Absolute Quantification of Proteins by LCMSE

Abstract

Relative quantification methods have dominated the quantitative proteomics field. There is a need, however, to conduct absolute quantification studies to accurately model and understand the complex molecular biology that results in proteome variability among biological samples. A new method of absolute quantification of proteins is described. This method is based on the discovery of an unexpected relationship between MS signal response and protein concentration: the average MS signal response for the three most intense tryptic peptides per mole of protein is constant within a coefficient of variation of less than ؎10%. Given an internal standard, this relationship is used to calculate a universal signal response factor. The universal signal response factor (counts/mol) was shown to be the same for all proteins tested in this study. A controlled set of six exogenous proteins of varying concentrations was studied in the absence and presence of human serum. The absolute quantity of the standard proteins was determined with a relative error of less than ؎15%. The average MS signal responses of the three most intense peptides from each protein were plotted against their calculated protein concentrations, and this plot resulted in a linear relationship with an R 2 value of 0.9939. The analyses were applied to determine the absolute concentration of 11 common serum proteins, and these concentrations were then compared with known values available in the literature. Additionally within an unfractionated Escherichia coli lysate, a subset of identified proteins known to exist as functional complexes was studied. The calculated absolute quantities were used to accurately determine their stoichiometry. Molecular & Cellular Proteomics 5:144 -156, 2006.The study of proteins is crucial in understanding and combating disease through identification of proteins, discovering disease biomarkers, studying protein involvement in specific metabolic pathways, and identifying protein targets in drug discovery (1, 2). An important technique that is used in these studies to quantify and identify peptides and/or proteins present in simple and complex mixtures is ESI-LCMS.To date a majority of the quantitative proteomic analyses have been performed using stable isotope labeling strategies such as ICAT (3), iTRAQ TM (4), SILAC (stable isotope labeling by amino acids in cell culture) (5), and 18 O labeling (6, 7). These methodologies require complex, time-consuming sample preparation and can be relatively expensive.Recently there have been numerous reports applying labelfree methods to monitor the relative abundance of protein between different conditions (8 -11). Relative quantification provides information regarding specific protein abundance changes between two conditions caused by an induced perturbation (environment-induced, drug-induced, and diseaseinduced). These studies require comparison of identical proteolytic peptides in each of the two experiments to accurately determine relative ratios of the particular protein(s) of interest.Rel...

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