Effect of the his residue on the cyclization of b ions

Focus: Mobile Proton Model

Abstract

The MSn spectra of the [M + H]+ and b5 peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b4 ions derived from the first four peptides. The MS2 spectra of the [M + H]+ ions show a substantial series of bn ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b tons when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b4 and b5 ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for bn ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b5 structures, the b4 ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b4 and b5 the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.

References

  1. 1.
    Larsen, M. R.; Roepstorff, P. Mass Spectrometric Identification of Proteins and Characterization of their Post-Translational Modifications. Fresenius J. Anal. Chem. 2000, 366, 677–690.CrossRefGoogle Scholar
  2. 2.
    Aebersold, R.; Goodlett, D. R. Mass Spectrometry in Proteomics. Chem. Rev. 2001, 101, 269–295.CrossRefGoogle Scholar
  3. 3.
    Medzihradszky, K. Peptide Sequence Analysis. Methods Enzymol. 2005, 402, 209–244.CrossRefGoogle Scholar
  4. 4.
    Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508–548.CrossRefGoogle Scholar
  5. 5.
    Roepstorff, P.; Fohlmann, J. Proposals for a Common Nomenclature for Sequence Ions in Mass Spectra of Peptides. Biomed. Mass Spectrom. 1984, 11, 601.CrossRefGoogle Scholar
  6. 6.
    Biemann, K. Contributions of Mass Spectrometry to Peptide and Protein Structure. Biomed. Env. Mass Spectrom. 1988, 16, 99–111.CrossRefGoogle Scholar
  7. 7.
    Harrison, A. G.; Young, A. B.; Bleiholder, C.; Suhai, S.; Paizs, B. Scrambling of Sequence Information in Collision-Induced Dissociation of Peptides. J. Am. Chem. Soc. 2006, 128, 10364–10365.CrossRefGoogle Scholar
  8. 8.
    Bleiholder, C.; Osburn, S.; Williams, T. D.; Suhai, S.; Van Stipdonk, M.; Harrison, A. G.; Paizs, B. Sequence-Scrambling Pathways of Protonated Peptides. J. Am. Chem. Soc. 2008, 130, 17774–17789.CrossRefGoogle Scholar
  9. 9.
    Mueller, D. R.; Eckersley, M.; Richter, W. Hydrogen Transfer Reactions in the Formation of “Y + 2” Sequence Ions from Protonated Peptides. Org. Mass Spectrom. 1988, 23, 217–222.CrossRefGoogle Scholar
  10. 10.
    Cordero, M. M.; Houser, J. J.; Wesdemiotis, C. The Neutral Products Formed During Backbone Cleavage of Protonated Peptides in Tandem Mass Spectrometry. Anal. Chem. 1993, 65, 1594–1601.CrossRefGoogle Scholar
  11. 11.
    Harrison, A. G. To b or not to b. The Ongoing Saga of Peptide b Ions. Mass Spectrom. Rev. 2009, 18, 640–654.CrossRefGoogle Scholar
  12. 12.
    Yalcin, T.; Khouw, C.; Csizmadia, I. G.; Peterson, M. R.; Harrison, A. G. Why are b Ions Stable Species in Peptide Mass Spectra? J. Am. Soc. Mass Spectrom. 1995, 6, 1165–1174.CrossRefGoogle Scholar
  13. 13.
    Yalcin, T.; Csizmadia, I. G.; Peterson, M. R.; Harrison, A. G. The Structures and Fragmentation of Bn (n ≥ 3) Ions in Peptide Mass Spectra. J. Am. Soc. Mass Spectrom. 1996, 7, 233–242.CrossRefGoogle Scholar
  14. 14.
    Mold, 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.CrossRefGoogle Scholar
  15. 15.
    Paizs, B.; Lendvay, G.; Vékey, K.; Suhai, S. Formation of b2+ Ions from Protonated Peptides. Rapid Commun. Mass Spectrom. 1999, 13, 523–533.CrossRefGoogle Scholar
  16. 16.
    Harrison, A. G.; Csizmadia, I. G.; Tang, T.-H. Structures and Fragmentation of b2 Ions in Peptide Mass Spectra. J. Am. Soc. Mass Spectrom. 2000, 11, 427–436.CrossRefGoogle Scholar
  17. 17.
