Collision-induced dissociation pathways of protonated Gly2NH2 and Gly3NH2 in the short time-scale limit by chemical dynamics and ion spectroscopy

International Journal of Mass Spectrometry

Volumn 388, Issue , 2015, Pages 40-52

  Spezia, Riccardo ^a   Martens, Jonathan ^b   Oomens, Jos ^b,c   Song, Kihyung ^d  

^a UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d Korea National University of Education   (South Korea)

Author keywords

Collision induced dissociation; Fragmentation mechanisms; IRMPD; Mass spectrometry; Peptides; QM + MM chemical dynamics

Indexed keywords

EID: 84940719098     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2015.07.025     Document Type: Article

References (85)

1. R. Aebersold, and D.R. Goodlett Mass spectrometry in proteomics Chem. Rev. 101 2001 269 295
2. K. Biemann Contributions of mass spectrometry to peptide and protein structure Biol. Mass Spectrom. 16 1988 99 111
3. B. Paizs, and S. Suhai Fragmentation pathways of protonated peptides Mass Spectrom. Rev. 24 2004 508 548
4. P. Roepstorff, and J. Fohlman Proposal for a common nomenclature for sequence ions in mass spectra of peptides Biomed. Mass Spectrom. 11 1984 601
5. A. Dongre, J. Jones, A. Somogyi, and V. Wysocki Influence of peptide composition, gas- phase basicity, and chemical modification on fragmentation efficiency: evidence for the mobile proton model J. Am. Chem. Soc. 118 1996 8365 8374
6. A.G. Harrison To b or not to b: The ongoing saga of peptide b ions Mass Spec. Rev. 28 2009 640 654
7. B.J. Bythell, P. Maître, and B. Paizs Cyclization and rearrangement reactions of an fragment ions of protonated peptides J. Am. Chem. Soc. 132 2010 14766 14779
8. 8 J. Am. Chem. Soc. 131 2009 18272 18282
9. X. Chen, M. Tirado, J.D. Steill, J. Oomens, and N.C. Polfer Cyclic peptide as reference system for b ion structural analysis in the gas phase J. Mass. Spectrom. 46 2011 1011 1015
10. + ion J. Am. Chem. Soc. 131 2009 17528 17529
11. K. Boutilier, M. Ross, A.V. Podtelejnikov, C. Orsi, R. Taylor, P. Taylor, and D. Figeys Comparison of different search engines using validated MS/MS test datasets Anal. Chim. Acta 534 2005 11 20
12. K.A. Resing, K. Meyer-Arendt, A.M. Mendoza, L.D. Aveline-Wolf, K.R. Jonscher, K.G. Pierce, W.M. Old, H.T. Cheung, S. Russell, J.L. Wattawa, G.R. Goehle, R.D. Knight, and N.G. Ahn Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics Anal. Chem. 76 2004 3556 3568
13. K. Forner, M. Lamarine, M. Guedj, J. Dauvillier, and J. Wojcik Universal false discovery rate estimation methodology for genome-wide association studies Hum. Hered. 65 2008 183 194
14. Y. Chen, W. Chen, M.H. Cobb, and Y. Zhao PTMap - A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites Proc. Nat. Acad. Sci. U.S.A. 106 2009 761 766
15. A.G. Harrison, A.B. Young, C. Bleiholder, S. Suhai, and B. Paizs Scrambling of sequence information in collision-induced dissociation of peptides J. Am. Chem. Soc. 128 2006 10364 10365
16. M. Tirado, and N.C. Polfer Defying entropy: forming large head-to-tail macrocycles in the gas phase Angew. Chem. Int. Ed. 51 2012 6436 6438
17. T. Yalcin, C. Khouw, I.G. Csizmadia, M.R. Peterson, and A. Harrison Why are B ions stable species in peptide spectra? J. Am. Soc. Mass Spectrom. 6 1995 1164 1174
18. P. de Sainte Claire, and W.L. Hase Thresholds for the collision-induced dissociation of clusters by rare gas impact J. Phys. Chem. 100 1996 8190 8196
19. 13 clusters J. Phys. Chem. 99 1995 81478161
