Abstract
In this work, we study the mechanism of peptide photodissociation by ultraviolet irradiation at 193 nm wavelength and discuss the role of ionization proton in this process. We found that substituting the ionization proton for the alkali metal cations (sodium) in the peptide ions results in significant changes of the photodissociation spectra. The experimental data obtained in this work revealed that the photodissociation process can be described using the mobile proton model introduced earlier for peptide collision dissociation. The results can be used in proteomics research for optimization of mass spectrometer’s parameters to increase the efficiency of peptide dissociation and in developing sequence-specific models for peptide fragmentation prediction.
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REFERENCES
R. Aebersold and M. Mann, Nature (London, U.K.) 537, 347 (2016).
P. E. Geyer, N. A. Kulak, G. Pichler, et al., Cell Syst. 2, 185 (2016).
L. C. Gillet, A. Leitner, and R. Aebersold, Ann. Rev. Anal. Chem. 9, 449 (2016).
E. S. Baker, T. Liu, V. A. Petyuk, et al., Genome Med. 4 (63), 1 (2012).
A. I. Nesvizhskii, O. Vitek, and R. Aebersold, Nat. Methods 4, 787 (2007).
J. Seidler, N. Zinn, M. E. Boehm, et al., Proteomics 10, 634 (2010).
J. K. Diedrich, A. F. M. Pinto, and J. R. Yates, J. Am. Soc. Mass Spectrom. 24, 1690 (2013).
Y. Zhang, S. B. Ficarro, S. Li, et al., J. Am. Soc. Mass Spectrom. 20, 1425 (2009).
A. S. C Silva, R. Bouwmeester, L. Martens, et al., Bioinformatics (2019).
G. Espadas, E. Borras, C. Chiva, et al., Proteomics 17, 1 (2017).
B. Paizs and S. Suhai, Mass Spectrom. Rev. 24, 508 (2005).
L. Sleno and D. A. Volmer, J. Mass Spectrom. 39, 1091 (2004).
J. V. Olsen, B. Macek, O. Lange, et al., Nat. Methods 4, 709 (2007).
P. Roepstorff and J. Fohlman, Biol. Mass Spectrom. 11, 601 (1984).
E. M. Marzluff and J. L. Beauchamp, Large Ions: Their Vaporization, Detection and Structural Analysis, Ed. by T. Baer, C. Y. Ng, and I. Powis (Wiley, New York, 1996).
