Feature based retention time alignment for improved HDX MS analysis

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 4, 2013, Pages 642-645

  Venable, John D ^a   Scuba, William ^b   Brock, Ansgar ^a  

^a GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^b OREI   (United States)

Author keywords

Chromatographic alignment; Fitting; Hydrogen deuterium exchange; Isotopic cluster; Mass spectrometry; Retention time correction

Indexed keywords

DEUTERIUM INCORPORATIONS; DISTANCE MINIMIZATIONS; FITTING; HYDROGEN-DEUTERIUM EXCHANGE; ISOTOPIC CLUSTER; PAIR-WISE COMPARISON; RETENTION TIME; RETENTION TIME ALIGNMENTS;

ALGORITHMS; DEUTERIUM; HYDROGEN; ITERATIVE METHODS; MASS SPECTROMETRY;

ALIGNMENT;

CYTOCHROME C; DEUTERIUM; HYDROGEN DEUTERIUM; UNCLASSIFIED DRUG;

ACCURACY; ALGORITHM; ARTICLE; AUTOMATION; CHROMATOGRAPHY; DATA ANALYSIS SOFTWARE; HYDROGEN DEUTERIUM EXCHANGE MASS SPECTROMETRY; MASS SPECTROMETRY; PREDICTION;

ALGORITHMS; CHROMATOGRAPHY, LIQUID; CLUSTER ANALYSIS; DEUTERIUM EXCHANGE MEASUREMENT; MASS SPECTROMETRY; MODELS, THEORETICAL; SOFTWARE; TIME FACTORS;

EID: 84879536137     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0566-9     Document Type: Article

References (11)

1. Zhang, Z.M.; Chen, S.; Liang, Y.Z.: Peak alignment using wavelet pattern matching and differential evolution. Talanta 83, 1108-1117 (2011)
2. Tomasi, G.; van der Berg, F.; Andersson, C.: Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data. J. Chemometr. 18, 231-241 (2004)
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)
4. Hoffmann, N.; Stoye, J.: ChromA: Signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics 25, 2080-2081 (2009)
5. Lommen, A.: MetAlign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal. Chem. 81, 3079-3086 (2009)
6. Wang, S.Y.; Ho, T.J.; Kuo, C.H.; Tseng, Y.J.: Chromaligner: A web server for chromatogram alignment. Bioinformatics 26, 2338-2339 (2010)
7. Konermann, L.; Pan, J.; Liu, Y.H.: Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem. Soc. Rev. 40, 1224-1234 (2011)
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)
10. Chik, J.K.; Graaf, J.L.V.; Schriemer, D.C.: Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data. Anal. Chem. 78, 207-214 (2006)
11. Chalmers, M.J.; Busby, S.A.; Pascal, B.D.; He, Y.; Hendrickson, C.L.; Marshall, A.G.; Griffin, P.R.: Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 78, 1005-1014 (2006)