20. +-Ne collisions J. Chem. Phys. 119 2003 3040 3050
21. 6 with Xe J. Chem. Phys. 123 2005 154311
22. O. Meroueh, Y. Wang, and W.L. Hase Direct dynamics simulations of collision- and surface- induced dissociation of N-protonated glycine, shattering fragmentation J. Phys. Chem. A 106 2002 9983 9992
23. D. Ortiz, P. Martin-Gago, A. Riera, K. Song, J.-Y. Salpin, and R. Spezia Gas-phase collision induced dissociation mechanisms of peptides. Theoretical and experimental study of N-formylalanylamide fragmentation Int. J. Mass Spectrom. 335 2013 33 44
24. Y. Wang, W.L. Hase, and K. Song Direct dynamics study of N-protonated diglycine surface-induced dissociation. Influence of collision energy J. Am. Soc. Mass Spectrom. 14 2003 1402 1412
25. K. Park, B. Deb, K. Song, and W.L. Hase Importance of shattering fragmentation in the surface-induced dissociation of protonated octaglycine J. Am. Soc. Mass Spectrom. 20 2009 939 948
26. G. Barnes, and W.L. Hase Energy transfer, unfolding, and fragmentation dynamics in collisions of N-protonated octaglycine with an H-SAM surface J. Am. Chem. Soc. 131 2009 17185 17193
27. G.L. Barnes, K. Young, L. Yang, and W.L. Hase Fragmentation and reactivity in collisions of protonated diglycine with chemically modified perfluorinated alkylthiolate-self-assembled monolayer surfaces J. Chem. Phys. 134 2011 094106
28. W. Ijaz, Z. Gregg, and G.L. Barnes Complex formation during SID and its effect on proton mobility J. Phys. Chem. Lett. 4 2013 3935 3939
29. Z. Gregg, W. Ijaz, S. Jannetti, and G.L. Barnes The role of proton transfer in surface-induced dissociation J. Phys. Chem. C 118 2014 22149 22155
30. V. Wysocki, G. Tsaprailis, L. Smith, and L. Breci Mobile and localized protons: a framework for understanding peptide dissociation J. Mass Spectrom. 35 2000 1399 1406
31. O. Burlet, C.Y. Yang, and S.J. Gaskell Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: evidence of intraionic interactions J. Am. Soc. Mass Spectrom. 3 1992 337 344
32. K.A. Cox, S.J. Gaskell, M. Morris, and A. Whiting Role of the site protonation in the low-energy decomposition of gas-phase peptide ions J. Am. Soc. Mass Spectrom. 7 1996 522 531
33. R. Spezia, J.-Y. Salpin, M.-P. Gaigeot, W.L. Hase, and K. Song Protonated urea collision-induced dissociation comparison of experiments and chemical dynamics simulations J. Phys. Chem. A 113 2009 13853 13862
34. + by collisional activation: evidence of nonstatistical behavior J. Phys. Chem. A 101 1997 6513 6522
35. ++ Ar. J. Chem. Phys. 121 2004 2571
36. + by collisional activation: evidence of nonstatistical behavior J. Phys. Chem. A 106 2002 9729 9736
37. U. Lourderaj, and W.L. Hase Theoretical and computational studies of Non-RRKM unimolecular dynamics J. Phys. Chem. A 113 2009 2236 2253
38. A. Martin-Somer, M. Yanez, M.-P. Gaigeot, and R. Spezia Unimolecular fragmentation induced by low energy collision: statistically or dynamically driven? J. Phys. Chem. A 118 2014 10882 10893
39. J. Laskin, T.H. Bailey, and J.H. Futrell Shattering of peptide ions on self-assembled monolayer surfaces J. Am. Chem. Soc. 125 2002 1625 1632
40. J.S. Klassen, and P. Kebarle Collision-induced dissociation threshold energies of protonated glycine, glycinamide, and some related small peptides and peptide amino amides J. Am. Chem. Soc. 119 1997 6552 6563
41. B. Paisz, and S. Suhai Theoretical study of the main fragmentation pathways for protonated glycylglycine Rapid Commun. Mass Spectrom. 15 2001 651 663
