Blood plasma high abundant protein depletion unintentionally carries over 100 proteins

Abstract

There is a constant interest in blood-based protein biomarkers, which can help to improve diagnosis and treatment outcomes of multifactorial human pathologies. In this regard, proteomic studies usually employ plasma immunoaffinity fractionation to deplete the most abundant plasma proteins, due to the high dynamic concentration range of proteins. The depletion of high abundant proteins allows to obtain less abundant and, oftentimes, more interesting proteins. However, the removal of the fraction of the high abundant plasma proteins - the depletome - may co-elute many unintended proteins due to protein-protein interactions. Little data is available about the depletome and potential protein biomarkers may be lost during this process. To visualize and characterize these proteins, we analyzed the depletome of 20 plasma samples by shotgun mass spectrometry-based proteomics. Thus, using immunoaffinity depletion followed by 2-D liquid chromatography coupled to an ion mobility-enhanced mass spectrometer, our analysis identified that over 100 proteins are co-eluting with the high abundant fraction. These proteins play roles in several biological processes, such as receptor-mediated endocytosis, complement activation, and regulation of immune response. This study supports that investigating the depletome is important in the quest for biomarkers.