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Sequence-specific fragmentation of deprotonated peptides containing H or alkyl side chains

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Journal of the American Society for Mass Spectrometry

Abstract

The [M − H]− ions of a variety of di- to pentapeptides containing H or alkyl side chains have been prepared by electrospray ionization and low-energy collision-induced dissociation (CID) of the deprotonated species carried out in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. Using the nomenclature applied to the fragmentation of protonated peptides, deprotonated dipeptides fragment to give a2 ions (CO2 loss) and y1 ions, where the y1 ion has two fewer hydrogens than the y ″1 ions formed from protonated peptides. Deprotonated tri- and tetrapeptides fragment to give primarily y1, c1, and sup″b2 ions, where the sup″b2 ion has two fewer hydrogens than the b2 ion observed for protonated peptides. More minor yields of y2, c2, and a2 ions also are observed. The a ion formed by loss of CO2 from the [M − H]- ion shows loss of the N-terminal residue for tripeptides and sequential loss of two amino acid residues from the N-terminus for tetrapeptides. The formation of cn ions and the sequential loss of N-terminus residues from the [M − H − CO2]sup− ion serves to sequence the peptide from the N-terminus, whereas the formation of yn ions serves to sequence the peptide from the C-terminus. It is concluded that low-energy CID of deprotonated peptides provides as much (or more) sequence information as does CID of protonated peptides, at least for those peptides containing H or alkyl side chains. Mechanistic aspects of the fragmentation reactions observed are discussed.

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References

  1. Tandem Mass Spectrometry; McLafferty, F. W., Ed; Wiley: New York, 1983.

    Google Scholar 

  2. Busch, K. L.; Glish, G. L.; McLuckey, S. A.Mass Spectrometry/ Mass Spectrometry: Techniques and Applications of Tandem Mass Spectrometry; VCH: New York, 1988.

    Google Scholar 

  3. Hunt, D. F.; Yates, J. R., III; Shabanowitz, J.; Winston, S.; Hauer, C. R. Protein sequencing by tandem mass spectrometry.Proc. Natl. Acad. Sci. USA 1986,83, 6233.

    Article  CAS  Google Scholar 

  4. Biemann, K. Sequencing of peptides by tandem mass spectrometry and high-energy collision-induced dissociation.Methods Enzymol. 1990,193, 455.

    Article  CAS  Google Scholar 

  5. Biemann, K. Primary studies of peptides and proteins. InBiological Mass Spectrometry: Present and Future; Matsuo, T.; Caprioli, R. M.; Gross, M. L.; Seyama, T., Eds.; Wiley: New York, 1993, p 275.

    Google Scholar 

  6. Pappayanopoulos, I. The interpretation of collision-induced dissociation tandem mass spectra of peptides.Mass Spectrom. Rev. 1995,14, 49.

    Article  Google Scholar 

  7. Roepstorff, P.; Fohlman, J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides.Biomed. Mass Spectrom. 1984,11, 601.

    Article  CAS  Google Scholar 

  8. Biemann, K. Contribution of mass spectrometry to peptide and protein structure.Biomed. Environ. Mass Spectrom. 1988,16, 99.

    Article  CAS  Google Scholar 

  9. Bradley, C. V.; Howe, I.; Beynon, J. H. Analysis of underivatized peptide mixtures by collision-induced dissociation of negative ions.J. Chem. Soc. Chem. Commun. 1980, ••, 502.

    Google Scholar 

  10. Bradley, C. V.; Howe, I.; Beynon, J. H. Sequence analysis of underivatized peptides by negative ion chemical ionization and collision-induced dissociation.Biomed. Mass Spectrom. 1981,8, 85.

    Article  CAS  Google Scholar 

  11. Kulik, W.; Heerma, W. The determination of the amino acid sequence in the fast atom bombardment mass spectra of dipeptides.Biomed. Environ. Mass Spectrom. 1988,17, 173.

    Article  CAS  Google Scholar 

  12. Kulik, W.; Heerma, W. Fast atom bombardment tandem mass spectrometry for amino acid determination in tripeptides.Biomed. Environ. Mass Spectrom. 1989,18, 910.

    Article  CAS  Google Scholar 

  13. van Setten, D.; Kulik, W.; Heerma, W. Isomeric tripeptides: A study on structure-spectrum relationship.Biomed. Environ. Mass Spectrom. 1990,19, 475.

    Article  Google Scholar 

  14. Eckersley, M.; Bowie, J. H.; Hayes, R. N. Collision-induced dissociation of deprotonated peptides: dipeptides and tripeptides with hydrogen and alkyl α-groups. An aid to structure determination.Org. Mass Spectrom. 1989,24, 597.

