Influence of secondary structure on the fragmentation of protonated peptides

Journal of the American Chemical Society

Volumn 121, Issue 22, 1999, Pages 5142-5154

  Tsaprailis, George ^a   Nair, Hari ^a   Somogyi, Árpád ^a   Wysocki, Vicki H ^a   Zhong, Wenqing ^b   Futrell, Jean H ^b   Summerfield, Scott G ^c   Gaskell, Simon J ^c  

^a University of Arizona   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; ASPARTIC ACID; CYSTEIC ACID; GLUTAMINE; PEPTIDE FRAGMENT; PROTON; SYNTHETIC PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; DISSOCIATION; MASS SPECTROMETRY; MOLECULAR MODEL; NONHUMAN; PEPTIDE SYNTHESIS; PROTEIN DEGRADATION; PROTEIN SECONDARY STRUCTURE; PROTON TRANSPORT;

EID: 0033538311     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja982980h     Document Type: Article

References (138)

1. Dyson, H. J.; Wright, D. E. Annu. Rev. Biophys. Chem. 1991, 20, 519-538.
2. Diffraction Methods for Biological Macromolecules. Methods Enzymol. 1985, 114 and 115 (special issues).
3. Burlet, O.; Yang, C.-Y.; Gaskell, S. J. J. Am. Soc. Mass Spectrom. 1992, 3, 337-344.
4. Gonzalez, J.; Besada, V.; Garay, H.; Reyes, O.; Padron, G.; Tambara, Y.; Takao, T.; Shimonishi, Y. J. Mass Spectrom. 1996, 31, 150-158.
5. Summerfield, S. G.; Whiting, A.; Gaskell, S. J. Int. J. Mass Spectrom. Ion Processes 1997, 162, 149-161.
6. Schnier, P. D.; Price, W. D.; Jockusch, R. A.; Williams, E. R. J. Am. Chem. Soc. 1996, 118, 7178-7189.
7. (a) Wyttenbach, T.; von Helden, G.; Bowers, M. T. J. Am. Chem. Soc. 1996, 118, 8355-8364.
8. (b) Wyttenbach, T.; Bushnell, J. E.; Bowers, M. T. J. Am. Chem. Soc. 1998, 120, 5098-5103.
9. Vachet, R. W.; Asam, M. R.; Glish, G. L. J. Am. Chem. Soc 1996, 118, 6252-6256.
10. Burlet, O.; Orkiszewski, R. S.; Ballard, K. D.; Gaskell, S. J. Rapid Commun. Mass Spectrom. 1992, 6, 658-662.
11. Price, W. D.; Jockusch, R. A.; Williams, E. R. J. Am. Chem. Soc. 1997, 119, 11988-11989.
12. Price, W. D.; Schnier, P. D.; Jockusch, R. A.; Strittmatter, E. F.; Williams, E. R. J. Am. Chem. Soc. 1996, 118, 10640-10644.
13. (a) Gross, D. S.; Williams, E. R. J. Am. Chem. Soc. 1995, 117, 883-890.
14. (b) Campbell, S.; Rodgers, M. T.; Marzluff, E. M.; Beauchamp, J. L. J. Am. Chem. Soc. 1995, 117, 12840-12854.
15. (c) Grese, R. P.; Cerny, R. L.; Gross, M. L. J. Am. Chem. Soc. 1989, 111, 2835-2842.
16. Lee, S.-W.; Kim, H. S.; Beauchamp, J. L. J. Am. Chem. Soc. 1998, 120, 3188-3195.
17. Barril, X.; Aleman, C.; Orozco, M., Luque, F. J. Proteins Struct. Fund. Genet. 1998, 32, 67-79.
18. Melo, A.; Ramos, M. J. Chem. Phys. Lett. 1995, 245, 498-502.
19. Winston, R. L.; Fitzgerald, M. C. Mass Spectrom. Rev. 1997, 16, 165-179.
20. (a) Karas, M.; Bachmna, U.; Hillenkamp, F. Int. J. Mass Spectrom. Ion Processes 1987, 78, 53-81.
21. (b) Hillenkamp, F.; Karas, M.; Beavis, R. C.; Chait, B. T. Anal. Chem. 1991, 63, 1193A-1203A.
22. (a) Dole, M.; Mack, L. L.; Hines, R. L.; Mobley, R. C.; Ferguson, L. D.; Alice, M. B. J. Chem. Phys. 1968, 49, 2240-2249.
