Electron capture dissociation mass spectrometry of tyrosine nitrated peptides

  • Andrew W. Jones
  • Victor A. Mikhailov
  • Jesus Iniesta
  • Helen J. Cooper
Article

Abstract

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.

Supplementary material

13361_2011_210200268_MOESM1_ESM.pdf (252 kb)
Supplementary material, approximately 258 KB.

References

  1. 1.
    Abello, N.; Kerstjens, H. A. M.; Postma, D. S.; Bischoff, R. Protein Tyrosine Nitration: Selectivity, Physicochemical, and Biological Consequences, Denitration, and Proteomics Methods for the Identification of Tyrosine Nitrated Proteins. J. Proteome Res. 2009, 8(7), 3222–3238.CrossRefGoogle Scholar
  2. 2.
    Beckman, J. S. Oxidative Damage and Tyrosine Nitration from Peroxynitrite. Chem. Res. Toxicol. 1996, 95, 836–844.CrossRefGoogle Scholar
  3. 3.
    Reiter, C. D.; Teng, R. J.; Beckman, J. S. Superoxide Reacts with Nitric Oxide to Nitrate Tyrosine at Physiological pH Via Peroxynitrite. J. Biol. Chem. 275, 42, 32460–32466.Google Scholar
  4. 4.
    Radi, R. Nitric Oxide, Oxidants, and Protein Tyrosine Nitration. Proc. Nat. Acad. Sci. USA. 2004, 1012, 4003–4008.CrossRefGoogle Scholar
  5. 5.
    Ischiropoulos, H. Biological Tyrosine nitration: A Pathophysiological Function of Nitric Oxide and Reactive Oxygen Species. Arch. Biochem. Biophys. 1998, 3561, 1–11.CrossRefGoogle Scholar
  6. 6.
    Ischiropoulos, H.; Almehdi, A. B. Peroxynitrite-Mediated Oxidative Protein Modifications. FEBS Lett. 1995, 364(3), 279–282.CrossRefGoogle Scholar
  7. 7.
    Shishehbor, M. H.; Aviles, R. J.; Brennan, M. L.; Fu, X. M.; Goormastic, M.; Pearce, G. L.; Gokce, N.; Keaney, J. F.; Penn, M. S.; Sprecher, D. L.; Vita, J. A.; Hazen, S. L. Association of Nitrotyrosine Levels with Cardiovascular Disease and Modulation by Statin Therapy. JAMA. 2003, 289(13), 1675–1680.CrossRefGoogle Scholar
  8. 8.
    Good, F.; Werner, P.; Hsu, A.; Olanow, C. W.; Perl, D. P. Evidence for Neuronal Oxidative Damage in Alzheimer’s Fisease. Am. J. Pathol. 1996, 149(1), 21–28.Google Scholar
  9. 9.
    Parastatidis, I.; Thomson, L.; Burke, A.; Chernysh, I.; Nagaswami, C.; Visser, J.; Stamer, S.; Liebler, D. C.; Koliakos, G.; Heijnen, H. F. G.; FitzGerald, G. A.; Weisel, J. W.; Ischiropoulos, H. Fibrinogen β-Chain Tyrosine Nitration Is a Prothrombotic Risk Factor. J. Biol. Chem. 283, 49, 33846–33853.Google Scholar
  10. 10.
    Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Protein Cations: A nonergodic process. J. Am. Chem. Soc. 1998, 120(13), 3265–3266.CrossRefGoogle Scholar
  11. 11.
    Cooper, H. J.; Hakansson, K.; Marshall, A. G. The Role of Electron Capture Dissociation in Biomolecular Analysis. Mass Spectrom. Rev. 2005, 24, 201–222.CrossRefGoogle Scholar
  12. 12.
    McLuckey, S. A.; Goeringer, D. E. Slow Heating Methods in Tandem Mass Spectrometry. J. Mass Spectrom. 1997, 3(5), 461–474.CrossRefGoogle Scholar
  13. 13.
    Little, D. P.; Speir, J. P.; Senko, M. W.; O’Connor, B.; McLafferty, F. W. Infrared Multiphoton Dissociation of Large Multiply-Charged Ions for Biomolecule Sequencing. Anal. Chem. 1994, 66(18), 2809–2815.CrossRefGoogle Scholar
  14. 14.
