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Submitted on September 5, 2006
Revised on January 4, 2007
Accepted on February 9, 2007

Comparison of full versus partial metabolic labeling for quantitative proteomic analysis in Arabidopsis thaliana

Edward L. Huttlin, Adrian D. Hegeman, Amy C. Harms, and Michael R. Sussman

Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706

Corresponding Author: hegeman{at}biochem.wisc.edu

In recent years a variety of quantitative proteomic techniques have been developed, allowing characterization of changes in protein abundance in a variety of organisms under various biological conditions. Because it allows excellent control for error at all steps in sample preparation and analysis, full metabolic labeling using 15N has emerged as an important strategy for quantitative proteomics, having been applied in a variety of organisms from yeast to Arabidopsis and even rats. However, challenges associated with complete replacement of 14N with 15N can make its application in many complex eukaryotic systems impractical on a routine basis. Extending a concept proposed by Whitelegge et al. [Phytochemistry (2004) 65:1507], we investigate an alternative strategy for quantitative proteomics that relies upon the subtle changes in isotopic envelope shape that result from partial metabolic labeling to compare relative abundances of labeled and unlabeled peptides in complex mixtures. We present a novel algorithm for the automated quantitative analysis of partial incorporation samples via LC-MS. We then compare the performance of partial metabolic labeling with traditional full metabolic labeling for quantification of controlled mixtures of labeled and unlabeled Arabidopsis peptides. Finally, we evaluate the performance of each technique for comparison of light versus dark-grown Arabidopsis with respect to reproducibility and numbers of peptide and protein identifications under more realistic experimental conditions. Overall full and partial metabolic labeling prove to be comparable with respect to dynamic range, accuracy and reproducibility, although partial metabolic labeling consistently allows quantification of a higher percentage of peptide observations across the dynamic range. This difference is especially pronounced at extreme ratios. Ultimately both full and partial metabolic labeling prove to be well suited for quantitative proteomic characterization.


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