Feature Based Retention Time Alignment for Improved HDX MS Analysis
- First Online:
- 333 Downloads
An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.
Key wordsHydrogen deuterium exchange Chromatographic alignment Retention time correction Isotopic cluster Fitting Mass spectrometry
- 3.Ahmad, I., Suits, F., Hoekman, B., Swertz, M.A., Byelas, H., Dijkstra, M., Hooft, R., Katsubo, D., van Breukelen, B., Bischoff, R., Horvatovich, P.: A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. Bioinformatics 27, 1176–1178 (2011)CrossRefGoogle Scholar
- 8.Center, S.P.: Software:ReAdW. (2012); Available at: http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW#Current_Version. Accessed September 3, 2012
- 9.Bellew, M., Coram, M., Fitzgibbon, M., Igra, M., Randolph, T., Wang, P., May, D., Eng, J., Fang, R., Lin, C., Chen, J., Goodlett, D., Whiteaker, J., Paulovich, A., McIntosh, M.: A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22, 1902–1909 (2006)CrossRefGoogle Scholar