    Woodin, R. L.; Bomse, D. S.; Beauchamp, J. L. Multi-Photon Dissociation of Molecules with Low-Power Continuous Wave Infrared-Laser Radiation. J. Am. Chem. Soc. 1978, 100(10), 3248–3250.CrossRefGoogle Scholar
  15. 15.
    Kruger, N. A.; Zubarev, R. A.; Carpenter, B. K.; Kelleher, N. L.; Horn, D. M.; McLafferty, F. W. Electron Capture Versus Energetic Dissociation of Protein Ions. Int. J. Mass Spectrom. 1999, 182, 1–5.CrossRefGoogle Scholar
  16. 16.
    Savitski, M. M.; Kjeldsen, F.; Nielsen, M. L.; Zubarev, R. A. Hydrogen Rearrangement to and from Radical z Fragments in Electron Capture Dissociation of Peptides. J. Am. Soc. Mass Spectrom. 2007, 18(1), 113–120.CrossRefGoogle Scholar
  17. 17.
    Zubarev, R. A.; Haselmann, K. F.; Budnik, B.; Kjeldsen, F.; Jensen, F. Towards an Understanding of the Mechanism of Electron-Capture Dissociation: A Historical Perspective and Modern Ideas. Eur. J. Mass Spectrom. 2002, 8(5), 337–349.CrossRefGoogle Scholar
  18. 18.
    Roepstorff, P.; Fohlman, J. Proposal for a Common Nomenclature for Sequence Ions in Mass-Spectra of Peptides. Biomed. Mass Spectrom. 1984, 11(11), 601.CrossRefGoogle Scholar
  19. 19.
    Leymarie, N.; Costello, C. E.; O’Connor, P. B. Electron Capture Dissociation Initiates a Free Radical Reaction Cascade. J. Am. Chem. Soc. 2003, 12(29), 8949–8958.CrossRefGoogle Scholar
  20. 20.
    Syrstad, E. A.; Turecek, F. Toward a General Mechanism of Electron Capture Dissociation. J. Am. Soc. Mass Spectrom. 2005, 16(2), 208–224.CrossRefGoogle Scholar
  21. 21.
    Chen, X.; Turecek, F. The Arginine Anomaly: Arginine Radicals are Poor Hydrogen Donors in Electron Transfer Induced Dissociations. J. Am. Chem. Soc. 2006, 128, 12520–12530.CrossRefGoogle Scholar
  22. 22.
    Sobczyk, M.; Anusiewicz, W.; Berdys-Kochanska, J.; Sawicka, A.; Skurski, P.; Simons, J. Coulomb-Assisted Dissociative Electron Attachment: Application to a Model Peptide. J. Phys. Chem. A. 2005, 109, 250–258.CrossRefGoogle Scholar
  23. 23.
    Cooper, H. J.; Hudgins, R. R.; Hakansson, K.; Marshall, A. G. Secondary Fragmentation of Linear Peptides in Electron Capture Dissociation. Int. J. Mass Spectrom. 2003, 228(2/3), 723–728.CrossRefGoogle Scholar
  24. 24.
    Zubarev, R. A.; Horn, D. M.; Fridriksson, E. K.; Kelleher, N. L.; Kruger, N. A.; Lewis, M. A.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations. Anal. Chem. 2000, 72(3), 563–573.CrossRefGoogle Scholar
  25. 25.
    Axelsson, J.; Palmblad, M.; Hakansson, K.; Hakansson, P. Electron Capture Dissociation of Substance P Using a Commercially Available Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Rapid Commun. Mass Spectrom. 1999, 13(6), 474–477.CrossRefGoogle Scholar
  26. 26.
    Kelleher, R. L.; Zubarev, R. A.; Bush, K.; Furie, B.; Furie, B. C.; McLafferty, F. W.; Walsh, C. T. Localization of Labile Post-Translational Modifications by Electron Capture Dissociation: The Case of γ-Carboxyglutamic Acid. Anal. Chem. 1999, 71(19), 4250–4253.CrossRefGoogle Scholar
  27. 27.