    Article  CAS  Google Scholar 

  15. Waugh, R. J.; Eckersley, M.; Bowie, J. H.; Hayes, R. N. Collision induced dissociation of deprotonated peptides: dipeptides containing serine or threonine.Int. J. Mass Spectrom. Ion Processes 1990,98, 135.

    Article  CAS  Google Scholar 

  16. Waugh, R. J.; Bowie, J. H.; Hayes, R. N. Collision-induced dissociation of deprotonated dipeptides containing aspartic or glutamic acids.Org. Mass Spectrom. 1991,26, 250.

    Article  CAS  Google Scholar 

  17. Waugh, R. J.; Bowie, J. H.; Hayes, R. N. Collision induced dissociations of deprotonated dipeptides. Dipeptides containing phenylalanine, tyrosine, histidine and tryptophan.Int. J. Mass Spectrom. Ion Processes 1991,107, 333.

    Article  CAS  Google Scholar 

  18. Waugh, R. J.; Bowie, J. H.; Gross, M. L. Collision-induced dissociations of deprotonated peptides. Dipeptides containing Asn, Arg, and Lys.Aust. J. Chem. 1993,46, 693.

    Article  CAS  Google Scholar 

  19. Waugh, R. J.; Bowie, J. H.; Gross, M. L. Collision-induced dissociation of deprotonated peptides. Dipeptides containing methionine or cysteine.Rapid Commun. Mass Spectrom. 1993,7, 623.

    Article  CAS  Google Scholar 

  20. Reiter, A.; Teesch, L. M.; Zhao, H.; Adams, J. Gas-phase fragmentation of anionic complexes of serine- and threoninecontaining peptides.Int. J. Mass Spectrom. Mass Spectrom. Ion Processes 1993,127, 17.

    Article  CAS  Google Scholar 

  21. Marzluff, E. M.; Campbell, S.; Rodgers, M. T.; Beauchamp, J. L. Low-energy dissociation pathways of small deprotonated peptides in the gas phase.J. Am. Chem. Soc. 1994,116, 7787.

    Article  CAS  Google Scholar 

  22. Harrison, A. G. Energy-resolved mass spectrometry. A comparison of quadrupole cell and cone-voltage collision-induced dissociation.Rapid Commun. Mass Spectrom. 1999,13, 1663.

    Article  CAS  Google Scholar 

  23. van Dongen, W. D.; van Wijk, J. I. T.; Green, B. N.; Heerma, W.; Haverkamp, J. Comparison between collision induced dissociation of electrosprayed protonated peptides in the up-front region and in a low-energy collision cell.Rapid Commun. Mass Spectrom. 1999,13, 1712.

    Article  Google Scholar 

  24. Harrison, A. G. Fragmentation reactions of alkylphenyl ammonium ions.J. Mass Spectrom. 1999,34, 1253.

    Article  CAS  Google Scholar 

  25. Donò, A.; Paradisi, C.; Scorrano, G. Abatement of volatile organic compounds by corona discharge. A study of the reactivity of trichloroethylene under atmospheric pressure ionization conditions.Rapid Commun. Mass Spectrom. 1997,11, 1687.

    Article  Google Scholar 

  26. Collette, C.; DePauw, E. Calibration of the internal energy of ions produced by electrospray.Rapid Commun. Mass Spectrom. 1998,12, 165.

    Article  CAS  Google Scholar 

  27. Collette, C.; Drahos, L.; DePauw, E.; Vèkey, K. Comparison of the internal energy distributions of ions produced by different electrospray sources.Rapid Commun. Mass Spectrom. 1998,12, 1673.

    Article  CAS  Google Scholar 

  28. Harrison, A. G.; Csizmadia, I. G.; Tang, T.-H. Structure and fragmentation of b2 ions in peptide mass spectra.J. Am. Soc. Mass Spectrom. 2000,11, 427.

    Article  CAS  Google Scholar 

  29. McLuckey, S. A.; Glish, G. L.; Cooks, R. G. Kinetic energy effects in mass spectrometry/mass spectrometry using a sector/quadrupole tandem instrument.Int. J. Mass Spectrom. Ion Phys. 1981,39, 219.

    Article  CAS  Google Scholar 

  30. Fetterolf, D. D.; Yost, R. A. Energy-resolved collision-induced dissociation in tandem mass spectrometry.Int. J. Mass Spectrom. Ion Phys. 1982,44, 37.

    Article  CAS  Google Scholar 

  31. McLuckey, S. A.; Cooks, R. G. Angle- and energy-resolved fragmentation spectra from tandem mass spectrometry. InTandem Mass Spectrometry; McLafferty, F. W., Ed.; Wiley: New York, 1983; p 303.

