Proteomics of human plasma: A critical comparison of analytical workflows in terms of effort, throughput and outcome

In this study, several workflows to analyze human plasma proteins with RP-LC MS/MS are evaluated. The impact of depletion of abundant proteins on the plasma proteome coverage was assessed together with the duration of RP-LC separation. An additional upstream liquid-based fractionation was evaluated. The applicability and feasibility of these technologies in large-scale clinical studies with respect to effort, throughput, and outcome are discussed. Label-free and isobaric tagging-based quantifications are examined in this perspective. We demonstrate that, despite the great improvement of proteomic technologies, significant trade-offs between effort and yield are still challenging the discovery of protein biomarkers in blood plasma.