Abstract
Odd-electron a+1 radical ions generated in the 157 nm photodissociation of peptide ions were investigated in an ion trap mass spectrometer. To localize the radical, peptide backbone amide hydrogens were replaced with deuterium. When the resulting radical ions underwent hydrogen elimination, no H/D scrambling was obvious, suggesting that without collisional activation, the radical resides on the terminal α-carbon. Upon collisional excitation, odd-electron radical ions dissociate through two favored pathways: the production of a-type ions at aromatic amino acids via homolytic cleavage of backbone Cα-C(O) bonds and side-chain losses at nonaromatic amino acids. When aromatic residues are not present, nonaromatic residues can also lead to a-type ions. In addition to a-type ions, serine and threonine yield c n−1 and a n−1+1 ions where n denotes the position of the serine or threonine. All of these fragments appear to be directed by the radical and they strongly depend on the amino acid side-chain structure. In addition, thermal fragments are also occasionally observed following cleavage of labile Xxx-Pro bonds and their formation appears to be kinetically competitive with radical migration.
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Halliwell, B.; Gutteridge, J. M. C. Free Radicals in Biology and Medicine; Oxford University Press: Oxford, 1999.
Pogozelski, W. K.; Tullius, T. D. Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety. Chem. Rev. 1998, 98, 1089–1107.
Stubbe, J.; van der Donk, W. A. Protein Radicals in Enzyme Catalysis. Chem. Rev. 1998, 98, 705–762.
Garrison, W. M. Reaction-Mechanisms in the Radiolysis of Peptides, Polypeptides, and Proteins. Chem. Rev. 1987, 87, 381–389.
Dean, R. T.; Fu, S.; Stocker, R.; Davies, M. J. Biochemistry and Pathology of Radical-mediated Protein Oxidation. Biochem. J. 1997, 324, 1–18.
Hawkins, C. L.; Davies, M. J. Generation and Propagation of Radical Reactions on Proteins. Biochim. Biophys. Acta. 2001, 1504, 196–219.
Rauk, A.; Yu, D.; Armstrong, D. A. Toward Site Specificity of Oxidative Damage in Proteins: C-H and C-C Bond Dissociation Energies and Reduction Potentials of the Radicals of Alanine, Serine, and Threonine Residues—An Ab Initio Study. J. Am. Chem. Soc. 1997, 119, 208–217.
Rauk, A.; Yu, D.; Armstrong, D. A. Oxidative Damage to and by Cysteine in Proteins: An Ab Initio Study of the Radicals Structures, C-H, S-H, and by Thiyl Radicals. J. Am. Chem. Soc. 1998, 120, 9949–8855.
Turecek, F.; Syrstad, E. A. Mechanism and Energetics of Intramolecular Hydrogen Transfer in Amide and Peptide Radicals and Cation Radicals. J. Am. Soc. Chem. 2003, 125, 3353–3369.
Chowdhury, S. K.; Katta, V.; Chait, B. T. Probing Conformational Changes in Proteins by Mass Spectrometry. J. Am. Chem. Soc. 1990, 112, 9012–9013.
Syka, J. E. P.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9528–9533.
Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Protein Cations: A Nonergodic Process. J. Am. Soc. Chem. 1998, 120, 3265–3266.
Chu, I. K.; Rodriquez, C. F.; Lau, T. C.; Hopkinson, A. C.; Siu, K. W. M. Molecular Radical Cations of Oligopeptides. J. Phys. Chem. B 2000, 104, 3393–3397.
Wee, S.; O’Hair, R. A. J.; McFadyen, W. D. Comparing the Gas-phase Fragmentation Reactions of Protonated and Radical Cations of the Tripeptides GXR. Int. J. Mass Spectrom. 2004, 234, 101–122.
Laskin, J.; Yang, Z.; Chu, I. K. Energetics and Dynamics of Electron Transfer and Proton Transfer in Dissociation of Metal III(Salen)-Peptide Complexes in the Gas Phase. J. Am. Soc. Chem. 2008, 130, 3218–3230.
Laskin, J.; Yang, Z.; Lam, C.; Chu, I. K. Charge-Remote Fragmentation of Odd-Electron Peptide Ions. Anal. Chem. 2007, 79, 6607–6614.
Hao, G.; Gross, S. S. Electrospray Tandem Mass Spectrometer Analysis of S- and N-Nitrosopeptides: Facile Loss of NO and Radical-Induced Fragmentation. J. Am. Soc. Mass Spectrom. 2006, 17, 1725–1730.
Hodyss, R.; Cox, H. A.; Beauchamp, J. L. Bioconjugates for Tunable Peptide Fragmentation: Free Radical Initiated Peptide Sequencing (FRIPS). J. Am. Chem. Soc. 2005, 127, 12436–12437.
Yin, H.; Chacon, A.; Porter, N. A.; Yin, H.; Masterson, D. S. Free Radical-Induced Site-Specific Peptide Cleavage in the Gas Phase: Low-Energy Collision-Induced Dissociation in ESI- and MALDI Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2007, 18, 807–816.
