Analytical and Bioanalytical Chemistry

, Volume 411, Issue 24, pp 6409–6417 | Cite as

Two-dimensional decomposition of H-D exchange mass spectra of multicharged ions of biopolymers and their separation into components with independent H-D substitutions

  • Valeriy Raznikov
  • Marina RaznikovaEmail author
  • Il’ya Sulimenkov
Research Paper


The work is aimed at developing a numerical method for analysing mass spectra of deutero-substituted multicharged ions of biopolymers to determine contributions of components presumably corresponding to different biomolecule conformations. The two-dimensional decomposition of the H-D exchange mass spectra of two, three and four charged apamin ions with their separation suggests that the reaction of apamin ions with ND3 molecules in the gas phase reveals hypothetically three different structural modifications of apamin ions. Usually for H-D exchange mass spectra, the presence of many resolvable protein structures was determined from measured distributions of peak intensities of ions with the same charge state. The method is new and has no published analogues.

Graphical abstract


Mass spectrometry H-D exchange Electrospray ionization (ESI) Multiply charged ions Decomposition of deutero-substituted charge-state distributions Retention probability for protons and deutrons 



The authors appreciate Dr. V.I. Kozlovskiy and Dr. A.V. Chudinov for their aid for getting experimental data for apamin. Our thanks to A.R. Piktelev for further development of his software for time-of-flight mass spectra data processing.

Funding information

This work was supported partially by the Russian Academy of Sciences (program no. 36). This work was performed in accordance with the state task, state registration N 0089-2019-0018.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.


