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Bioinformatics Advance Access originally published online on January 28, 2009
Bioinformatics 2009 25(5):650-654; doi:10.1093/bioinformatics/btn663
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Serial dilution curve: a new method for analysis of reverse phase protein array data

Li Zhang 1,*, Qingyi Wei 2, Li Mao 3, Wenbin Liu 1,4, Gordon B. Mills 4 and Kevin Coombes 1

1Department of Bioinformatics and Computational Biology, 2Department of Epidemiology, 3Department of Thoracic and Head and Neck Medical Oncology and 4Department of Systems Biology, The University of Texas MD Anderson Cancer Center, 1400 Pressler street, Unit 1410, Houston, TX 77030, USA

*To whom correspondence should be addressed.


  Abstract

Reverse phase protein arrays (RPPAs) are a powerful high-throughput tool for measuring protein concentrations in a large number of samples. In RPPA technology, the original samples are often diluted successively multiple times, forming dilution series to extend the dynamic range of the measurements and to increase confidence in quantitation. An RPPA experiment is equivalent to running multiple ELISA assays concurrently except that there is usually no known protein concentration from which one can construct a standard response curve. Here, we describe a new method called ‘serial dilution curve for RPPA data analysis’. Compared with the existing methods, the new method has the advantage of using fewer parameters and offering a simple way of visualizing the raw data. We showed how the method can be used to examine data quality and to obtain robust quantification of protein concentrations.

Availability: A computer program in R for using serial dilution curve for RPPA data analysis is freely available at http://odin.mdacc.tmc.edu/~zhangli/RPPA.

Contact: lzhangli{at}mdanderson.org

Associate Editor: Jonathan Wren

Received on April 25, 2008; revised on December 3, 2008; accepted on December 27, 2008

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E. S. Neeley, S. M. Kornblau, K. R. Coombes, and K. A. Baggerly
Variable slope normalization of reverse phase protein arrays
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[Abstract] [Full Text] [PDF]


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