Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles

Human plasma is a rich source of biomedical information and biomarkers. However, the enormous dynamic range of plasma proteins limits its accessibility to mass spectrometric (MS) analysis. Here, we show that enrichment of extracellular vesicles (EVs) by ultracentrifugation increases plasma proteome...

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Bibliographic Details
Published in:	Proteomics (Weinheim) Vol. 23; no. 7-8; pp. e2200039 - n/a
Main Authors:	Kverneland, Anders H., Østergaard, Ole, Emdal, Kristina Bennet, Svane, Inge Marie, Olsen, Jesper Velgaard
Format:	Journal Article
Language:	English
Published:	Germany Wiley Subscription Services, Inc 01-04-2023
Subjects:	Biomarkers Blood plasma cancer immune therapy Extracellular vesicles Extracellular Vesicles - metabolism Fractionation Humans Immunotherapy Liquid chromatography Mass spectrometry Mass Spectrometry - methods Mass spectroscopy Melanoma Plasma proteins plasma proteomics Proteins Proteome - analysis Proteomes Proteomics Proteomics - methods Ultracentrifugation Vesicles Workflow cancer immune therapy extracellular vesicles plasma proteomics biomarkers
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Summary:	Human plasma is a rich source of biomedical information and biomarkers. However, the enormous dynamic range of plasma proteins limits its accessibility to mass spectrometric (MS) analysis. Here, we show that enrichment of extracellular vesicles (EVs) by ultracentrifugation increases plasma proteome depth by an order of magnitude. With this approach, more than two thousand proteins are routinely and reproducibly quantified by label‐free quantification and data independent acquisition (DIA) in single‐shot liquid chromatography tandem mass spectrometry runs of less than one hour. We present an optimized plasma proteomics workflow that enables high‐throughput with very short chromatographic gradients analyzing hundred samples per day with deep proteome coverage, especially when including a study‐specific spectral library generated by repeated injection and gas‐phase fractionation of pooled samples. Finally, we test the workflow on clinical biobank samples from malignant melanoma patients in immunotherapy to demonstrate the improved proteome coverage supporting the potential for future biomarker discovery.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1615-9853 1615-9861
DOI:	10.1002/pmic.202200039