    Hakansson, K.; Cooper, H. J.; Emmett, M. R.; Costello, C. E.; Marshall, A. G.; Nilsson, C. L. Electron Capture Dissociation and Infrared Multiphoton Dissociation MS/MS of an N-Glycosylated Tryptic Peptide to Yield Complementary Sequence Information. Anal. Chem. 2001, 73(18), 4530–4536.CrossRefGoogle Scholar
  28. 28.
    Mirgorodskaya, E.; Roepstorff, P.; Zubarev, R. A. Localization of O-Glycosylation Sites in Peptides by Electron Capture Dissociation in a Fourier Transform Mass Spectrometer. Anal. Chem. 1999, 71(20), 4431–4436.CrossRefGoogle Scholar
  29. 29.
    Shi, S. D. H.; Hemling, M. E.; Carr, S. A.; Horn, D. M.; Lindh, I.; McLafferty, F. W. Phosphopeptide/Phosphoprotein Mapping by Electron Capture Dissociation Mass Spectrometry. Anal. Chem. 2001, 73(1), 19–22.CrossRefGoogle Scholar
  30. 30.
    Stensballe, A.; Jensen, O. N.; Olsen, J. V.; Haselmann, K. F.; Zubarev, R. A. Electron Capture Dissociation of Singly and Multiply Phosphorylated Peptides. Rapid Commun. Mass Spectrom. 2000, 14(19), 1793–1800.CrossRefGoogle Scholar
  31. 31.
    Guan, Z. Q. Identification and Localization of the Fatty Acid Modification in Ghrelin by Electron Capture Dissociation. J. Am. Soc Mass Spectrom. 2002, 13(12), 1443–1447.CrossRefGoogle Scholar
  32. 32.
    Guan, Z. Q.; Yates, N. A.; Bakhtiar, R. Detection and Characterization of Methionine Oxidation in Peptides by Collision-Induced Dissociation and Electron Capture Dissociation. J. Am. Soc. Mass Spectrom. 2003, 14(6), 605–613.CrossRefGoogle Scholar
  33. 33.
    Cooper, H. J.; Heath, J. K.; Jaffray, E.; Hay, R. T.; Lam, T. T.; Marshall, A. G. Identification of Sites of Ubiquitination in Proteins: A Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Approach. Anal. Chem. 2004, 76, 6982–6988.CrossRefGoogle Scholar
  34. 34.
    Cooper, H. J.; Tatham, M. H.; Jaffray, E.; Heath, J. K.; Lam, T. T.; Marshall, A. G.; Hay, R. T. FT-ICR Mass Spectrometry for the Analysis of SUMO Modification: Identification of Lysines in RanBP2 and SUMO Targeted for Modification During the E3 AutoSUMOylation reaction. Anal. Chem. 2005, 77, 6310–6319.CrossRefGoogle Scholar
  35. 35.
    Creese, A. J.; Cooper, H. J. The Effect of Phosphorylation on the Electron Capture Dissociation of Peptide Ions. J. Am. Soc. Mass Spectrom. 2008, 19, 1263–1274.CrossRefGoogle Scholar
  36. 36.
    Sohn, C. H.; Chung, C. K.; Yin, S.; Ramachandran, P.; Loo, J. A.; Beauchamp, J. L. Probing the Mechanism of Electron Capture and Electron Transfer Dissociation Using Tags with Variable Electron Affinity. J. Am. Chem. Soc. 2009, 131(15), 5444–5459.CrossRefGoogle Scholar
  37. 37.
    Desfrancois, C.; Periquet, V.; Lyapustina, S. A.; Lippa, T. P.; Robinson, D. W.; Bowen, K. H.; Nonaka, H.; Compton, R. N. Electron Binding to Valence and Multipole States of Molecules: Nitrobenzene, Para- and Meta-Dinitrobenzenes. J. Chem. Phys. 1999, 111(10), 4569–4576.CrossRefGoogle Scholar
  38. 38.
    Fukuda, E. K.; McIver, R. T. Relative Electron Affinities of Substituted Benzophenones, Nitrobenzenes, and Quinones. J. Am. Chem. Soc. 1985, 107, 2291–2296.CrossRefGoogle Scholar
  39. 39.
    Horn, D. M.; Ge, Y.; McLafferty, F. W. Activated Ion Electron Capture Dissociation for Mass Spectral Sequencing of Larger (42 kDa) Proteins. Anal. Chem. 2000, 73, 4778–4784.CrossRefGoogle Scholar
