Backbone and side-chain specific dissociations of z ions from non-tryptic peptides

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 8, 2010, Pages 1279-1295

  Chung, Thomas W ^a   Tureček, František ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON DIOXIDE; CHAINS; DISSOCIATION; FREE RADICAL REACTIONS; PEPTIDES; POTENTIAL ENERGY; QUANTUM CHEMISTRY; RATE CONSTANTS;

COLLISIONAL ACTIVATION; DISSOCIATION PRODUCTS; ELECTRON STRUCTURES; ELECTRON-TRANSFER DISSOCIATION; OPTIMIZED STRUCTURES; PEPTIDE ION FRAGMENTATION; PROTONATED PEPTIDES; UNIMOLECULAR RATE CONSTANTS;

IONS;

ALANYLALANYLHISTIDINYLALANYLLEUCINE; ALANYLHISTIDINYLALANYLASPARTYLLEUCINE; ALANYLHISTIDINYLASPARTYLALANYLLEUCINE; CARBON DIOXIDE; POLYPEPTIDE; RADICAL; UNCLASSIFIED DRUG; ION; PEPTIDE; PROTON;

ARTICLE; CALCULATION; CARBOXY TERMINAL SEQUENCE; CHEMICAL BOND; CHEMICAL REACTION; CHEMICAL STRUCTURE; COLLISIONALLY ACTIVATED DISSOCIATION; DENSITY FUNCTIONAL THEORY; ELECTRON TRANSFER DISSOCIATION; ENERGY TRANSFER; KINETICS; MASS SPECTROMETRY; PEPTIDE ANALYSIS; PROTEIN DEGRADATION; PROTON TRANSPORT; SURFACE CHARGE; SURFACE PROPERTY; CHEMISTRY; METHODOLOGY; PROTEIN CONFORMATION; THERMODYNAMICS;

CARBON DIOXIDE; IONS; KINETICS; MASS SPECTROMETRY; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTONS; THERMODYNAMICS;

EID: 79955676557     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1016/j.jasms.2010.02.018     Document Type: Article

References (62)