42. B. Paizs, I.P. Csonka, G. Lendvay, and S. Suhai Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RRKM study Rapid Commun. Mass Spectrom. 15 2011 637 650
43. C.F. Rodriquez, A. Cunje, T. Shoeib, I.K. Chu, A.C. Hopkinson, and K.W.M. Siu Proton migration and tautomerism in protonated triglycine J. Am. Chem. Soc. 123 2001 3006 3012
44. H. El Aribi, C.F. Rodriquez, D.R.P. Almeida, Y. Ling, W.W.-N. Mak, A.C. Hopkinson, and K.W.M. Siu Elucidation of fragmentation mechanisms of protonated peptide ions and their products: a case study on glycylglycylglycine using density functional theory and threshold collision-induced dissociation J. Am. Chem. Soc. 125 2003 9229 9236
45. P.B. Armentrout, and A.L. Heaton Thermodynamics and mechanisms of protonated diglycine decomposition: a computational study J. Am. Soc. Mass Spectrom. 23 2012 621 631
46. P.B. Armentrout, and A.L. Heaton Thermodynamics and mechanisms of protonated diglycine decomposition: a guided ion beam study J. Am. Soc. Mass Spectrom. 23 2012 632 643
47. I.P. Csonka, B. Paizs, G. Lendvay, and S. Suhai Proton mobility in protonated peptides: a joint molecular orbital and RRKM study Rapid Commun. Mass Spectrom. 14 2000 417 431
48. K. Biemann Contributions of mass spectrometry to peptide and protein structure Biomed. Environ. Mass Spectrom. 16 1988 99 111
49. A.D. Becke A new mixing of Hartree-Fock and local density-functional theories J. Chem. Phys. 98 1993 1372 1377
50. C.T. Lee, W.T. Yang, and R.G. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 37 1988 785 789
51. S. Grimme, J. Antony, S. Ehrlich, and H. Krieg A consistent and accurate ab initio parameterization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu J. Chem. Phys. 132 2010 154104
52. J.P.P. Stewart Optimization of parameters for semiempirical methods I. Method J. Comp. Chem. 10 1989 209 220
53. D.A. Case, T.E. Cheatham III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossváry, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman AMBER 2012 2012
54. J.K. Martens, J. Grzetic, G. Berden, and J. Oomens Gas-phase conformations of small polyprolines and their fragment ions by IRMPD spectroscopy Int. J. Mass Spectrom. 377 2015 179 187
55. T. Baer, and W.L. Hase Unimolecular Reaction Dynamics. Theory and experiments, New York 1996
56. L. Zhu, and W.L. Hase A General RRKM Program QCPE 14 1994 644
57. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, and D.J. Fox Gaussian 09, Revision D.01 2009 Gaussian, Inc. Wallingford CT
58. O. Meroueh, and W.L. Hase Collisional activation of small peptides J. Phys. Chem. A 103 1999 3981 3990
59. 2: effects of rotational energy on reactivity and energy transfer via chemical dynamics simulations Int. J. Mass Spectrom. 308 2011 289 298
60. 2+ gas phase unimolecular reactivity via chemical dynamics simulations Phys. Chem. Chem. Phys. 14 2012 11724 11736
61. D. Ortiz, J.-Y. Salpin, K. Song, and R. Spezia Galactose 6-sulfate collision induced dissociation using QM + MM chemical dynamics simulations and ESI-MS/MS experiments Int. J. Mass Spectrom. 358 2014 25 35
62. 2 and its isotopic variants J. Chem. Phys. 62 1975 2890 2899
63. 3Cl association and direct substitution-reactions J. Chem. Phys. 98 1993 8626 8639
64. C.S. Sloane, and W.L. Hase On the dynamics of state selected unimolecular reactions: chloroacetylene dissociation and predissociation J. Chem. Phys. 66 1977 1523 1533
65. X.C. Hu, W.L. Hase, and T. Pirraglia Vectorization of the general Monte Carlo classical trajectory program VENUS J. Comput. Chem. 12 1991 1014 1024
