Algorithms for Extracting Rate Constants and Protection Factors

3 Algorithms for Extracting Rate Constants and Protection Factors 

Before attempting to derive the rate constant information based on Equation 7.5 and measured deuterium uptake levels, one must consider the fact that the measured deuterium uptake in a peptide is not the actual deuterium uptake after an exchange time t described in Equation 7.5, due to the significant level of deuterium back-exchange during digestion and LC-MS analysis (see Section 2.3.8). The back-exchange must be corrected, or considered by other means, before a reasonable attempt can be made to derive the rate constants. 

A simple way to correct for the back-exchange is by analyzing a nondeuterated control and a fully deuterated control [1] together with all other labeling time points. The back-exchange corrected deuterium incorporation level in a peptide can then be calculated by Equation 7.6, 

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