Determination of Relative Protein Abundance by Internally Normalized Ratio Algorithm with Antibody Arrays

In this paper, we report an experimental setup and mathematical algorithm for determination of relative protein abundance from directly labeled native protein samples applied to an array of antibodies. The application of the proposed experimental system compensates internally at each array element f...

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Bibliographic Details
Published in:Journal of proteome research 2005-05, Vol.4 (3), p.758-767
Main Authors: Andersson, Oskar, Kozlowski, Mark, Garachtchenko, Tatiana, Nikoloff, Corina, Lew, Nancy, Litman, David J, Chaga, Grigoriy
Format: Article
Language:English
Subjects:
Algorithms
Antibodies, Monoclonal
Cell Extracts - chemistry
Electrophoresis, Polyacrylamide Gel
HeLa Cells
Humans
Immunoassay
Indicators and Reagents
Jurkat Cells
Protein Array Analysis
Proteins - analysis
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Summary:In this paper, we report an experimental setup and mathematical algorithm for determination of relative protein abundance from directly labeled native protein samples applied to an array of antibodies. The application of the proposed experimental system compensates internally at each array element for a number of deficiencies in array experiments such as differential labeling efficiency in dual color assay systems, differential solubility of protein molecules in dual color assay systems, and differential affinity of capture reagents toward proteins labeled with two different fluorescent dyes. This system offers full compensation for variable amounts of capture reagents on separate array structures, as well as limited compensation for nonspecific interactions between capture reagents and analytes. The proposed experimental strategy enables the use of a large number of capture reagents to develop a true multiplex analysis system that will yield complete relative protein abundance information in two biological systems. Keywords: antibody array • dual color detection • protein abundance • multiplex protein analyses • internally normalized ratio
ISSN:1535-3893
1535-3907
DOI:10.1021/pr049776f