23. (b) Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Science 1989, 246, 64-71.
24. (c) Mann, M.; Meng, C. K.; Fenn, J. B. Anal. Chem. 1989, 61, 1702-1708.
25. Smith, R. D.; Loo, J. A.; Edmonds, C. G.; Barinaga, C. J.; Udseth, H. R. Anal. Chem. 1990, 62, 882-899.
26. Smith, R. D.; Loo, J. A.; Barinaga, C. J.; Edmonds, C. G.; Udseth, H. R. J. Am. Soc. Mass Spectrom. 1990, 1, 53-65.
27. (a) Fye, J. L.; Woenckhaus, J.; Jarrold, M. F. J. Am. Chem. Soc. 1998, 120, 1327-1328.
28. (b) Chowdhury, S. K.; Katta, V.; Chait, B. T.; Williams, E. R. Rapid Commun. Mass Spectrom. 1990, 4, 81-87.
29. (c) Rodriquez-Cruz, S. E.; Klassen, J. S.; Williams, E. R. J. Mass Spectrom. 1997, 8, 565-568.
30. (d) Woenckhaus, J.; Hudgins, R. R.; Jarrold, M. F. J. Am. Chem. Soc. 1997, 119, 9586-9587.
31. (a) Busch, K. L.; Glish, G. L.; McLuckey, S. A. Mass Spectrometry/ Mass Spectrometry: Techniques and Applications of Tandem Mass Spectrometry; VCH Publishers: New York, 1988.
32. (b) Siuzdak, G. Mass Spectrometry for Biotechnology; Academic Press: San Diego, CA, 1996.
33. (c) Protein and Peptide Analysis by Mass Spectrometry; Chapman, J. R., Ed.; Humana Press: Towada, NJ, 1996.
34. (d) Yates, J. R. Methods Enzymol. 1996, 271, 351-377.
35. (e) Gillece-Castro, B. L.; Stults, J. T. Methods Enzymol. 1996, 271, 427-448.
36. (a) Eng, J. E.; McCormack, A. L.; Yates, J. R., III. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
37. (b) Yates, J. R.; Eng, J. E.; McCormack, A. L.; Schieltz, D. Anal. Chem. 1995, 67, 1426-1436.
38. (c) Yates, J. R., III; Speicher, S.; Griffin, P. R.; Hunkapiller, T. Anal. Biochem. 1993, 214, 397-408.
39. (d) Yates, J. R., III. Protein. Chem. 1997, 16, 495-497.
40. (e) Yates, J. R., III; Eng, A. L.; McCormack, A. L. Anal. Chem. 1995, 67, 3202-3210.
41. (a) Mann, M.; Wilm, M. Anal. Chem. 1994, 66, 4390-4399.
42. (b) Clauser, K. R.; Baker, P., Burlingame, A. L. In Proceedings of the 44th ASMS Conference on Mass Spectrometry and Allied Topics, Portland, OR, 1996; p 365.
43. Hunt, D. F.; Yates, J. R., III; Shabanowitz, J.; Winston, S.; Hauer, C. R. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 6233-6237.
44. Biemann, K. Biomed. Environ. Mass Spectrom. 1988, 16, 99-110.
45. Biemann, K. Methods Enzymol. 1990, 193, 351-360, 455-479.
46. Biemann, K.; Stoble, H. A. Science 1987, 237, 992-998.
47. Roepstroff, P.; Fohlman, J. J. Biomed. Mass Spectrom. 1984, 11, 601-603.
48. (a) Medzihradszky, K. F.; Burlingame, A. L. Methods Enzymol. 1994, 6, 284-303.
49. (b) McCormack, A. L.; Eng, J.; Yates, J. R., III. Methods Enzymol. 1994, 6, 274-283.
50. (c) Hunt, D. F.; Shabanowitz, J.; Yates, J. R., III. J. Chem. Soc. Chem. Commun. 1987, 548-550.
51. (d) Biemann, K.; Martin, S. A. Mass Spectrom. Rev. 1987, 6, 1-76.
52. Papayannopoulos, I. A. Mass Spectrom. Rev. 1995, 14, 49-73.
53. Johnson, R. S.; Martin, S. A.; Biemann, K., Stults, J. T.; Watson, J. T. Anal. Chem. 1987, 59, 2621-2625.
