Hexicon 2: Automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation

Journal of the American Society for Mass Spectrometry

Volumn 25, Issue 6, 2014, Pages 1018-1028

  Lindner, Robert ^a   Lou, Xinghua ^b   Reinstein, Jochen ^a   Shoeman, Robert L ^a   Hamprecht, Fred A ^b   Winkler, Andreas ^a  

^a MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Chromatogram alignment; Data analysis; Hydrogen deuterium exchange; Software

Indexed keywords

ALIGNMENT; ATOMS; AUTOMATION; BENCHMARKING; CHROMATOGRAPHIC ANALYSIS; COMPUTER SOFTWARE; DATA REDUCTION; DECONVOLUTION; DEUTERIUM; HYDROGEN; ITERATIVE METHODS; MASS SPECTROMETRY; PEPTIDES;

AUTOMATED DATA ANALYSIS; CONTINUOUS IMPROVEMENTS; DISTRIBUTION ESTIMATION; HYDROGEN-DEUTERIUM EXCHANGE; ITERATIVE DECONVOLUTION ALGORITHMS; MASS SPECTROMETRY DATA; SOLVENT ACCESSIBILITY; STANDALONE APPLICATIONS;

DATA VISUALIZATION;

DEUTERIUM; HYDROGEN; PEPTIDES AND PROTEINS; PEPTIDE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOANALYSIS; AUTOMATION; DATA ANALYSIS; DATA PROCESSING; DEUTERIUM HYDROGEN EXCHANGE; HEXICON 2; MASS SPECTROMETRY; NOISE; PROTEIN DENATURATION; PROTEIN STRUCTURE; QUALITY CONTROL; WORKFLOW; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; IMAGE PROCESSING; PROCEDURES; SEQUENCE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DEUTERIUM EXCHANGE MEASUREMENT; IMAGE PROCESSING, COMPUTER-ASSISTED; MASS SPECTROMETRY; MODELS, MOLECULAR; PEPTIDES; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84901036938     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-014-0850-y     Document Type: Article

References (38)

