TY - JOUR
T1 - Mass-Spectrometry Based Proteome Comparison of Extracellular Vesicle Isolation Methods
T2 - Comparison of ME-kit, Size-Exclusion Chromatography, and High-Speed Centrifugation
AU - Askeland, Anders
AU - Borup, Anne
AU - Østergaard, Ole
AU - Olsen, Jesper V
AU - Lund, Sigrid M
AU - Christiansen, Gunna
AU - Kristensen, Søren R
AU - Heegaard, Niels H H
AU - Pedersen, Shona
PY - 2020
Y1 - 2020
N2 - Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells' biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation (PAP/ME kit) for subsequent MS-based proteome analysis. Successful EV isolation was evaluated by nanoparticle-tracking analysis, immunoblotting, and transmission electron microscopy, while EV abundance, EV subtypes, and contamination was evaluated by label-free tandem MS. High-speed centrifugation and SEC isolates showed high EV abundance at the expense of contamination by non-EV proteins and lipoproteins, respectively. These two methods also resulted in EVs of a similar type, however, with smaller EVs in SEC isolates. PAP isolates had a relatively low EV abundance and high contamination. We consider high-speed centrifugation and SEC suitable as EV isolation for MS biomarker studies, where the choice between the two should depend on the scientific questions and whether the focus is on larger or smaller EVs or a combination of both.
AB - Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells' biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation (PAP/ME kit) for subsequent MS-based proteome analysis. Successful EV isolation was evaluated by nanoparticle-tracking analysis, immunoblotting, and transmission electron microscopy, while EV abundance, EV subtypes, and contamination was evaluated by label-free tandem MS. High-speed centrifugation and SEC isolates showed high EV abundance at the expense of contamination by non-EV proteins and lipoproteins, respectively. These two methods also resulted in EVs of a similar type, however, with smaller EVs in SEC isolates. PAP isolates had a relatively low EV abundance and high contamination. We consider high-speed centrifugation and SEC suitable as EV isolation for MS biomarker studies, where the choice between the two should depend on the scientific questions and whether the focus is on larger or smaller EVs or a combination of both.
U2 - 10.3390/biomedicines8080246
DO - 10.3390/biomedicines8080246
M3 - Journal article
C2 - 32722497
VL - 8
JO - Biomedicines
JF - Biomedicines
SN - 2227-9059
IS - 8
M1 - 246
ER -