  40. 40.
    Kendall, G.; Cooper, H. J.; Heptinstall, J.; Derrick, J.; Walton, D. J.; Peterson, I. R. Specific Electrochemical Nitration of Horse Heart Myoglobin. Arch. Biochem. Biophys. 2001, 392(2), 169–179.CrossRefGoogle Scholar
  41. 41.
    Mikhailov, V. A.; Cooper, H. J. Activated Ion Electron Capture Dissociation (AI ECD) of Proteins: Synchronization of Infrared and Electron Irradiation with Ion Magnetron Motion. J. Am. Soc. Mass Spectrom. 2009, 20(5), 763–771.CrossRefGoogle Scholar
  42. 42.
    Chalkley, R. J.; Baker, R.; Medzihradszky, K. F.; Lynn, A. J.; Burlingame, A. L. In-Depth Analysis of Tandem Mass Spectrometry Data from Disparate Instrument Types. Mol. Cell. Proteom. 2008, 7(12), 2386–2398.CrossRefGoogle Scholar
  43. 43.
    Breuker, K.; Oh, H.; Cerda, B.; Horn, D. M.; McLafferty, F. W. Hydrogen Atom Loss in ECD: A Fourier Transform Ion Cyclotron Resonance Study with Single Isotopomeric Ions. Eur. J. Mass Spectrom. 2002, 8, 177–180.CrossRefGoogle Scholar
  44. 44.
    Polasek, M.; Turecek, F. Hydrogen Atom Adducts to Nitrobenzene: Formation of the Phenylnitronic Radical in the Gas Phase and Energetics of Wheland Intermediates. J. Am. Chem. Soc. 2000, 122(39), 9511–9524.CrossRefGoogle Scholar
  45. 45.
    Sokolovsky, M.; Riordan, J. F.; Vallee, B. L. Conversion of 3-Nitrotyrosine to 3-Aminotyrosine in Peptides and Proteins. Biochem. Biophys. Res. Commun. 1967, 27(1), 20–25.CrossRefGoogle Scholar
  46. 46.
    De Filippis, V.; Frasson, R.; Fontana, A. 3-Nitrotyrosine as a Spectroscopic Probe for Investigating Protein—Protein Interactions. Protein Sci. 2006, 15(5), 976–986.CrossRefGoogle Scholar
  47. 47.
    Hamidane, H. B.; Chiappe, D.; Hartmer, R.; Vorobyev, A.; Moniatte, M.; Tsybin, Y. O. Electron Capture and Transfer Dissociation: Peptide Structure Analysis at Different Ion Internal Energy Levels. J. Am. Soc. Mass Spectrom. 2009, 20, 567–575.CrossRefGoogle Scholar
  48. 48.
    Hudgins, R. R.; Ratner, M. A.; Jarrold, M. F. Design of Helices that are Stable In Vacuo. J. Am. Chem. Soc. 1998, 120, 12974–12975.CrossRefGoogle Scholar
  49. 49.
    Hamidane, H. B.; He, H.; Tsybin, O. Y.; Emmett, M. R.; Hendrickson, C. L.; Marshall, A. G.; Tsybin, Y. O. Periodic Sequence Distribution of Product Ion Abundances in Electron Capture Dissociation of Amphipathic Peptides and Proteins. J. Am. Soc. Mass Spectrom. 2009, 20, 1182–1192.CrossRefGoogle Scholar
  50. 50.
    Sobczyk, M.; Simons, J. Distance Dependence of Through-Bond Electron Transfer Rates in Electron-Capture and Electron-Transfer Dissociation. Int. J. Mass Spectrom. 2006, 253, 274–280.CrossRefGoogle Scholar
  51. 51.
    Mikhailov, V. A.; Iniesta, J.; Jones, A. W.; Cooper, H. J. unpublished (manuscript in preparation).Google Scholar

Copyright information

© American Society for Mass Spectrometry 2010

Authors and Affiliations

  • Andrew W. Jones
    • 1
  • Victor A. Mikhailov
    • 1
  • Jesus Iniesta
    • 2
  • Helen J. Cooper
    • 1
  1. 1.School of BiosciencesUniversity of BirminghamEdgbastonUK
  2. 2.Department of Physical ChemistryUniversity of AlicanteAlicanteSpain

Personalised recommendations