Ly, T.; Julian, R. R. Residue-Specific Radical-Directed Dissociation of Whole Proteins in the Gas Phase. J. Am. Soc. Chem. 2008, 130, 351–358.
Oh, H. B.; Breuker, K.; Sze, S. K.; Ge, Y.; Carpenter, B. K.; McLafferty, F. W. Secondary and Tertiary Structures of Gaseous Protein Ions Characterized by Electron Capture Dissociation Mass Spectrometry and Photofragment Spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15863–15868.
Breuker, K.; Oh, H. B.; Horn, D. M.; Cerda, B. A.; McLafferty, F. W. Detailed Unfolding and Folding of Gaseous Ubiquitin Ions Characterized by Electron Capture Dissociation. J. Am. Soc. Chem. 2002, 127, 6407–6420.
Swaney, D. L.; McAlister, G. C.; Wirtala, M.; Schwartz, J. C.; Syka, J. E. P.; Coon, J. J. Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors. Anal. Chem. 2007, 79, 477–485.
Barlow, C. K.; McFadyen, W. D.; O’Hair, R. A. J. Formation of Cationic Peptide Radicals by Gas-Phase Redox Reactions with Trivalent Chromium, Manganese, Iron, and Cobalt Complexes. J. Am. Soc. Chem. 2005, 127, 6109–6115.
Sun, Q.; Nelson, H.; Ly, T.; Stoltz, B. M.; Julian, R. R. Side Chain Chemistry Mediates Backbone Fragmentation in Hydrogen Deficient Peptide Radicals. J. Proteome Res. 2008, 8, 958–966.
Ly, T.; Julian, R. R. Tracking Radical Migration in Large Hydrogen Deficient Peptides with Covalent Labels: Facile Movement Does Not Equal Indiscriminate Fragmentation. J. Am. Soc. Mass Spectrom. 2009, In press.
Burlet, O.; Orkiszewski, R. S.; Ballard, K. D.; Gaskell, S. J. Charge Promotion of Low-energy Fragmentation of Peptide ions. Rapid Commun. Mass Spectrom. 1992, 6, 658–662.
Dongre, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model. J. Am. Soc. Chem. 1996, 118, 8365–8374.
Kapp, E. A.; Schutz, F.; Reid, G. E.; Eddes, J. S.; Moritz, R. L.; O’Hair, R. A. J.; Speed, T. P.; Simpson, R. J. Mining a Tandem Mass Spectrometry Database to Determine the Trends and Global Factors Influencing Peptide Fragmentation. Anal. Chem. 2003, 75, 6251–6264.
Paizs, B.; Suhai, S. Towards Understanding the Tandem Mass spectra of Protonated Oligopeptides: 1: Mechanism of Amide Bond Cleavage. J. Am. Soc. Mass Spectrom. 2004, 15, 103–113.
Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Mobile and Localized Protons: A Framework for Understanding Peptide Dissociation. J. Mass Spectrom. 2000, 35, 1399–1406.
Cooper, H. J.; Hudgins, R. R.; Hakansson, K.; Marshall, A. G. Characterization of Amino Acid Side-Chain Losses in Electron Capture Dissociation. J. Am. Soc. Mass Spectrom. 2002, 13, 241–249.
Leymarie, N.; Costello, C. E.; O’Connor, P. B. Electron Capture Dissociation Initiates a Free Radical Reaction Cascade. J. Am. Chem. Soc. 2003, 125, 8949–8958.
Fung, Y. M. E.; Chan, T. W. D. Experimental and Theoretical Investigations of the Loss of Amino Acid Side Chains in Electron Capture Dissociation of Model Peptides. J. Am. Soc. Mass Spectrom. 2005, 16, 1523–1535.
Zubarev, R. A.; Kruger, N. A.; Fridriksson, E. K.; Lewis, M. A.; Horn, D. M.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation of Gaseous Multiply-Charged Proteins Is Favored at Disulfide Bonds and Other Sites of High Hydrogen Atom Affinity. J. Am. Chem. Soc. 1999, 121, 2857–2862.
O’Connor, P. B.; Lin, C.; Cournoyer, J. J.; Pittman, J. L.; Belyayev, M.; Budnik, B. A. Long-Lived Electron Capture Dissociation Product Ions Experience Radical Migration via Hydrogen Abstraction. J. Am. Soc. Mass Spectrom. 2006, 17, 576–585.
Han, H.; Xia, Y.; McLuckey, S. A. Ion Trap Collisional Activation of c and z Ions Formed via Gas-Phase Ion/Ion Electron-Transfer Dissociation. J. Proteome Res. 2007, 6, 3062–3069.
Cui, W.; Thompson, M. S.; Reilly, J. P. Pathways of Peptide Ion Fragmentation Induced by Vacuum Ultraviolet Light. J. Am. Soc. Mass Spectrom. 2005, 16, 1384–1398.
Zhang, L.; Cui, W.; Thompson, M. S.; Reilly, J. P. Structures of a-Type Ions Formed in the 157 nm Photodissociation of Singly-Charged Peptide Ions. J. Am. Soc. Mass Spectrom. 2006, 17, 1315–1321.
