What is the structure of b2 ions generated from doubly protonated tryptic peptides?

Articles
  • 194 Downloads

Abstract

A recent statistical study (Savitski, M. M.; Falth, M.; Eva Fung, Y. M.; Adams, C. M.; Zubarev, R. A. J. Am. Soc. for Mass Spectrom. doi: 10.1016/j.jasms.2008.08.003) of a large spectral database indicated that the product ion spectra of doubly protonated tryptic peptides fall into two distinct classes. The main factor distinguishing the two classes is the relative abundance of the yN-2 fragment: for Class I spectra yN-2 is the most abundant y fragment while for Class II other y ions dominate the corresponding spectra. To explain the dominance of yN-2 for Class I spectra formation of a nontraditional b2 ion with a diketopiperazine (6-membered cyclic peptide) rather than an oxazolone structure was proposed. Here we present evidence from tandem mass spectrometry, hydrogen/deuterium exchange, and density functional calculations that do not support this proposal. Namely, that CID of doubly protonated YIGSR, YGGFLR, and YIYGSFK produce Class I product ion spectra, yet the b2 fragment is shown to have the traditional oxazolone structure.

Supplementary material

13361_2011_200400618_MOESM1_ESM.pdf (1.5 mb)
Supplementary material, approximately 1561 KB.