1. Engen, J.R.: Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS. Anal. Chem. 81, 7870-7875 (2009)
2. Krishna, M.M.G., Hoang, L., Lin, Y., Englander, S.W.: Hydrogen exchange methods to study protein folding. Methods 34, 51-64 (2004)
3. Marcsisin, S.R., Engen, J.R.: Hydrogen exchange mass spectrometry: what is it and what can it tell us? Anal. Bioanal. Chem. 397, 967-972 (2010)
4. Zhang, Z., Smith, D.L.: Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2, 522-531 (1993)
5. Zhang, Z., Guan, S., Marshall, A.G.: Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution. J. Am. Soc. Mass Spectrom. 8, 659-670 (1997)
6. Palmblad, M., Buijs, J., Håkansson, P.: Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions. J. Am. Soc. Mass Spectrom. 12, 1153-1162 (2001)
7. Hotchko, M., Anand, G.S., Komives, E.A., Ten Eyck, L.F.: Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci. 15, 583-601 (2006)
8. Chik, J.K., van der Graaf, J.L., 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)
9. Weis, D.D., Engen, J.R., Kass, I.J.: Semi-automated data processing of hydrogen exchange mass spectra using HX-Express. J. Am. Soc. Mass Spectrom. 17, 1700-1703 (2006)
10. Guttman, M., Weis, D.D., Engen, J.R., Lee, K.K.: Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra. J. Am. Soc. Mass Spectrom. 24, 1906-1912 (2013)
11. Venable, J.D., Scuba, W., Brock, A.: Feature-based retention time alignment for improved HDX MS analysis. J. Am. Soc. Mass Spectrom. 24, 642-645 (2013)
12. Slysz, G.W., Baker, C.A., Bozsa, B.M.: Hydra - software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinforma. 10, 162 (2009)
13. Burns, K.M., Rey, M., Baker, C.A.H., Schriemer, D.C.: Platform dependencies in bottom-up hydrogen/deuterium exchange mass spectrometry. Mol. Cell. Proteom 12, 539-548 (2013)
14. Kan, Z.-Y., Mayne, L., Sevugan Chetty, P., Englander, S.W.: ExMS: data analysis for HX-MS experiments. J. Am. Soc. Mass Spectrom. 22, 1906-1915 (2011)
15. Miller, D.E., Prasannan, C.B., Villar, M.T.: HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry. J. Am. Soc. Mass Spectrom. 23, 425-429 (2011)
16. Pascal, B.D., Willis, S., Lauer, J.L.: HDX workbench: software for the analysis of H/D exchange MS data. J. Am. Soc. Mass Spectrom. 23, 1512-1521 (2012)
17. Pascal, B.D., Chalmers, M.J., Busby, S.A., Griffin, P.R.: HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J. Am. Soc. Mass Spectrom. 20, 601-610 (2009)
18. Lou, X., Kirchner, M., Renard, B.Y.: Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinformatics 26, 1535-1541 (2010)
19. Renard, B.Y., Kirchner, M., Steen, H.: NITPICK: peak identification for mass spectrometry data. BMC Bioinforma. 9, 355 (2008)
20. Zhang, J., Ramachandran, P., Kumar, R., Gross, M.L.: H/D exchange centroid monitoring is insufficient to show differences in the behavior of protein states. J. Am. Soc. Mass Spectrom. 24, 450-453 (2013)
21. Kreshuk, A., Stankiewicz, M., Lou, X.: Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon. Int. J. Mass Spectrom. 302, 125-131 (2011)
22. Kazazic, S., Zhang, H.M., Schaub, T.M.: Automated data reduction for hydrogen/deuterium exchange experiments, enabled by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. J. Am. Soc. Mass Spectrom. 21, 550-558 (2010)
23. Gomelsky, M., Kaplan, S.: Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J. Bacteriol. 179, 128-134 (1997)
24. Winkler, A., Heintz, U., Lindner, R., Reinstein, J., Shoeman, R.L., Schlichting, I.: A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression. Nat. Struct. Mol. Biol. 20, 859-867 (2013)
25. Senko, M.W., Beu, S.C., McLafferty, F.W.: Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6, 229-233 (1995)
26. Tibshirani, R.: Regression shrinkage and selection via the lasso. J. Royal. Stat. Soc. (Series B) 58, 267-288 (1996)
27. Efron, B.: Least angle regression. Ann. Stat. 32, 407-499 (2004)
28. Schwarz, G.: Estimating the dimension of a model. Ann. Stat. 6, 461-464 (1978)
29. Hamuro, Y., Coales, S.J., Molnar, K.S.: Specificity of immobilized porcine pepsin in H/D exchange compatible conditions. Rapid Commun. Mass Spectrom. 22, 1041-1046 (2008)
30. Kirchner, M., Xu, B., Steen, H., Steen, J.A.J.: libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. Bioinformatics 27, 1166-1167 (2011)
31. Abzalimov, R.R., Kaltashov, I.A.: Extraction of local hydrogen exchange data from HDX CAD MS measurements by deconvolution of isotopic distributions of fragment ions. J. Am. Soc. Mass Spectrom. 17, 1543-1551 (2006)
32. Morháč, M.: Deconvolution methods and their applications in the analysis of gamma-ray spectra. Nucl. Instrum. Methods Phys. Res. A. 559, 119-123 (2006)
33. Morháč, M., Kliman, J., Matoušek, V.: Efficient one- and two-dimensional gold deconvolution and its application to γ-ray spectra decomposition. Nucl. Instrum. Methods Phys. Res. A. 401, 385-408 (1997)
34. Morháč, M., Matoušek, V., Kliman, J.: Efficient algorithm of multidimensional deconvolution and its application to nuclear data processing. Digital. Signal. Proc. 13, 144-171 (2003)
35. Wu, J., van der Rest, G.: Improvement of Peptic Peptide Identification for Amide H/D Exchange using High Mass Accuracy Combined with a Statistical Approach. 61st ASMS Conference, Minneapolis, MN (2013)
36. Weis, D.D., Wales, T.E., Engen, J.R.: Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J. Am. Soc. Mass Spectrom. 17, 1498-1509 (2006)
37. The PyMOL Molecular Graphics System, version 1.2r3pre, Schrödinger, L.L.C. Available at: http://www.pymol.org/. Accessed 16 July (2012)
38. Winkler, A., Udvarhelyi, A., Hartmann, E.: Characterization of elements involved in allosteric light regulation of phosphodiesterase activity by comparison of different functional BlrP1 states. J. Mol. Biol. 426, 853-868 (2014)