Thompson, M. S.; Cui, W.; Reilly, J. P. Fragmentation of Singly Charged Peptide Ions by Photodissociation at λ=157 nm. Angew. Chem. Int. Edit. 2004, 43, 4791–4794.
Kim, T. Y.; Thompson, M. S.; Reilly, J. P. Peptide Photodissociation at 157 nm in a Linear Ion Trap Mass Spectrometer. Rapid Commun. Mass Spectrom. 2005, 19, 1657–1665.
Chu, I. K.; Zhao, J.; Xu, M.; Siu, S. O.; Hopkinson, A. C.; Siu, K. W. M. Are the Radical Centers in Peptide Radical Cations Mobile?: The Generation, Tautomerism, and Dissociation of Isomeric α-Carbon-Centered Triglycine Radical Cations in the Gas Phase. J. Am. Soc. Chem. 2008, 130, 7862–7872.
Chu, I. K.; Rodriguez, C. F.; Hopkinson, A. C.; Siu, K. W. M.; Lau, T. C. Formation of Molecular Radical Cations of Enkephalin Derivatives Via Collisional-Induced Dissociation of Electrospray-generated Copper (II) Complex Ions of Amines and Peptides. J. Am. Soc. Mass Spectrom. 2001, 12, 1114–1119.
Hopkinson, A. C.; Siu, K. W. M. In Principles of Mass Spectrometry Applied to Biomolecules; Laskin, J.; Lifshitz, C., Eds.; Wiely-Interscience: Hoboken, NJ, 2006; p 301–335.
Wee, S.; O’Hair, R. A. J.; McFadyen, W. D. The Role of the Position of the Basic Residue in the Generation and Fragmentation of Peptide Radical Ions. Int. J. Mass Spectrom. 2006, 249, 171–183.
Moran, D.; Jacob, R.; Wood, G. P. F.; Coote, M. L.; Davies, M. J.; O’Hair, R. A. J.; Easton, C. J.; Radom, L. Rearrangements in Model Peptide-Type Radicals Via Intramolecular Hydrogen-Atom Transfer. Helv. Chim. Acta. 2006, 89, 2254–2272.
Wee, S.; O’Hare, R. A. J.; McFadyen, W. D. Side-Chain Radical Losses from Radical Cations Allows Distinction of Leucine and Isoleucine Residues in the Isomeric Peptide Gly-XXX-Arg. Rapid Commun. Mass Spectrom. 2002, 16, 884–890.
Peter, M. G. Chemical Modifications of Biopolymers by Quinones and Quinone Methides. Angew. Chem. Int. Edit. 1989, 28, 555–570.
Kjeldsen, F.; Haselmann, K. F.; Sorensen, E. S.; Zubarev, R. A. Distinguishing of Ile/Leu Amino Acid Residues in the PP3 Protein by (Hot) Electron Capture Dissociation in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 2003, 75, 1267–1274.
Wood, G. P. F.; Moran, D.; Jacob, R.; Radom, L. Bond Dissociation Energetics and Radical Stabilization Energies Associated with Model Peptide-Backbone Radicals. J. Phys. Chem. A. 2005, 109, 6318–6325.
Wood, G. P. F.; Easton, C. J.; Rauk, A.; Davies, M. J.; Radom, L. Effect of Side Chains on Competing Pathways for β-Scission Reactions of Peptide-Backbone Alkoxyl Radicals. J. Phys. Chem. A. 2006, 110, 10316–10323.
Smith, L. L.; Herrmann, K. A.; Wysocki, V. H. Investigation of Gas Phase Ion Structure for Proline-Containing b2 Ion. J. Am. Soc. Mass Spectrom. 2006, 17, 20–28.
Wood, G. P. F.; Easton, C. J.; Rauk, A.; Davies, M. J.; Radom, L. Effect of Side Chains on Competing Pathways for β-Scission Reactions of Peptide-Backbone Alkoxyl Radicals. J. Phys. Chem. A. 2008, 110, 10316–10323.
Karnezis, A.; Barlow, C. K.; O’Hair, R. A. J.; McFadyen, W. D. Peptide Derivatization as a Strategy to Form Fixed-Charge Peptide Radicals. Rapid Commun. Mass Spectrom. 2006, 20, 2865–2870.
Tsaprailis, G.; Somogyi, A.; Nikolaev, E. N.; Wysocki, V. H. Refining the Model for Selective Cleavage at Acidic Residues in Arginine-Containing Protonated Peptides. Int. J. Mass Spectrom. 2000, 195/196, 467–479.
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Published online April 5, 2009
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Zhang, L., Reilly, J.P. Radical-driven dissociation of odd-electron peptide radical ions produced in 157 nm photodissociation. J Am Soc Mass Spectrom 20, 1378–1390 (2009). https://doi.org/10.1016/j.jasms.2009.03.026
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DOI: https://doi.org/10.1016/j.jasms.2009.03.026