66. W.L. Hase, R.J. Duchovic, X. Hu, A. Komornicki, K. Lim, D.-H. Lu, G.H. Peslherbe, K.N. Swamy, S.R. Vande Linde, H. Wang, and R.J. Wolf VENUS96, a general chemical dynamics computer program QCPE Bull. 16 1996
67. J.J.P. Stewart MOPAC-a semiempirical molecular-orbital program J. Comput. -Aided Mol. Des. 4 1990 1 45
68. J.J. Valle, J.R. Eyler, J. Oomens, D.T. Moore, A.F.G. van der Meer, G. von Helden, G. Meijer, C.L. Hendrickson, A.G. Marshall, and G.T. Blakney Free electron laser-Fourier transform ion cyclotron resonance mass spectrometry facility for obtaining infrared multiphoton dissociation spectra of gaseous ions Rev. Sci. Instrum. 76 2005 023103
69. R. Wu, and T.B. McMahon Infrared multiple photon dissociation spectroscopy as structural confirmation for GlyGlyGlyH+ and AlaAlaAlaH+ in the gas phase, evidence for amide oxygen as the protonation site J. Am. Chem. Soc. 129 2007 11312 11313
70. R. Wu, and T.B. McMahon Protonation sites and conformations of peptides of glycine (Gly1 - 5H +) by IRMPD spectroscopy J. Phys. Chem. B 113 2009 8767 8775
71. C.F. Rodriquez, A. Cunje, T. Shoeib, I.K. Chu, A.C. Hopkinson, and K.W.M. Siu Proton migration and tautomerism in protonated triglycine J. Am. Chem. Soc. 123 2001 3006 3012
72. J. Mosley, J. Young, and M. Duncan Infrared spectroscopy of the acetyl cation and its protonated ketene isomer J. Chem. Phys. 141 2014 024306
73. R.M. Forck, J.M. Dieterich, C.C. Pradzynski, A.L. Huchting, R.A. Mata, and T. Zeuch Structural diversity in sodium doped water trimer Phys. Chem. Chem. Phys. 14 2012 9054 9057
74. B. Yang, and M.T. Rodgers Alkali metal cation binding affinities of cytosine in the gas phase: revisited Phys. Chem. Chem. Phys. 16 2014 16110 16120
75. 2+ revealed by cold ion spectroscopy coupled with FAIMS J. Am. Soc. Mass Spectrom. 23 2012 1173 1182
76. K. Fort, J. Silveira, N. Pierson, K. Servage, D. Clemmer, and D. Russell From solution to the gas phase: factors that influence kinetic trapping of substance P in the gas phase J. Phys. Chem. B 118 2014 14336 14344
77. J. Silveira, K. Fort, D. Kim, K. Servage, N. Pierson, D. Clemmer, and D. Russell From solution to the gas phase: stepwise dehydration and kinetic trapping of substance P reveals the origin of peptide conformations J. Am. Chem. Soc. 135 2013 19147 19153
78. 1 clusters: evidence of high-energy conformers from infrared spectra J. Phys. Chem. Lett. 2 2011 1444 1448
79. V. Brites, A. Cimas, R. Spezia, N. Sieffert, J.M. Lisy, and M.-P. Gaigeot Stalking higher energy conformers on the potential energy surface of charged species J. Chem. Theory Comput. 11 2015 871 883
80. L. Yang, R. Sun, and W.L. Hase Use of direct dynamics simulations to determine unimolecular reaction paths and Arrhenius parameters for large molecules J. Chem. Theory Comput. 7 2011 3478 3483
81. 2 ions Rapid Commun. Mass Spectrom. 16 2002 375 389
82. U.H. Verkerk, J. Zhao, M.J. Van Stipdonk, B.J. Bythell, J. Oomens, A.C. Hopkinson, and K.W.M. Siu Structure of the [M+H-H2O]+ ion from tetraglycine: a revisit by means of density functional theory and isotope labeling J. Phys. Chem. A 115 2011 6683 6687
83. n (n ≥ 3) ions in peptide spectra J. Am. Soc. Mass Spectrom. 7 1996 233 242
84. + ions of protonated peptides. An ab initio study Rapid Commun. Mass Spectrom. 14 2000 746 755
85. E. Martinez-Nunez An automated transition state search using classical trajectories initialized at multiple minima Phys. Chem. Chem. Phys. 17 2015 14912 14921