    Rodriquez, C. F.; Shoeib, T.; Chu, I. K.; Siu, K. W. M.; Hopkinson, A. C. Comparison Between Protonation, Lithiation and Argentination of 5-Oxazolones. A Study of a Key Intermediate in Gas-Phase Peptide Sequencing. J. Phys. Chem. A 2000, 104, 5335–5342.CrossRefGoogle Scholar
  18. 18.
    Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. Spectroscopic and Theoretical Evidence for Oxazolone Ring Formation in Collision-Induced Dissociation of Peptides. J. Am. Chem. Soc. 2005, 127, 17154–17155.CrossRefGoogle Scholar
  19. 19.
    Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. Infrared Spectroscopy and Theoretical Studies on Gas-Phase Protonated Leu-Enkephalin and Its Fragments: Direct Experimental Evidence for the Mobile Proton. J. Am. Chem. Soc. 2007, 129, 5887–5897.CrossRefGoogle Scholar
  20. 20.
    Yoon, S. H.; Chamot-Rooke, J.; Perkins, B. R.; Hilderbrand, A. E.; Poutsma, I. C.; Wysocki, V. H. IRMPD. Spectroscopy Shows That AGG Forms an Oxazolone b2 Ion. J. Am. Chem. Soc. 2008, 130, 17644–17645.CrossRefGoogle Scholar
  21. 21.
    Oomens, J.; Young, S.; Molesworth, S.; Van Stipdonk, M. Spectroscopic Evidence for an Oxazolone Structure of the b2 Ion from Protonated Tri-Alanine. J. Am. Soc. Mass Spectrom. 2009, 20, 334–339.CrossRefGoogle Scholar
  22. 22.
    Bythell, B. J.; Erlekam, U.; Paizs, B.; Maitre, P. Infrared Spectroscopy of Fragments Derived from Tryptic Peptides. Chem. Phys. Chem. 2009, 10, 883–885.Google Scholar
  23. 23.
    Bythell, B. I.; Somogyi,,Á.; Paizs, B. What is the Structure of b2 Ions Generated from Doubly Protonated Tryptic Peptides? J. Am. Soc. Mass Spectrom. 2009, 10, 618–624.CrossRefGoogle Scholar
  24. 24.
    Yalcin, T.; Harrison, A. G. Ion Chemistry of Protonated Lysine Derivatives. J. Mass Spectrom. 1996, 31, 1237–1243.CrossRefGoogle Scholar
  25. 25.
    Tu, Y.-P.; Harrison, A. G. The b1 Ion Derived from Methionine is a Stable Species. Rapid Commun. Mass Spectrom. 1998, 12, 849–851.CrossRefGoogle Scholar
  26. 26.
    Yu, W.; Vath, J. E.; Huberty, M. C.; Martin, S. A. Identification of the Facile Gas-phase Cleavage of the Asp-Pro and Asp-Xxx Peptide Bonds in Matrix-assisted Laser Desorption Time-of-flight Mass Spectrometry. Anal. Chem. 1993, 65, 3015–3023.CrossRefGoogle Scholar
  27. 27.
    Farrugia, J. M.; Taverner, T.; O’Hair, R. A. J. Side-Chain Involvement in the Fragmentation Reactions of Protonated Methyl Esters of Histidine and its Peptides. Int. J. Mass Spectrom. 2001, 209, 99–112.CrossRefGoogle Scholar
  28. 28.
    Farrugia, J. M.; O’Hair, R. A. J.; Reid, G. A. Do All b2 Ions Have Oxazolone Structures? Multistage Mass Spectrometry and Ab Initio Studies on Protonated N-Acyl Amino Acid Methyl Ester Model Systems. Int. J. Mass Spectrom. 2001, 210/211, 71–87.CrossRefGoogle Scholar
  29. 29.
    Csonka, I. P.; Paizs, B.; Lendvay, G.; Suhai, S. Proton Mobility and Main Fragmentation Pathways of Protonated Lysylglycine. Rapid Commun. Mass Spectrom. 2001, 15, 1457–1472.CrossRefGoogle Scholar
  30. 30.
    Knapp-Mohammady, M.; Young, A. B.; Paizs, B.; Harrison, A. G. Fragmentation of Doubly-Protonated Pro-His-Xaa Tripeptides: Formation of b22+ Ions. J. Am. Soc. Mass Spectrom. 2009, 10, 2135–2143.CrossRefGoogle Scholar
  31. 31.
    Bythell, B. J.; Csonka, I. P.; Suhai, S.; Barofsky, D. F.; Paizs, B. Gas-Phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-Terminal Arginine J. Phys. Chem. A, unpublished (submitted).Google Scholar
  32. 32.
    Allen, J. M.; Racine, A. H.; Berman, A. M.; Johnson, J. S.; Bythell, B. J.; Paizs, B.; Glish, G. L. Why are a3 Ions Rarely Observed? J. Am. Soc. Mass Spectrom. 2008, 19, 1764–1770.CrossRefGoogle Scholar