  1. 1.
    Kostyukevich Y, Acter T, Zherebker A, Ahmed A, Kim S, Nikolaev E. Hydrogen/deuterium exchange in mass spectrometry. Mass Spectrom Rev. 2018:1–43.
  2. 2.
    Wales TE, Engen JR. Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom Rev. 2006;25:158–70. Scholar
  3. 3.
    Englander SW, Mayne L, Bai Y, Sosnick TR. Hydrogen exchange: the modern legacy of Linderstrom–Lang. Protein Sci. 1997;6:1101–9.CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Katta V, Chait BT. Hydrogen-deuterium exchange electrospray ionization mass-spectrometry: a method for probing protein conformational changes in solution. J Am Chem Soc. 1993;115:6317–21.CrossRefGoogle Scholar
  5. 5.
    Zhang ZQ, Smith DL. Determination of amide hydrogen-exchange by mass-spectrometry: a new tool for protein-structure elucidation. Protein Sci. 1993;2:522–31.CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Konermann L, Pan JX, Liu YH. Hydrogen exchange mass spectrometry for studying protein structure and dynamics. Chem Soc Rev. 2011;40:1224–34.CrossRefPubMedGoogle Scholar
  7. 7.
    Green MK, Lebrilla CB. Ion-molecule reactions as probes of gas phase structures of peptides and proteins. Mass Spectrom Rev. 1997;16:53–71.CrossRefPubMedGoogle Scholar
  8. 8.
    Xiao H, Hoerner JK, Eyles SJ, Dobo A, Voigtman E, Melcuk AI, et al. Mapping Protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. a generalized model for a two-state protein and comparison with experiment. Protein Sci. 2005;14(2):543–57.Google Scholar
  9. 9.
    Abzalimov RR, Kaltashov IA. Extraction of local hydrogen exchange data from HDX CAD MS measurements by deconvolution of isotopic distributions of fragment ions. J Am Soc Mass Spectrom. 2006 Nov;17(11):1543–51. Scholar
  10. 10.
    Kostyukevich Y, Kononikhin A, Popov I, Nikolaev E. Simple atmospheric hydrogen/deuterium exchange method for enumeration of labile hydrogens by electrospray ionization mass spectrometry. Anal Chem. 2013;85:5330–4.CrossRefPubMedGoogle Scholar
  11. 11.
    Kostyukevich Y, Kononikhin A, Popov I, Kharybin O, Konstantinov AI, Zaitsev KV, et al. Enumeration of labile hydrogens in natural organic matter by use of hydrogen/deuterium exchange Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem. 2013;85:11007–13.Google Scholar
  12. 12.
    Kostyukevich Y, Kononikhin A, Popov I, Spasskiy A, Nikolaev E. In ESI-source H/D exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa: the role of the temperature of the desolvating capillary on H/D exchange. J Mass Spectrom. 2015;50:49–55.CrossRefPubMedGoogle Scholar
  13. 13.
    Valentine SJ, Clemmer DE. H/D exchange levels of shape-resolved cytochrome C conformers in the gas phase. J Am Chem Soc. 1997;119:3558–66.CrossRefGoogle Scholar
  14. 14.
    Mohimen A, Dobo A, Hoerner JK, Kaltashov IA. A chemometric approach to detection and characterization of multiple protein conformers in solution using electrospray ionisation mass spectrometry. Anal Chem. 2003;75:4139–47.CrossRefPubMedGoogle Scholar
  15. 15.
    Raznikova MO, Raznikov VV. Evaluating the probability of protonation of amino acids in peptides and proteins according to their electrospray mass spectra. Khim Fiz. 2001;20:13–7 (in Russian).Google Scholar
  16. 16.
    Raznikova MO, Raznikov VV. Determination of the activity of H-atoms of ions of polyfunctional compounds on the basis of mass spectra of H/D exchange. J Adv Chem Phys. 2005;4:16–22.Google Scholar
  17. 17.
    Raznikova MO, Raznikov VV. A new approach to the analysis of the kinetics of H/D exchange processes of active hydrogen atoms of polyfunctional compounds. Mass-spectrometriya. 2006;3:193–200.Google Scholar
  18. 18.
    Raznikov VV, Raznikova MO. Decomposition of charge-state distributions for better understanding of electrospray mass spectra of bioorganic compounds. Part 1. Basic formalism. Eur J Mass Spectrom. 2009;15:367–75. Scholar
  19. 19.
    Raznikov VV, Raznikova MO. Decomposition of charge-state distributions for better understanding of electrospray mass spectra of bioorganic compounds. Part 2. Application of the method. Eur J Mass Spectrom. 2009;15:377–83. Scholar
  20. 20.
    Raznikov VV, Raznikova MO. Use of decomposition of ion charge-state distributions for the interpretation of electrospray ionization mass spectra of bioorganic compounds. J Anal Chem. 2012;13:974–80. Scholar
  21. 21.
    Raznikova MO, Raznikov VV. Probabilistic calculations of biomolecule charge states that generate mass spectra of multiply charged ions. Mol Biol. 2015;49:728–34. Scholar
  22. 22.
    Raznikov VV, Raznikova MO. Decomposition of multi-dimensional charge-state distributions of ions produced by electrospray ionization of bioorganic compounds. Part 2. Testing of the method for one-dimensional distributions. J Anal Chem. 2014;15:1278–84. Scholar
  23. 23.
    Raznikov VV, Raznikova MO. Decomposition of multi-dimensional charge-state distributions of ions produced by electrospray ionization of bioorganic compounds. Part 1. Basic formalism and implementation of the method. J Anal Chem. 2014;15:1270–7. Scholar
  24. 24.
    Raznikov VV, Raznikova MO, Pridatchenko ML. Disentangling of information about the structure of biomolecules based on the decomposition and separation of two-dimentional charge distributions of ions. J Anal Chem. 2017;72:1300–6. Scholar
  25. 25.
    Raznikov VV, Raznikova MO. Characterization of the structural forms of biomolecules based on the decomposition and separation of the charge-state distributions of their ions. Mass-spektrometriya 2018;15:152–161 (in Russian). English version of the paper will appear in J Anal Chem. 2019 (in one of the last two issues).Google Scholar
  26. 26.
    Raznikova MO, Raznikov VV. Calculation of the characteristics of the ionic states of cytochrome C biomolecules by decomposition method with separation of one- and two-dimensional ion charge distributions. Russ J Phys Chem B. 2018;12:271–80. Scholar
  27. 27.
    Korn GA, Korn TM. Mathematical handbook for scientists and engineers. New York: cMGRAW-HILL BOOK COMPANY, INC; 1961, 18.3-8(e) Google Scholar
  28. 28.
    Claesen J, Dittwald P, Burzykowski T, Valkenborg D. An efficient method to calculate the aggregated isotopic distribution and exact center-masses. J Am Soc Mass Spectrom. 2012;23:753–63.CrossRefPubMedGoogle Scholar
  29. 29.
    Sadygov RJ. Poisson model to generate isotope distribution for biomolecules. J Proteome Res. 2018;17:751–8.CrossRefPubMedGoogle Scholar
  30. 30.
    Raznikov VV, Raznikova MO. Deconvolution of overlapping mass spectral peaks following ion counting data acquisition. Int J Mass Spectrom Ion Process. 1985;63:157–86.CrossRefGoogle Scholar
  31. 31.
    Raznikov VV, Dodonov AF, Zelenov VV. Disentangling the fine structure of ionization efficiency curves. Int J Mass Spectrom Ion Process. 1986;71:1–27.CrossRefGoogle Scholar
  32. 32.
    Raznikov VV, Dodonov AF, Lanin EV. Data acquisition and processing in high-resolution mass spectrometry using ion counting. Int J Mass Spectrom Ion Phys. 1977;25:295–313.CrossRefGoogle Scholar
  33. 33.
    Chudinov AV, Sulimenkov IV, Pikhtelev AR, Kozlovskii VI. Study of H/D_exchange reaction kinetics of polypeptides. J Anal Chem. 2010;65:1517–23.CrossRefGoogle Scholar
  34. 34.
    Dodonov AF, Kozlovski VI, Sulimenkov IV, Raznikov VV, Loboda AV, Zhen Z, et al. High-resolution electrospray ionization orthogonal-injection time-of-flight mass spectrometer. Eur J Mass Spectrom. 2000;6:481–90.Google Scholar
  35. 35.
    Chudinov AV, Martynovich YG, Sulimenkov IV, Brusov VS, Filatov VV, Pikhtelev AR, et al. Study of the dependence of peptide collision cross section on the ion bunch drift velocity in nitrogen. J Anal Chem. 2015;70:1647–53.Google Scholar
  36. 36.
    Wood T, Chorush R, Wampler F, Little D, Oconnor P, McLafferty F. Gas-phase folding and unfolding of cytochrome-C cations. Proc Natl Acad Sci U S A. 1995;92:2451–4.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    McLafferty FW, Guan ZQ, Haupts U, Wood TD, Kelleher NL. Gaseous conformational structures of cytochrome C. J Am Chem Soc. 1998;120:4732–40.CrossRefGoogle Scholar
  38. 38.
    Meija J. Mathematical tools in analytical mass spectrometry. Anal Bioanal Chem. 2006;385:486–99.CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Valeriy Raznikov
    • 1
  • Marina Raznikova
    • 2
    Email author
  • Il’ya Sulimenkov
    • 1
  1. 1.Chernogolovka Branch of the N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of SciencesChernogolovka, Moscow regionRussia
  2. 2.Institute of Problems of Chemical Physics, Russian Academy of SciencesChernogolovka, Moscow regionRussia

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