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Bioinformatics Advance Access published online on July 24, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn385
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

An Integrated Approach for Automating Validation of Extracted Ion Chromatographic Peaks

William D. Nelson 1,*, Kert Viele 2 and Bert C. Lynn 3

Departments of 1Biology, 2Statistics, and 3Chemistry, University of Kentucky, Lexington, KY 40506, USA

*To whom correspondence should be addressed. William D. Nelson, E-mail: wnels2{at}uky.edu


  Abstract

Summary: Accurate determination of extracted ion chromatographic peak areas in isotope labeled quantitative proteomics is difficult to automate. Manual validation of identified peaks is typically required. We have integrated a peak confidence scoring algorithm into existing tools which are compatible with analysis pipelines based on the standards from the Institute for Systems Biology. This algorithm automatically excludes incorrectly identified peaks, improving the accuracy of the final protein expression ratio calculation.

Contact: wnels2{at}uky.edu

Source and Supplementary Information: http://www.chem.uky.edu/research/lynn/Nelson.pdf

Associate Editor: Prof. David Rocke

Received on March 21, 2008; revised on July 18, 2008; accepted on July 22, 2008

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