References

  1. 1.
    Aebersold, R.; Goodlett, D. R. Mass Spectrometry in Proteomics. Chem. Rev. 2001, 101, 269–295.CrossRefGoogle Scholar
  2. 2.
    Hunt, D. F.; Yates, John R. III; Shabanovitz, J.; Winston, S.; Hauer, C. R. Protein Sequencing by Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 6233–6237.CrossRefGoogle Scholar
  3. 3.
    Steen, H.; Mann, M. The ABCs (and XYZs) of Peptide Sequencing. Nat. Rev. Mol. Cell. Biol. 2004, 5, 699–711.CrossRefGoogle Scholar
  4. 4.
    Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Electrospray Ionization for Mass-Spectrometry of Large Biomolecules. Science 1989, 246, 64–71.CrossRefGoogle Scholar
  5. 5.
    Vékey, K.; Candido, M.; Traldi, P. Use of Charge-Separation Reactions for Sequencing Peptides. Rapid Commun. Mass Spectrom. 1990, 4, 74–76.CrossRefGoogle Scholar
  6. 6.
    Tang, X.; Boyd, R. K. An Investigation of Fragmentation Mechanisms of Doubly Protonated Tryptic Peptides. Rapid Commun. Mass Spectrom. 1992, 6, 651–657.CrossRefGoogle Scholar
  7. 7.
    Tang, X.-J.; Thibault, P.; Boyd, R. K. Fragmentation Reactions 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
  8. 8.
    Burlet, O.; Orkiszewski, R. S.; Ballard, K. D.; Gaskell, S. J. Charge Promotion of Low-Energy Fragmentations of Peptide Ions. Rapid Commun. Mass Spectrom. 1992, 6, 658–662.CrossRefGoogle Scholar
  9. 9.
    Mann, M.; Wilm, M. Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags. Anal. Chem. 1994, 66, 4390–4399.CrossRefGoogle Scholar
  10. 10.
    Adams, J.; Strobel, F. H.; Reiter, A.; Sullards, M. C. The Importance of Charge-Separation Reactions in Tandem Mass Spectrometry of Doubly Protonated Angiotensin II Formed by Electrospray Ionization: Experimental Considerations and Structural Implications. J. Am. Soc. Mass Spectrom. 1996, 7, 30–41.CrossRefGoogle Scholar
  11. 11.
    Kapp, E. A.; Schutz, F.; Reid, G. E.; Moritz, R. L.; O’Hair, R. A. J.; 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.CrossRefGoogle Scholar
  12. 12.
    Huang, Y. Y.; Triscari, J. M.; Tseng, G. C.; Pasa-Tolic, L.; Smith, R. D.; Wysocki, V. H. Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns. Anal. Chem. 2005, 77, 5800–5813.CrossRefGoogle Scholar
  13. 13.
    Martin, D. B.; Eng, J. K.; Nesvizhskii, A. I.; Aebersold, R. Investigation of Neutral Loss During Collision-Induced Dissociation of Peptide Ions. Anal. Chem. 2005, 77, 4870–4882.CrossRefGoogle Scholar
  14. 14.
    Savitski, M. M.; Kjeldsen, F.; Nielsen, M. L.; Garbuzynskiy, S. O.; Galzitskaya, O. V.; Surin, A. K.; Zubarev, R. A. Backbone Carbonyl Group Basicities are Related to Gas-Phase Fragmentation of Peptides and Protein Folding. Angew. Chem. Int. Ed. 2007, 46, 1481–1484.CrossRefGoogle Scholar
  15. 15.
    Savitski M. M.; Falth M.; Eva Fung Y. M.; Adams C. M.; Zubarev R. A. Bifurcating Fragmentation Behavior of Gas-Phase Tryptic Peptide Dications in Collisional Activation. J. Am. Soc. Mass Spectrom. 2008, doi: 10.1016/j.jasms 2008.08.003.Google Scholar
  16. 16.
    Bleiholder, C.; Suhai, S.; Somogyi, A.; Paizs, B. Fragmentation Pathways of Doubly Protonated Tryptic Peptides. J. Am. Soc. Mass Spectrom, unpublished.Google Scholar
  17. 17.
    Cordero, M. M.; Houser, J. J.; Wesdemiotis, C. The Neutral Products Formed During Backbone Fragmentations of Protonated Peptides in Tandem Mass Spectrometry. Anal. Chem. 1993, 65, 1594–1601.CrossRefGoogle Scholar
  18. 18.
    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.CrossRefGoogle Scholar
  19. 19.
    Yalcin, T.; Csizmadia, I. G.; Peterson, M. R.; Harrison, A. G. The Structure and Fragmentation of B − n (n < 3) Ions in Peptide Spectra. J. Am. Soc. Mass Spectrom. 1996, 7, 233–242.CrossRefGoogle Scholar
  20. 20.
    Yalcin, T.; Khouw, C.; Csizmadia, 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.CrossRefGoogle Scholar
  21. 21.
    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
  22. 22.
    Paizs, B.; Lendvay, G.; Vékey, K.; Suhai, S. Formation of b2+ Ions from Protonated Peptides: An Ab Initio Study. Rapid Commun. Mass Spectrom. 1999, 13, 525–533.CrossRefGoogle Scholar
  23. 23.
    Paizs, B.; Suhai, S. Combined Quantum Chemical and RRKM Modeling of the Main Fragmentation Pathways of Protonated GGG: I. Cis-trans Isomerization Around Protonated Amide Bonds. Rapid Commun. Mass Spectrom. 2002, 15, 2307–2323.CrossRefGoogle Scholar
  24. 24.
    Paizs, B.; Suhai, S. Combined Quantum Chemical and RRKM Modeling of the Main Fragmentation Pathways of Protonated GGG: II. Formation of b2, y1, and y2 ions. Rapid Commun. Mass Spectrom. 2002, 16, 375–389.CrossRefGoogle Scholar
  25. 25.
    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, 103–112.CrossRefGoogle Scholar
  26. 26.
    Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508–548.CrossRefGoogle Scholar
  27. 27.
    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 Model Systems. Int. J. Mass Spectrom. 2001, 210/211, 71–87.CrossRefGoogle Scholar
  28. 28.
    Somogyi, Á. Probing Peptide Fragment Ion Structures by Combining Sustained Off-Resonance Collision Induced Dissociation and Gas-Phase H/D Exchange (SORI-HDX) in Fourier Transform Ion-Cyclotron Resonance (FT-ICR) Instruments. J. Am. Soc. Mass Spectrom. doi:10.1016/j.jasms. 2008.08.012.Google Scholar
  29. 29.
    Jiao, C. Q.; Ranatunga, D. R. A.; Vaugn, W. E.; Freiser, B. S. A Pulsed-Leak Valve for Use with Ion Trapping Mass Spectrometers. J. Am. Soc. Mass Spectrom. 1996, 7, 118–122.CrossRefGoogle Scholar
  30. 30.
    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. J.; 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. In: AMBER 99; University of California: San Francisco, 1999.Google Scholar
  31. 31.
    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.; 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 2004, Rev. C; Gaussian, Inc: Wallingford, CT, 2004.Google Scholar
  32. 32.
    Campbell, S.; Rodgers, M. T.; Marzluff, E. M.; Beauchamp, J. L. Structural and Energetic Constraints on Gas Phase Hydrogen/Deuterium Exchange Reactions of Protonated Peptides with D2O, CD3OD, CD3CO2D, and ND3. J. Am. Chem. Soc. 1994, 116, 9765–9766.CrossRefGoogle Scholar
  33. 33.
    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
  34. 34.
    Harrison, A. G.; Young, A. B.; Schnoelzer, M.; Paizs, B. Formation of Iminium Ions by Fragmentation of a2 Ions. Rapid Commun. Mass Spectrom. 2004, 18, 1635–1640.CrossRefGoogle Scholar
  35. 35.
    Allen, J. M.; Black, D. 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

Copyright information

© American Society for Mass Spectrometry 2009

Authors and Affiliations

  1. 1.Department of Molecular BiophysicsGerman Cancer Research Centr (DKFZ)HeidelbergGermany
  2. 2.Department of ChemistryUniversity of ArizonaTucsonUSA

Personalised recommendations