V. H. Wysocki, G. Tsaprailis, L. L. Smith, et al., J. Mass Spectrom. 35, 1399 (2000).
B. L. Schwartz and M. M. Bursey, Biol. Mass Spectrom. 21, 92 (1992).
C. Gu, A. Somogyi, V. H. Wysocki, et al., Anal. Chim. Acta 397, 247 (1999).
R. S. Johnson, D. Krylov, and K. A. Walsh, J. Mass Spectrom. 30, 386 (1995).
B. Paizs, I. P. Csonka, G. Lendvay, et al., Rapid Commun. Mass Spectrom. 15, 637 (2001).
M. P. Jedrychowski, E. L. Huttlin, W. Haas, et al., Mol. Cell. Proteomics 10, M111.009910 (2011).
M. L. Nielsen, M. M. Savitski, and R. A. Zubarev, Mol. Cell. Proteomics 4, 835 (2005).
J. A. Madsen, T. S. Kaoud, K. N. Dalby, et al., Proteomics 11, 1329 (2011).
R. Parthasarathi, Y. He, J. P. Reilly, et al., J. Am. Chem. Soc. 132, 1606 (2010).
T. Fellers, B. P. Early, P. M. Thomas, et al., J. Am. Chem. Soc. 135, 12646 (2014).
J. A. Madsen, D. R. Boutz, and J. S. Brodbelt, J. Proteome Res. 9, 4205 (2010).
T. Ly and R. R. Julian, Angew. Chem. Int. Ed. 48, 7130 (2009).
J. P. Reilly, Mass Spectrom. Rev. 28, 425 (2016).
L. Zhang and J. P. Reilly, Anal. Chem. 81, 7829 (2009).
E. M. Solovyeva, V. N. Kopysov, A. Y. Pereverzev, et al., Anal. Chem. 91, 6709 (2019).
K. L. Fort, A. Dyachenko, C. M. Potel, et al., Anal. Chem. 88, 2303 (2016).
T. P. Cleland, C. J. Dehart, R. T. Fellers, et al., J. Proteome Res. 16, 2072 (2017).
X. Dang and N. L. Young, Proteomics 14, 1128 (2014).
S. M. Greer and J. S. Brodbelt, J. Proteome Res. 17, 11385 (2018).
M. B. Robin, Higher Excited States of Polyatomic Molecules (Academic, New York, 1974).
R. R. Julian, J. Am. Soc. Mass Spectrom. 28, 1823 (2017).
P. R. Stannard and W. M. Gelbart, J. Phys. Chem. 85, 3592 (1981).
Y. Hu, B. Hadas, M. Davidovitz, et al., J. Phys. Chem. A 107, 6507 (2003).
H. M. Rosenstock, M. B. Wallenstein, A. L. Wahrhaftig, et al., Proc. Natl. Acad. Sci. 38, 667 (1952).
K. M. Choi, S. H. Yoon, M. Sun, et al., J. Am. Soc. Mass Spectrom. 17, 1643 (2006).
J. H. Moon, S. H. Yoon, Y. J. Bae, et al., J. Am. Soc. Mass Spectrom. 21, 1151 (2010).
J. H. Moon, S. H. Yoon, and M. S. Kim, Rapid Commun. Mass Spectrom. 19, 3248 (2005).
W. Cui, M. S. Thompson, and J. P. Reilly, J. Am. Soc. Mass Spectrom. 16, 1384 (2005).
J. Y. Oh, J. H. Moon, and M. S. Kim, J. Mass Spectrom. 40, 899 (2005).
M. Yamashita and J. B. Fenn, J. Phys. Chem. 88, 4451 (1984).
V. Kopysov, A. Makarov, and O. V. Boyarkin, Anal. Chem. 87, 4607 (2015).
T. Lin, A. H. Payne, and G. L. Glish, J. Am. Soc. Mass Spectrom. 12, 497 (2001).
W. Yong, S. Gronert, K. A. Fletcher, et al., Int. J. Mass Spectrom. 222, 117 (2003).
S. M. Greer, D. D. Holden, R. Fellers, et al., J. Am. Soc. Mass Spectrom. 28, 1587 (2017).
N. M. Emanuel und D. G. Knorre, Chemical Kinetics (Wiley, New York, 1973).
W. Stiller, Arrhenius Equation and Non-Equilibrium Kinetics (BSB B. G. Teubner, Leipzig, 1989).
G. H. Beaven and E. R. Holiday, Ultraviolet Absorption Spectra of Proteins and Amino Acids (Academic, New York, 1952), p. 319.
A. P. Demchenko, Ultraviolet Spectroscopy of Proteins (Springer, Berlin, 1986).
C. Bleiholder, S. Suhai, and B. Paizs, J. Am. Soc. Mass Spectrom. 17, 1275 (2006).
G. Tsaprailis, H. Nair, A. Somogyi, et al., J. Am. Chem. Soc. 121, 5142 (1999).
Funding
This work was supported by the Program for Basic Research of Russian State Academies of Sciences for 2013–2020 (no. 0068-2019-0011). A.Y.P. and O.V.B. thank Swiss National Science Foundation (grants 206021_164101).
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Solovyeva, E.M., Pereverzev, A.Y., Gorshkov, M.V. et al. Ultraviolet Photodissociation of Peptides: New Insight on the Mobile Proton Model. J. Exp. Theor. Phys. 130, 626–632 (2020). https://doi.org/10.1134/S1063776120030164
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DOI: https://doi.org/10.1134/S1063776120030164