  33. 33.
    Erlekam, U.; Bythell, B. J.; Scuderi, D.; Van Stipdonk, M.; Paizs, B.; Maitre, P. Infrared Spectroscopy of Fragments of Protonated Peptides. Direct Evidence for Macrocyclic Structure of b 5 Ions. J. Am. Chem. Soc. 2009, 131, 11503–11508.CrossRefGoogle Scholar
  34. 34.
    Tang, X.-J.; Thibault, P.; Boyd, R. K. Fragmentation of Multiply-Protonated Peptides and Implications for Sequencing by Tandem Mass Spectrometry with Low-Energy Collision-Induced Dissociation. Anal. Chem. 1993, 65, 2824–2834.CrossRefGoogle Scholar
  35. 35.
    Tang, X.-J.; Boyd, R. K. Rearrangement of Doubly-Charged Acylium Ions from Lysyl and Ornithyl Peptides. Rapid Commun. Mass Spectrom. 1994, 8, 678–686.CrossRefGoogle Scholar
  36. 36.
    Yague, J.; Paradela, A.; Ramos, M.; Ogueta, S.; Marina, A.; Barabona, F.; Lopez de Castro, J. A.; Vazquez, J. Peptide Rearrangement During Ion Trap Fragmentation: Added Complexity to MS/MS Spectra. Anal. Chem. 2003, 75, 1524–1535.CrossRefGoogle Scholar
  37. 37.
    Mouls, L.; Aubagnac, J. L.; Enjalbal, C. Low Energy Peptide Fragmentations in an ESI-Q-TOF Type Mass Spectrometer, J. Proteome Res. 2007, 6, 1378–1391.CrossRefGoogle Scholar
  38. 38.
    Harrison, A. G. Sequence Scrambling Through Cyclization of b 5 Ions. J. Am. Soc. Mass Spectrom. 2008, 19, 1776–1780.CrossRefGoogle Scholar
  39. 39.
    Molesworth, S.; Osburn, S.; Van Stipdonk, M. Influence of Size on Apparent Scrambling of Sequence During CID of b-Type Ions. J. Am. Soc. Mass Spectrom. 2009, 10, 2174–2181.CrossRefGoogle Scholar
  40. 40.
    Riba-Garcia, I.; Giles, K.; Bateman, R. H.; Gaskell, S. J. Evidence for Structural Variants of a- and b-Type Peptide Fragment Ions Using Combined Ion Mobility/Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2008, 19, 609–613.CrossRefGoogle Scholar
  41. 41.
    Harrison, A. G. Cyclization of Peptide b9 Ions. J. Am. Soc. Mass Spectrom. 2009, 10, 2248–2253.CrossRefGoogle Scholar
  42. 42.
    Fattahi, A.; Zekavat, B.; Solouki, T. H/D Exchange Kinetics: Experimental Evidence for Formation of Different b Fragment Ion Conformers/ Isomers During the Gas-Phase Peptide Sequencing. J. Am. Soc. Mass Spectrom. 2010, 21, 358–369.CrossRefGoogle Scholar
  43. 43.
    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.CrossRefGoogle Scholar
  44. 44.
    Wyttenbach, T.; Paizs, B.; Barran, P.; Breci, L. A.; Liu, D.; Suhai, S.; Wysocki, V. H.; Bowers, M. T. The Effect of the Initial Water of Hydration on the Energetics, Structures, and H/D-exchange Mechanism of a Family of Pentapeptides: An Experimental and Theoretical Study. J. Am. Chem. Soc. 2003, 123, 13768–13775.CrossRefGoogle Scholar
  45. 45.
    Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E. III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. T.; Crowley, M.; Tsui, V.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I. G.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollmann, P. A. AMBER 99; University of California: San Francisco, 1999.Google Scholar
  46. 46.
    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.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, 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.; Parkas, 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, L.; 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 C2; Gaussian Inc.: Wallingford CT, 2004.Google Scholar
  47. 47.
