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

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

doi:10.1371/journal.pone.0024442

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

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

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

PloS one, Vol.6(9), pp.e24442-e24442

09/07/2011

DOI: 10.1371/journal.pone.0024442

PMCID: PMC3168506

PMID: 21931718

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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 <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.

Biology

Medicine

Details

Title: Subtitle: A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery
Creators: Amit Kumar Yadav - Institute of Genomics and Integrative Biology
Gourav Bhardwaj - Institute of Genomics and Integrative Biology
Trayambak Basak - Institute of Genomics and Integrative Biology
Dhirendra Kumar - Institute of Genomics and Integrative Biology
Shadab Ahmad - Institute of Genomics and Integrative Biology
Ruby Priyadarshini - Institute of Genomics and Integrative Biology
Ashish Kumar Singh - Institute of Genomics and Integrative Biology
Debasis Dash - Institute of Genomics and Integrative Biology
Shantanu Sengupta - Institute of Genomics and Integrative Biology
Resource Type: Journal article
Publication Details: PloS one, Vol.6(9), pp.e24442-e24442
DOI: 10.1371/journal.pone.0024442
PMID: 21931718
PMCID: PMC3168506
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Publisher: Public Library of Science
Alternative title: Immunodepleted Plasma: Analysis of Eluted Fraction
Language: English
Date published: 09/07/2011
Academic Unit: Internal Medicine
Record Identifier: 9984359808102771

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