Amit Yadav - A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery

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  Amit Kumar Yadav1#,   Gourav Bhardwaj2#,   Trayambak Basak2#,   Dhirendra Kumar1,   Shadab Ahmad2,   Ruby Priyadarshini2,   Ashish Kumar Singh1,   Debasis Dash1*,Shantanu   Sengupta2*

  Citation: Yadav AK, Bhardwaj G, Basak T, Kumar   D, Ahmad S, et al. (2011) A Systematic Analysis of Eluted   Fraction of Plasma Post Immunoaffinity Depletion: Implications in   Biomarker Discovery. PLoS ONE 6(9): e24442.   doi:10.1371/journal.pone.0024442


  Plasma is the most easily accessible source for biomarker   discovery in clinical proteomics. However, identifying potential   biomarkers from plasma is a challenge given the large dynamic   range of proteins. The potential biomarkers in plasma are   generally present at very low abundance levels and hence   identification of these low abundance proteins necessitates the   depletion of highly abundant proteins. Sample pre-fractionation   using immuno-depletion of high abundance proteins using   multi-affinity removal system (MARS) has been a popular method to   deplete multiple high abundance proteins. However, depletion of   these abundant proteins can result in concomitant removal of low   abundant proteins. Although there are some reports suggesting the   removal of non-targeted proteins, the predominant view is that   number of such proteins is small. In this study, we identified   proteins that are removed along with the targeted high abundant   proteins. Three plasma samples were depleted using each of the   three MARS (Hu-6, Hu-14 and Proteoprep 20) cartridges. The   affinity bound fractions were subjected to gelC-MS using an   LTQ-Orbitrap instrument. Using four database search algorithms   including MassWiz (developed in house), we selected the peptides   identified at <1% FDR. Peptides identified by at least two   algorithms were selected for protein identification. After this   rigorous bioinformatics analysis, we identified 101 proteins with   high confidence. Thus, we believe that for biomarker discovery   and proper quantitation of proteins, it might be better to study   both bound and depleted fractions from any MARS depleted plasma   sample.

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