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

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  • Amit Kumar Yadav
  • Gourav Bhardwaj
  • Trayambak Basak
  • Dhirendra Kumar
  • Shadab Ahmad
  • Ruby Priyadarshini
  • Ashish Kumar Singh
  • Debasis Dash
  • Shantanu Sengupta

Abstract

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

Suggested Citation

  • Amit Kumar Yadav & Gourav Bhardwaj & Trayambak Basak & Dhirendra Kumar & Shadab Ahmad & Ruby Priyadarshini & Ashish Kumar Singh & Debasis Dash & Shantanu Sengupta, 2011. "A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-9, September.
    • Handle: RePEc:plo:pone00:0024442
    DOI: 10.1371/journal.pone.0024442
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    1. Lin Wang & Chuanhao Tang & Bin Xu & Lin Yang & Lili Qu & Liangliang Li & Xiaoyan Li & Weixia Wang & Haifeng Qin & Hongjun Gao & Kun He & Xiaoqing Liu, 2017. "Mass spectrometry-based serum peptidome profiling accurately and reliably predicts outcomes of pemetrexed plus platinum chemotherapy in patients with advanced lung adenocarcinoma," PLOS ONE, Public Library of Science, vol. 12(6), pages 1-15, June.

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