Journal article
Challenges and Opportunities in State-of-the-Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles
Proteomics (Weinheim), Vol.26(2-3), pp.9-20
02/2026
DOI: 10.1002/pmic.70036
PMCID: PMC12604859
PMID: 40955644
Abstract
Extracellular vesicles (EVs) are membrane-bound particles secreted by cells, playing crucial roles in intercellular communication. The composition of EVs can undergo changes in response to stress and disease conditions, making them excellent biomarker candidates. However, extracting protein information from EVs can be challenging due to their low abundance in complex biofluids and copurification with contaminant proteins and particles. Techniques to enrich EVs have their strengths and limitations, without one being able to purify EVs to complete homogeneity. This can lead to compromised recovery rates and increased complexity, making data interpretation difficult. In this viewpoint article, we explore the concept that better characterization of EV composition, followed by quantification of EV proteins in complex samples, might be a more viable route for biomarker development. Mass spectrometers can provide reproducible deep coverage of the EV proteome, despite sample impurities. This paradigm shift presents opportunities to integrate advanced bioinformatics tools to refine the EV proteome landscape, identify novel biomarkers, and streamline validation processes in biomarker development. By focusing on leveraging technology rather than achieving absolute purity, this approach can transform current practices and open opportunities for robust biomarker discovery. Herein, we highlight not only such opportunities but also challenges to implement this concept.
Details
- Title: Subtitle
- Challenges and Opportunities in State-of-the-Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles
- Creators
- Panshak P. Dakup - Pacific Northwest National LaboratoryIvo Diaz Ludovico - Pacific Northwest National LaboratoryYoungki You - Pacific Northwest National LaboratoryChaitra Rao - Indiana University School of MedicineJavier Flores - Pacific Northwest National LaboratoryLisa M. Bramer - Pacific Northwest National LaboratoryMarian Rewers - University of Colorado Anschutz Medical CampusBobbie-Jo M. Webb-Robertson - Pacific Northwest National LaboratoryThomas O. Metz - Pacific Northwest National LaboratoryRaghavendra G. Mirmira - University of ChicagoEmily K. Sims - Indiana University School of MedicineErnesto S. Nakayasu - Pacific Northwest National Laboratory
- Resource Type
- Journal article
- Publication Details
- Proteomics (Weinheim), Vol.26(2-3), pp.9-20
- DOI
- 10.1002/pmic.70036
- PMID
- 40955644
- PMCID
- PMC12604859
- NLM abbreviation
- Proteomics
- ISSN
- 1615-9853
- eISSN
- 1615-9861
- Publisher
- Wiley
- Number of pages
- 12
- Grant note
- Catalyst Award from the Human Islet Research Network
- Language
- English
- Electronic publication date
- 09/16/2025
- Date published
- 02/2026
- Academic Unit
- Biostatistics
- Record Identifier
- 9985113183402771
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