A software system capable of extracting and cataloging the large number of data points obtained during each experiment has been developed . The automated system streamlines most data handling steps and reduces the potential for errors associated with manual manipulation of large data sets. In the first processing step, the centroid mass value is obtained for the isotopic envelope of each peptide ion observed in every LC-MS data file associated with the experiment. This step includes peak detection, selection of retention time window, selection of m/z range, and calculation of envelope centroid. The second step involves correction for deuterium losses subsequent to sample quench by reference to measured peptide-specific losses [1, 8]. After calculating the percent deuterium incorporation for each peptide at each time point, H/D exchange data is displayed in a number of formats, often as a stacked bar chart that is aligned with the protein primary sequence.
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