    Tsaprailis, G.; Nair, H.; Zhong, W.; Kuppannan, K.; Futrell, J. H.; Wysocki, V. H. A Mechanistic Investigation of the Enhanced Cleavage at Histidine in the Gas-Phase Dissociation of protonated Peptides. Anal. Chem. 2004, 76, 2083–2094.CrossRefGoogle Scholar
  48. 48.
    Paizs, B.; Suhai, S. Towards Understanding Some Ion Intensity Relationships for the Tandem Mass Spectra of Protonated Peptides. Rapid Commun. Mass Spectrom. 2002, 16, 1699–1702.CrossRefGoogle Scholar
  49. 49.
    Bleiholder, C.; Suhai, S.; B. Paizs. Revising the Proton Affinity Scale of the Naturally Occurring α-Amino Acids. J. Am. Soc. Mass Spectrom. 2006, 17, 1275–1281.CrossRefGoogle Scholar
  50. 50.
    Harrison, A. G.; Young, A. B. Fragmentation of Protonated Oligo-Alanines: Amide Bond Cleavage and Beyond. J. Am. Soc. Mass Spectrom. 2004, 15, 1810–1819.CrossRefGoogle Scholar
  51. 51.
    Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Commentary— Mobile and Localized Protons: A Framework for Understanding Peptide Dissociation. J. Mass Spectrom. 2000, 35, 1399–1406.CrossRefGoogle Scholar
  52. 52.
    Ballard, K. D.; Gaskell, S. J. Dehydration of Peptide [M + H]+ Ions in the Gas Phase. J. Am. Soc. Mass Spectrom. 1993, 4, 477–481.CrossRefGoogle Scholar
  53. 53.
    Reid, G. E.; Simpson, R. J.; O’Hair, R. A. J. Probing the Fragmentation Reactions of Protonated Glycine Oligomers Via Multistage Mass Spectrometry and Gas Phase Ion Molecule Hydrogen/Deuterium Exchange Int. J. Mass Spectrom. 1999, 190/191, 209–230.CrossRefGoogle Scholar
  54. 54.
    Bythell, B. J.; Dain, R. P.; Curtice, S. S.; Oomens, J.; Steill, J. D.; Groenewold, G. S.; Paizs, B.; Van Stipdonk, M. J. Structure of [M + H − H2O]+ from Protonated Tetraglycine Revealed by Landem Mass Spectrometry and IRMPD Spectroscopy J. Phys. Chem. A 2010, 114, 5076–5082.CrossRefGoogle Scholar
  55. 55.
    Cooper, T.; Talaty, E.; Grove, J.; Van Stipdonk, M.; Suhai, S.; Paizs, B. Isotope Labeling and Theoretical Study of the Formation of a3* Ions from Protonated Tetragiycine. J. Am. Soc. Mass Spectrom. 2006, 17, 1654–1664.CrossRefGoogle Scholar
  56. 56.
    Harrison, A. G. Fragmentation Reactions of Some Peptide b3 Ions: An Energy-Resolved Study. Rapid Commun. Mass Spectrom. 2009, 13, 1298–1302.CrossRefGoogle Scholar
  57. 57.
    Bythell, B. J.; Molesworth, S.; Osburn, S.; Cooper, T.; Paizs, B.; Van Stipdonk, M. Structure and Reactivity of an and an* Peptide Fragments Investigated Using Isotope Labeling, Tandem Mass Spectrometry and Density Functional Theory Calculations. J. Am. Soc Mass Spectrom. 2008, 19, 1788–1798.CrossRefGoogle Scholar
  58. 58.
    Chen, X.; Yu, L.; Steill, J. D.; Oomens, J.; Polfer, N. C. Effect of Peptide Fragment Size on the Propensity of Cyclization in Collision-Induced Dissociation: Oligoglycine b2-bs. J. Am. Chem Soc., 2009, 131, 18272–18282.CrossRefGoogle Scholar
  59. 59.
    Paizs, B.; Szlávik, Z.; Lendvay, G.; Vékey, K.; Suhai, S. Formation of a2+ Ions of Protonated Peptides. An Ab Initio Study. Rapid Commun. Muss Spectrom. 2000, 14, 746–755.CrossRefGoogle Scholar
  60. 60.
    El Aribi, H.; Orlova, G.; Rodriquez, C. F.; Almeida, D. R. P.; Hopkinson, A. C.; Siu, K. W. M. Fragmentation Mechanisms of Product Ions from Protonated Tripeptides. J. Phys. Chem. B 2004, 108, 18743–18749.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2010

Authors and Affiliations

  1. 1.Computational Proteomics GroupGerman Cancer Research Center (DKFZ)HeidelbergGermany
  2. 2.Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
  3. 3.Department of ChemistryUniversity of TorontoTorontoCanada

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