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.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
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.
Beckman, J. S. Oxidative Damage and Tyrosine Nitration from Peroxynitrite. Chem. Res. Toxicol. 1996, 95, 836–844.
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.
Radi, R. Nitric Oxide, Oxidants, and Protein Tyrosine Nitration. Proc. Nat. Acad. Sci. USA. 2004, 1012, 4003–4008.
Ischiropoulos, H. Biological Tyrosine nitration: A Pathophysiological Function of Nitric Oxide and Reactive Oxygen Species. Arch. Biochem. Biophys. 1998, 3561, 1–11.
Ischiropoulos, H.; Almehdi, A. B. Peroxynitrite-Mediated Oxidative Protein Modifications. FEBS Lett. 1995, 364(3), 279–282.
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.
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.
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.
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.
Cooper, H. J.; Hakansson, K.; Marshall, A. G. The Role of Electron Capture Dissociation in Biomolecular Analysis. Mass Spectrom. Rev. 2005, 24, 201–222.
McLuckey, S. A.; Goeringer, D. E. Slow Heating Methods in Tandem Mass Spectrometry. J. Mass Spectrom. 1997, 3(5), 461–474.
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.
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.
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.
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.
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.
Roepstorff, P.; Fohlman, J. Proposal for a Common Nomenclature for Sequence Ions in Mass-Spectra of Peptides. Biomed. Mass Spectrom. 1984, 11(11), 601.
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.
Syrstad, E. A.; Turecek, F. Toward a General Mechanism of Electron Capture Dissociation. J. Am. Soc. Mass Spectrom. 2005, 16(2), 208–224.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Fukuda, E. K.; McIver, R. T. Relative Electron Affinities of Substituted Benzophenones, Nitrobenzenes, and Quinones. J. Am. Chem. Soc. 1985, 107, 2291–2296.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Mikhailov, V. A.; Iniesta, J.; Jones, A. W.; Cooper, H. J. unpublished (manuscript in preparation).
Author information
Authors and Affiliations
Corresponding author
Additional information
Published online October 22, 2009
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Jones, A.W., Mikhailov, V.A., Iniesta, J. et al. Electron capture dissociation mass spectrometry of tyrosine nitrated peptides. J Am Soc Mass Spectrom 21, 268–277 (2010). https://doi.org/10.1016/j.jasms.2009.10.011
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1016/j.jasms.2009.10.011