    Google Scholar 

  32. Young, A. B.; Harrison, A. G. Energy dependence of the fragmentation of ester enolate ions.Org. Mass Spectrom. 1987,22, 622.

    Article  Google Scholar 

  33. Mercer, R. S.; Harrison, A. G. Fragmentation of alkoxide ions following collisional activation. An energy-resolved study.Can. J. Chem. 1988,66, 2947.

    Article  CAS  Google Scholar 

  34. Chowdhury, S.; Harrison, A. G. Fragmentation of the enolate ions of some cycloalkanones. A comparison of high-energy and low-energy collisional activation.J. Am. Chem. Soc. 1988,110, 7345.

    Article  CAS  Google Scholar 

  35. Chowdhury, S. K.; Mercer, R. S.; Harrison, A. G.; Barlow, S. E.; DePuy, C. H. An energy-resolved study of the fragmentation of some 2-substituted 2-propoxide ions and the rates of proton abstraction from acetone.Int. J. Mass Spectrom. Ion Processes 1989,95, 55.

    Article  CAS  Google Scholar 

  36. Arnott, D.; Kottmeir, D.; Yates, N.; Shabanowitz, J.; Hunt, D. F. Fragmentation of multiply protonated peptides under low energy conditions.Proceedings of the 42nd ASMS Conference on Mass Spectrometry; Chicago, June, 1994; p 470.

  37. 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. 1996,6, 1165.

    Article  Google Scholar 

  38. Yalcin, T.; Csizmadia, I. G.; Peterson, M. R.; Harrison, A. G. The structure and fragmentation of B n (n ≥ 3) ions in peptide mass spectra.J. Am. Soc. Mass Spectrom. 1996,7, 293.

    Article  Google Scholar 

  39. 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.

    Article  CAS  Google Scholar 

  40. Reid, G. E.; Simpson, R. J.; O’Hair, R. A. J. A mass spectrometric and ab initio study for the dehydration of simple glycine and cysteine-containing peptide [M + H]+ ions.J. Am. Soc. Mass Spectrom. 1998,9, 945.

    Article  CAS  Google Scholar 

  41. Paisz, B.; Lendvay, G.; Vékey, K.; Suhai, S. Formation of b +1 ions from protonated peptides: an ab initio study.Rapid Commun. Mass Spectrom. 1999,13, 525.

    Article  Google Scholar 

  42. 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.

    Article  CAS  Google Scholar 

  43. Harrison, A. G.; Yalcin, T. Proton mobility in protonated amino acids and peptides.Int. J. Mass Spectrom. Ion Processes 1997,165/166, 339.

    Article  CAS  Google Scholar 

  44. Tsang, C. W.; Harrison, A. G. The chemical ionization of amino acids.J. Am. Chem. Soc. 1976,98, 1301.

    Article  CAS  Google Scholar 

  45. Bouchonnet, S.; Bourcier, S.; Hoppilliard, Y.; Mauriac, C. Leucine and isoleucine in chemical ionization and plasma desorption mass spectrometry. A comparative study.Org. Mass Spectrom. 1993,28, 1064.

    Article  Google Scholar 

  46. Biemann, K. Sequencing of peptides by tandem mass spectrometry and high-energy collision-induced dissociation.Methods Enzymol. 1990,193, 455.

    Article  CAS  Google Scholar 

  47. Wang, W.; Meadows, L. R.; den Haan, J. M. M.; Sherman, N. E.; Chen, Y.; Blokland, E.; Shabanowitz, J.; Agulnik, A. I.; Hendrikson, R. C.; Bishop, C. E.; Hunt, D. F.; Goulmy, E.; Engelhard, V. H. Human H-Y. A male specific histocampatibility antigen derived from the SMCY protein.Science 1995,269, 1588.

    Article  CAS  Google Scholar 

  48. Waugh, R. J.; Bowie, J. H. A review of the collision-induced dissociation of deprotonated dipeptides and tripeptides. An aid to structure identification.Rapid Commun. Mass Spectrom. 1994,8, 169.

    Article  CAS  Google Scholar 

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  1. Department of Chemistry, University of Toronto, 80 St. George Street, M5S 3H6, Toronto, Ontario, Canada

    Alex G. Harrison

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Harrison, A.G. Sequence-specific fragmentation of deprotonated peptides containing H or alkyl side chains. J. Am. Soc. Spectrom. 12, 1–13 (2001). https://doi.org/10.1016/S1044-0305(00)00199-9

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  • DOI: https://doi.org/10.1016/S1044-0305(00)00199-9

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