Towards understanding the tandem mass spectra of protonated oligopeptides. 1: Mechanism of amide bond cleavage

Journal of the American Society for Mass Spectrometry

Volumn 15, Issue 1, 2004, Pages 103-113

  Paizs, Béla ^a   Suhai, Sándor ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHEMICAL BONDS; ELECTRIC EXCITATION; ENTROPY; FREE ENERGY; MASS SPECTROMETRY; OXYGEN; REACTION KINETICS;

PROTONATION;

POLYPEPTIDES;

ALANINE; AMIDE; NITROGEN; OLIGOPEPTIDE;

MASS SPECTROMETRY;

ARTICLE; BINDING AFFINITY; CHEMICAL BOND; CHEMICAL STRUCTURE; ENERGY TRANSFER; ENTROPY; KINETICS; PROTON TRANSPORT; TANDEM MASS SPECTROMETRY;

EID: 0345862097     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2003.09.010     Document Type: Article

References (33)

1. Fenn J.B., Mann M., Meng C.K., Wong S.F., Whitehouse C.M. Electrospray Ionization for Mass-Spectrometry of Large Biomolecules. Science. 246:1989;64.
2. Karas M., Hillenkamp F. Laser Desorption Ionization of Proteins with Molecular Masses Exceeding 10,000 Da. Anal. Chem. 60:1988;2299.
3. Roepstorff P., Fohlman J. Proposal for a Common Nomenclature for Sequence Ions in Mass Spectra of Peptides. Biomed. Mass Spectrom. 11:1984;601.
4. Biemann K. Contributions of Mass Spectrometrey to Peptide and Protein Structure. Biomed. Env. Mass Spectrom. 16:1988;99.
5. Mann M., Wilm M. Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags. Anal. Chem. 66:1994;4390.
6. Eng J.K., McCormack A.L., Yates J.R.I.I.I. An Approach to Correlate Tandem Mass Spectra Data of Peptides with Amino Acid Sequences in a Protein Database. J. Am. Soc. Mass Spectrom. 5:1994;976.
7. Perkins D.N., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-Based Protein Identification by Searcheing Sequence Databases Using Mass Spectrometry Data. Electrophoresis. 20:1999;3551-3567.
8. Clauser K.R., Baker P.R., Burlingame A.L. Role of Accurate Mass Measurement (+/- 10 ppm) in Protein Identification Strategies Employing MS or MS MS and Database Searching. Anal. Chem. 71:1999;2871.
9. Baer T., Hase W.L. Unimolecular Reaction Dynamics. 1996;Oxford University Press, Oxford.
10. Frisch, M. J. Gaussian-98, Rev. A9. Gaussian, Inc.: Pittsburgh PA, 1995.
11. Dongré A.R., Jones J.L., Somogyi Á., Wysocki V.H. 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.
12. Harrison A.G., Yalcin T. Proton Mobility in Protonated Amino Acids and Peptides. Int. J. Mass Spectrom. Ion Processes. 165/166:1997;339.
13. Csonka I.P., Paizs B., Lendvay G., Suhai S. Proton Mobility in Protonated Peptides A Joint Molecular Orbital and RRKM Study . Rapid. Commun. Mass Spectrom. 14:2000;417.
14. Paizs B., Csonka I.P., Lendvay G., Suhai S. Proton Mobility in Protonated Glycylglycine and N-Formylglycylglycinamide A Combined Quantum Chemical and RKKM Study . Rapid Commun. Mass Spectrom. 15:2001;637.
15. Paizs B., Suhai S. Theoretical Study of the Main Fragmentation Pathways for Protonated Glycylglycine. Rapid Commun. Mass Spectrom. 15:2001;651.
16. 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. 15:2001;2307.
17. 2 Ions. Rapid Commun. Mass Spectrom. 16:2002;375.
18. Cordero M.M., Houser J.J., Wesdemiotis C. The Neutral Products Formed During Backbone Fragmentations of Protonated Peptides in Tandem Mass Spectrometry. Anal. Chem. 65:1993;1594.
19. 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. 6:1995;1165.
20. n (n ≧ 3) Ions in Peptide Spectra. J. Am. Soc. Mass Spectrom. 7:1996;233.
21. 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. 164:1997;137.
22. Polce M.J., Ren D., Wesdemiotis C. Dissociation of the Peptide Bond in Protonated Peptides. J. Mass Spectrom. 35:2000;1391.
23. + Ions from Protonated Peptides An ab Initio Study . Rapid Commun. Mass Spectrom. 13:1999;525.
24. Paizs B., Suhai S. Towards Understanding Some Ion Intensity Relationships for the Tandem Mass Spectra of Protonated Peptides. Rapid Commun. Mass Spectrom. 16:2002;1699.
25. Harrison A.G. Linear Free Energy Correlations in Mass Spectrometry. J. Mass Spectrom. 34:1999;577.
26. Csonka I.P., Paizs B., Lendvay G., Suhai S. Proton Mobility and Main Fragmentation Pathways of Protonated Lysylglycine. Rapid. Commun. Mass Spectrom. 15:2001;1457.
27. Jegorov A., Paizs B., Zabka M., Kuzma M., Giannakopulos A.E., Derrick P.J., Havlicek V. Profiling of Cyclic Hexadepsipeptides Roseotoxins Synthesized in Vitro and in Vivo A Combined Tandem Mass Spectrometry and Quantum Chemical Study . Eur. J. Mass Spectrom. 9:2003;105.
28. Paizs, B., Suhai, S., Harrison, A. G. Experimental and Theoretical Investigation of the Main Fragmentation Pathways of Protonated H-Gly-Gly-Sar-OH and H-Gly-Sar-Sar-OH, in press.
29. 3. J. Am. Chem. Soc. 117:1995;12840.
30. 2O, unpublished.
31. Wyttenbach, T.; Paizs, B.; Barran, P.; Breci, L.; 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, in press.
32. Harrison A.G. The Gas-Phase Basicities and Proton Affinities of Amino Acids and Peptides. Mass Spectrom. Rev. 116:1997;201.
33. Cassady C.J., Carr S.R., Zhang K., Chung-Phillips A. Experimental and ab Initio Studies on Protonations of Alanine and Small Peptides of Alanine and Glycine. J. Org. Chem. 60:1995;1704.