A comparison of size exclusion chromatography-based tandem strategies for plasma exosome enrichment and proteomic analysis

Proteomic analysis of exosomes from human plasma faces a tremendous challenge mainly due to the low abundance of the exosome itself and the complexity of the plasma matrix. Therefore, enrichment of exosomes from human plasma is an essential and indispensable step for large scale and in depth proteomic analysis. Size exclusion chromatography (SEC) is one of the most extensively used methods for exosome isolation from human plasma and many SEC-based tandem methods were established in order to increase the purity of the enriched exosomes and thus the accuracy of the proteomic analysis. To compare the advantages and disadvantages of the different isolation methods and subsequently to promote the establishment of a standardized method for plasma proteomic research, the capacities of the direct SEC method, the combination of SEC with ultracentrifugation (SEC-UC), ultrafiltration (SEC-UF), and titanium dioxide microspheres (SEC-TiO2) were systematically evaluated for exosome isolation from human plasma and thus proteomic analysis. The results demonstrated that the SEC-based tandem methods were superior to the direct SEC method in the purity of exosomes isolated from human plasma. Additionally, the SEC-UC method possessed the highest number of the total identified proteins and the overlapped proteins with the top 100 exosome markers in comparison with the other methods. The SEC-TiO2 method displayed the biggest capacity for plasma protein deleting. We expect that the research will have more beneficial values in the field of exosome research.