1. 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.
2. Coon, J. J.; Ueberheide, B.; Syka, J. E. P.; Dryhurst, D. D.; Ausio, J.; Shabanowitz, J.; Hunt, D. F. Protein Identification Using Sequential Ion/Ion Reactions and Tandem Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 9463-9468.
3. 2 - Anal. Chem. 2005, 77, 1831-1839.
4. McLafferty, F. W.; Tureček, F. Interpretation of Mass Spectra, 4th ed.; University Science Books: Mill Valley, CA, 1993; p. 37-38.
5. Hubler, S. L.; Jue, A.; Keith, J.; McAlister, G. C.; Craciun, G.; Coon, J. J. Valence Parity Renders z-Type Ions Chemically Distinct. J. Am. Chem. Soc. 2008, 130, 6388-6394.
6. 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.
7. 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.
8. Cooper, H. J.; Hakansson, K.; Marshall, A. G.; Hudgins, R. R.; Haselmann, K. F.; Kjeldsen, F.; Budnik, B. A.; Polfer, N. C.; Zubarev, R. A. Letter: The Diagnostic Value of Amino Acid Side-Chain Losses in Electron Capture Dissociation of Polypeptides. Comment on: "Can the (M.bul.-X) Region in Electron Capture Dissociation Provide Reliable Information on Amino Acid Composition of Polypeptides?" Eur. J. Mass Spectrom. 2002, 8, 461-469.
9. Eur. J. Mass Spectrom. 2003, 9, 221-222.
10. Kjeldsen, F.; Haselmann, K. F.; Sørensen, 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.
11. Kjeldsen, F.; Zubarev, R. A. Secondary Losses Via γ-Lactam Formation in Hot Electron Capture Dissociation: A Missing Link to Complete de Novo Sequencing of Proteins? J. Am. Chem. Soc. 2003, 125, 6628-6629.
12. 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.
13. Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. Side-Chain Losses in Electron Capture Dissociation To Improve Peptide Identification. Anal. Chem. 2007, 79, 2296-2302.
14. 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, 563-573.
15. Frison, G.; Bull, A.; van der Rest, G.; Tureček, F.; Besson, T.; Lemaire, J.; Maître, P.; Chamot-Rooke, J. Structure of ECD Fragments from Charge- Tagged Peptides Probed by Tunable IRMPD. J. Am. Chem. Soc. 2008, 130, 14916-14917.
16. + Cation Radical. J. Mass Spectrom. 2003, 38, 1093-1104.
17. (a) Tureček, F.; Carpenter, F. H.; Polce, M. J.; Wesdemiotis, C. Glycyl Radical Is a Stable Species in the Gas Phase. J. Am. Chem. Soc. 1999, 121, 7955-7956.
18. (b) Carpenter, F. H.; Tureček, F. Glycine Radicals in the Gas Phase. J. Chem. Soc. Perkin Trans. 1999, 2, 2315-2323.
19. (c) O'Hair, R. A. J.; Blanksby, S. J.; Styles, M.; Bowie, J. H. Characterization of [M - H] Cations, Radicals, and Anions of Glycine in the Gas Phase: A combined Experimental and Ab Initio Study. Int. J. Mass Spectrom. 1999, 182/183, 203-211.
20. 2NCH+COOH): Generation and Characterization in the Gas Phase. J. Am. Soc. Mass Spectrom. 1999, 10, 1241-1247.
21. Tureček, F.; Chung, T. W.; Wyer, J. A.; Ehlerding, A.; Zettergen, H.; Nielsen, S. B.; Hvelplund, P.; Chamot-Rooke, J.; Bythell, B.; Paizs, B. ECD and ETD are Different. Keynote lecture presented at the 7th UPPCON Conference, Nara, Japan, December, 2009.
22. 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.
23. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A. Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austn, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision B 05; Gaussian, Inc.; Pittsburgh, PA, 2003.
24. (a) Becke, A. D. A New Mixing of Hartree-Fock and Local Density- Functional Theories. J. Chem. Phys. 1993, 98, 1372-1377.
25. (b) Becke, A. D. Density Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648-5652.
26. (c) Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 1994, 98, 11623-11627.
27. Møller, C.; Plesset, M. S. A Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. 1934, 46, 618-622.
28. (a) Schlegel, H. B. Potential Energy Curves Using Unrestricted Moller- Plesset Perturbation Theory with Spin Annihilation. J. Chem. Phys. 1986, 84, 4530-4534.
29. (b) Mayer, I. Spin-Projected UHF Method. IV. Comparison of Potential Curves Given by Different One-Electron Methods. Adv. Quantum Chem. 1980, 12, 189-262.
30. + Ions. A Comparative G2(MP2) Ab Initio and Density Functional Theory Study. J. Phys. Chem. A 1998, 102, 4703-4713.
31. Gilbert, R.G.; Smith, S. C. Theory of Unimolecular and Recombination Reactions; Blackwell Scientific Publications: Oxford, 1990; p. 52-132.
32. Zhu, L.; Hase, W. L. Quantum Chemistry Program Exchange; Indiana University: Bloomington, 1994; Program No. QCPE 644.
33. Frank, A. J.; Sadílek, M.; Ferrier, J. G.; Tureček, F. Sulfur Oxyacids and Radicals in the Gas Phase. A Variable-Time Neutralization- Photoexcitation-Reionization Mass Spectrometric and Ab Initio/ RRKM Study. J. Am. Chem. Soc. 1997, 119, 12343-12353.
34. 15N-Labeling and Crown-Ether Complexation. J. Phys. Chem. A 2007, 111, 9641-9643.
35. Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
36. (a) Yalcin, T.; Khouw, C.; Czizmadia, I. G.; Peterson, M. R.; Harrison, A. G. Why Are b Ions Stable Species in Peptide Spectra? J. Am. Soc. Mass Spectrom. 1995, 6, 1165-1174.
37. (b) Rodriquez, C. F.; Shoeib, T.; Chu, I. K.; Siu, K. W. M.; Hopkinson, A. C. Comparison Between Protonation, Lithiation, and Argentation of 5-Oxazolones: A Study of a Key Intermediate in Gas-Phase Peptide Sequencing. J. Phys. Chem. A 2000, 104, 5335-5342.
38. + Ions of Protonated Peptides. An Ab Initio Study. Rapid Commun. Mass Spectrom. 2000, 14, 746-755.
39. (d) Nold, M. J.; Wesdemiotis, C.; Yalcin, T.; Harrison, A. G. Amide Bond Dissociation in Protonated Peptides. Structures of the N-Terminal Ionic and Neutral Fragments. Int. J. Mass Spectrom. Ion Processes. 1997, 164, 137-153.
40. 2 Ions Generated from Doubly Protonated Tryptic Peptides? J. Am. Soc. Mass Spectrom. 2009, 20, 618-624.
41. (f) Cooper, H. J. Investigation of the Presence of b Ions in Electron Capture Dissociation Mass Spectra. J. Am. Soc. Mass Spectrom. 2005, 16, 1932-1940.
42. Chen, X.; Tureček, F. Simple. b Ions Have Oxazolone Structures. A Neutralization-Reionization and Computational Study of Oxazolone Radicals. J. Am. Soc. Mass Spectrom. 2005, 16, 1941-1956.
43. Farrugia, J. M.; O'Hair, R. A. J.; Reid, G. E. Do All b2 Ions Have Oxazolone Structures? Multistage Mass Spectrometry and Ab Initio Studies on Protonated N-Acyl Amino Acid Methyl Ester. Int. J. Mass Spectrom. 2001, 210/211, 71-87.
44. + Ion. J. Am. Chem. Soc. 2009, 131, 17528-17529.
45. Seymour, J. L.; Tureček, F. Structure, Energetics, and Reactivity of Ternary Complexes of Amino Acids with Cu(II) and 2,2=-Bipyridine by Density Functional Theory. A Combination of Radical-Induced and Spin-Remote Fragmentations. J. Mass Spectrom. 2002, 37, 533-540.
46. (a) Pople, J. A.; Head-Gordon, M.; Fox, D. J.; Raghavachari, K.; Curtiss, L. A. Gaussian-1 Theory: A General Procedure for Prediction of Molecular Properties. J. Chem. Phys. 1989, 90, 5622-5629.
47. (b) Curtiss, L. A.; Jones, C.; Trucks, G. W.; Raghavachari, K.; Pople, J. A. Gaussian-1 Theory of Molecular Energies for Second-Row Compounds. J. Chem. Phys. 1990, 93, 2537-2545.
48. (c) Curtiss, L. A.; Raghavachari, K.; Pople, J. A. Gaussian-2 Theory Using Reduced Møller-Plesset Orders. J. Chem. Phys. 1993, 98, 1293-1298.
49. (d) Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Rassolov, V.; Pople, J. A. Gaussian-3 (G3) Theory for Molecules Containing First and Second Row Atoms. J. Chem. Phys. 1998, 109, 764-7776.
50. Reed, A. E.; Weinstock, R. B.; Weinhold, F. Natural Population Analysis. J. Chem. Phys. 1985, 83, 735-746.
51. (a) Syrstad, E. A.; Tureček, F. Hydrogen Atom Adducts to the Amide Bond. Generation and Energetics of the Amino(hydroxy)Methyl Radical in the Gas Phase. J. Phys. Chem. A 2001, 105, 11144-11155.
52. (b) Syrstad, E. A.; Stephens, D. D.; Tureček, F. Hydrogen Atom Adducts to the Amide Bond. Generation and Energetics of Amide Radicals in the Gas Phase. J. Phys. Chem. A 2003, 107, 115-126.
53. (c) Tureček, F.; Syrstad, E. A. Mechanism and Energetics of Intramolecular Hydrogen Transfer Atom Transfer in Amide and Peptide Radicals and Cation-Radicals. J. Am. Chem. Soc. 2003, 125, 3353-3369.
54. α Bond Dissociation Energies and Kinetics in Amide and Peptide Radicals. Is the Dissociation a Non-Ergodic Process? J. Am. Chem. Soc. 2003, 125, 5954-5963.
55. (e) Tam, F.; Syrstad, E. A.; Chen, X.; Tureček, F. Electron-Rich Radicals by Neutralization-Reionization Mass Spectrometry. Generation, Dissociations, and Energetics of the Hydrogen Atom Adduct to Acetamide. Eur. J. Mass Spectrom. 2004, 10, 869-879.
56. Yu, D.; Rauk, A.; Armstrong, D. A. Radicals and Ions of Glycine: An Ab Initio Study of the Structures and Gas-Phase Thermochemistry. J. Am. Chem. Soc. 1995, 117, 1789-1796.
57. 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.
58. Jhon, J. S.; Kang, Y. K. Imide Cis-Trans Isomerization of N-Acetyl-N=- Methylprolineamide and Solvent Effects. J. Phys. Chem. A 1999, 103, 5436-5439.
59. Shi, T.; Spain, S. M.; Rabenstein, D. L. Unexpectedly Fast Cis-Trans Isomerization of Xaa-Pro Peptide Bonds in Disulfide-Constrained Cyclic Peptides. J. Am. Chem. Soc. 2004, 126, 790-796.
60. Fischer, G. Chemical Aspects of Peptide Bond Isomerization. Chem. Soc. Rev. 2000, 29, 119-127.
61. Hayakawa, S.; Hashimoto, M.; Matsubara, H.; Tureček, F. Dissecting the Proline Effect: Dissociations of Proline Radicals Formed by Electron Transfer to Protonated Pro-Gly and Gly-Pro Dipeptides in the Gas Phase. J. Am. Chem. Soc. 2007, 129, 7936-7949.
62. 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. Chem. Soc. 2008, 130, 7862-7872.