PXD061653

PXD061653 is an original dataset announced via ProteomeXchange.

Title	Tetraspanin-based immunocapture for high-depth proteomic profiling of extracellular vesicles from cerebrospinal fluid for biomarker discovery
Description	Due to its proximity to cells of the central nervous system, cerebrospinal fluid (CSF) is an important source of novel biomarkers for neurological diseases. Membrane-bound extracellular vesicles (EVs) are enriched for proteins of intracellular and membrane origin, implicated in the pathogenesis of some neurological diseases and secreted into CSF. Proteomic profiling of CSF-EVs, however, is limited by the large volumes required for typical EV isolation protocols. We appraised the performance of tetraspanin-based immunocapture to reduce required sample volume for EV isolation and subsequent proteomic profiling by library-free data independent-acquisition (DIA) mass spectrometry. Immunocapture was effective using CSF volumes as low as 200 µL, consistently detecting core EV markers and reducing relative levels of non-vesicular proteins such as Apolipoprotein B and galectin 3 binding protein (LGALS3BP) compared with size-exclusion chromatography (SEC). Proteomic depth reached 811±14 protein groups in EVs from 200 µL CSF, increasing to 1285±224 when using feature alignment across runs with up to 1000 µL starting volume. Increased depth was observed for both transmembrane and secreted proteins using immunocapture compared with SEC, with proportional enrichment of transmembrane proteins. Abundance and precursor peptide locations for potential neuronal-specific immunocapture targets described in the literature were assessed, including L1CAM and ATP1A3. This work demonstrates the effectiveness of tetraspanin immunocapture for proteomic profiling of EVs in small volumes of CSF that can be adapted to use with cell-type-specific markers of choice.
HostingRepository	PRIDE
AnnounceDate	2026-02-23
AnnouncementXML	Submission_2026-02-22_16:24:02.980.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	iolanda Vendrell
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-10 08:36:19	ID requested
⏵ 1	2026-02-22 16:24:03	announced

Dellar ER, Vendrell I, Fischer R, Thompson AG, Tetraspanin-based immunocapture for high-depth proteomic profiling of extracellular vesicles from cerebrospinal fluid for biomarker discovery. Clin Proteomics, 23(1):8(2026) [pubmed]

10.1186/s12014-025-09579-9;

submitter keyword: cerebrospinal fluid, proteomics, tetraspanin,Extracellular vesicle, immunocapture.

Alexander G Thompson
contact affiliation	Nuffield Department of Clinical Neurosciences, University of Oxford
contact email	alexander.thompson@ndcn.ox.ac.uk
lab head
iolanda Vendrell
contact affiliation	Target Discovery Institute, NDMRB
contact email	iolanda.vendrell@ndm.ox.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD061653
     1. Label: PRIDE project
     2. Name: Tetraspanin-based immunocapture for high-depth proteomic profiling of extracellular vesicles from cerebrospinal fluid for biomarker discovery