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BioMed Research International
Volume 2014 (2014), Article ID 971857, 7 pages
Research Article

O18Quant: A Semiautomatic Strategy for Quantitative Analysis of High-Resolution 16O/18O Labeled Data

1Center for Quantitative Sciences, Vanderbilt University, Nashville, TN 37027, USA
2Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
3Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China

Received 28 February 2014; Accepted 18 April 2014; Published 11 May 2014

Academic Editor: Leng Han

Copyright © 2014 Yan Guo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Proteolytic 18O-labeling has been widely used in quantitative proteomics since it can uniformly label all peptides from different kinds of proteins. There have been multiple algorithms and tools developed over the last few years to analyze high-resolution proteolytic 16O/18O labeled mass spectra. We have developed a software package, O18Quant, which addresses two major issues in the previously developed algorithms. First, O18Quant uses a robust linear model (RLM) for peptide-to-protein ratio estimation. RLM can minimize the effect of outliers instead of iteratively removing them which is a common practice in other approaches. Second, the existing algorithms lack applicable implementation. We address this by implementing O18Quant using C# under framework and R. O18Quant automatically calculates the peptide/protein relative ratio and provides a friendly graphical user interface (GUI) which allows the user to manually validate the quantification results at scan, peptide, and protein levels. The intuitive GUI of O18Quant can greatly enhance the user’s visualization and understanding of the data analysis. O18Quant can be downloaded for free as part of the software suite ProteomicsTools.