellular vesicles (EVs) are a heterogeneous group of membrane-enclosed vesicles released by cells. They play important roles in intercellular communication and contribute to several physiological and pathological processes. Cells release subpopulations of EVs with distinct biogenesis and functions, however, we currently have few markers to differentiate them. This study therefore aimed to determine proteomic and lipidomic differences among four EV subpopulations of varying sizes and densities. Methods: Large and small EVs (L-EVs and S-EVs) were isolated from two immune cell lines by differential ultracentrifugation at 16,500 × g and 118,000 × g, respectively. The crude EVs were then further separated by density cushion centrifugation. EVs were isolated from the interphase between 1.079-1.146 and 1.146-1.185 g/ml, hereafter referred to as low density (LD) and high density (HD), respectively. This resulted in four subpopulations of EVs, namely, L-EV LD, L-EV HD, S-EV LD, and S-EV HD. The purity, morphology, size, and yield of EVs were determined by nanoparticle tracking analysis, electron microscopy, and western blot. The proteome and lipidome of the four subpopulations of EVs were determined with mass spectrometry. Results: A total of 5364 proteins were quantified in the dataset. L-EV and S-EVs as well as LD and HD were well separated. Briefly, L-EVs LD were enriched in mitochondrial proteins such as the TIMM/TOMM complex, MICOS, and ATP5 proteins, while L-EVs HD were enriched in proteins associated with the cytoskeleton, such as KIF proteins. Furthermore, S-EVs LD were enriched in tetraspanins and ESCRT machinery proteins, while S-EVs HD were enriched in histones, CCT proteins, and proteins from the complement pathway. While proteins such as flotillins, RABs, annexins, and integrins were enriched in two or several subpopulations. Our study quantified 108 lipids, and the most abundant lipids in EVs were phosphatidylcholine (PC), sphingomyelin, and phosphatidylethanolamine (PE). The most profound difference was that PE was less abundant in L-EVs LD as compared to the other EV subtypes and ceramides were enriched in L-EVs as compared to S-EVs. Conclusion: This study demonstrates that the proteome strongly differs in EV subpopulations separated at different densities. Furthermore, it validates several protein groups that have previously been suggested to be enriched in either S-EVs or L-EVs.
HostingRepository	PRIDE
AnnounceDate	2026-03-16
AnnouncementXML	Submission_2026-03-16_04:41:58.267.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Proteomics Core Facility
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	methylthiolated residue; monohydroxylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-25 06:04:47	ID requested
⏵ 1	2026-03-16 04:41:59	announced

10.1002/pmic.70096;

submitter keyword: Protein cargo, Microvesicles, Extracellular Vesicles,Exosomes, Lipid composition

Cecilia Lässer
contact affiliation	Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
contact email	cecilia.lasser@gu.se
lab head
Proteomics Core Facility
contact affiliation	SAMBIO Core Facilities, Sahgrenska Academy, University of Gothenburg
contact email	gupcf@outlook.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/2026/03/PXD063334

PRIDE project URI

• PRIDE
  1. PXD063334
     1. Label: PRIDE project
     2. Name: Proteomic and lipidomic profiling of immune cell-derived subpopulations of extracellular vesicles