54. Wysocki, V. H. In Proceedings of the NATO Advanced Study Institute on Mass Spectrometry in the Biological Sciences: A Tutorial; Gross, M. L., Ed.; Kluwer Academic Publishers: Hingham, MA, 1992; pp 59-77.
55. Alexander, A. J.; Thibault, P.; Boyd, R. K.; Curtis, J. M.; Rinehart, K. L. Int. J. Mass Spectrom. Ion Processes 1990, 98, 107-143.
56. Ballard, K. D.; Gaskell, S. J. Int. J. Mass Spectrom. Ion Processes 1991, 111, 173-189.
57. Wysocki, V. H.; Jones, J. L.; Dongré, A. R.; Somogyi, Á.; McCormack, A. L. In Biological Mass Spectrometry: Present and Future; Matsuo, T., Caprioli, R. M., Gross, M. L., Seyana, Y., Eds.; John Wiley and Sons Ltd.: New York, 1994; Chapter 2.14, pp 249-254.
58. Jones, J. L.; Dongré, A. R.; Somogyi, Á.; Wysocki, V. H. J. Am. Chem. Soc. 1994, 116, 8368-8369.
59. Dongré, A. R.; Jones, J. L.; Somogyi, Á.; Wysocki, V. H. J. Am. Chem Soc. 1996, 118, 8365-8374.
60. McCormack, A. L.; Somogyi, Á.; Dongré, A. R.; Wysocki, V. H. Anal. Chem. 1993, 65, 2859-2872.
61. McCormack, A. L.; Jones, J. L.; Wysocki, V. H. J. Am. Soc. Mass Spectrom. 1992, 3, 859-862.
62. Nair, H., Somogyi, Á.; Wysocki, V. H. J. Mass Spectrom. 1996, 31, 1141-1148.
63. Nair, H.; Wysocki, V. H. Int. J. Mass Spectrom. Ion. Processes 1998, 174, 95-100.
64. Burlingame, A. L.; Boyd, R. K.; Gaskell, S. J. Anal. Chem. 1996, 68, 599-561 and references therein.
65. Biemann, K. In Mass Spectrometry; McCloskey, J. A., Ed.; Academic Press: New York, 1990; pp 455-479.
66. Bean, M. F.; Carr, S. A.; Thorne, G. C.; Reilly, M. H.; Gaskell, S. J. Anal. Chem. 1991, 63, 1473-1481.
67. Poulter, L.; Taylor, L. C. E. Int. J. Mass Spectrom. Ion Processes 1989, 91, 183-197.
68. Ballard, K. D.; Gaskell, S. J. J. Am. Chem. Soc. 1992, 114, 64-71.
69. (a) Hunt, D. F.; Kishnamurthy, T.; Shabanowitz, J.; Griffin, P.; Yates, J. R., III; Martino, P. A.; McCormack, A. L.; Hauer, C. R. In Mass Spectrometry of Peptides; Desiderio, D., Ed.; CRC Press: Boca Raton, FL, 1990; p 139.
70. (b) Hunt, D. F.; Alexander, J. E.; McCormack, A. L.; Martino, P. A.; Michel, H.; Shabanowitz, J. In Protein Chemistry Techniques II; Villafranca, J. J., Ed.; Academic Press: New York, 1991; pp 455-465.
71. (c) Hunt, D. F.; Henderson, R. A.; Shabanowitz, J.; Sakaguchi, K.; Michel, H.; Sevilir, N.; Cox, A. L.; Appella, E.; Engelhard, V. H. Science 1992, 255, 1261-1263.
72. (d) Hunt, D. F.; Michel, H.; Dickinson, T. A.; Shabanowitz, J.; Cox, A. L.; Sakaguchi, K.; Appella, E.; Grey, H. M.; Sette, A. Science 1992, 256, 1817-1820.
73. Dongré, A. R.; Somogyi, Á., Wysocki, V. H. J. Mass Spectrom. 1996, 31, 339-350.
74. Nold, M. J.; Wesdemiotis, C.; Yalcin, T.; Harrison, A. G. Int. J. Mass Spectrom. Ion Processes. 1997, 164, 137-153.
75. Harrison, A. G.; Yalcin, T. Int. J. Mass Spectrom. Ion Processes 1997. 165/167, 339-347.
76. Mueller, D. R.; Eckersley, M.; Richter, W. Org. Mass Spectrom. 1988, 23, 217-222.
77. Johnson, R. S.; Krylov, D.; Walsh, K. A. J. Mass Spectrom. 1995, 30, 386-387.
78. Vaisar, T.; Urban, J. J. Mass Spectrom. 1998, 33, 505-524.
79. Cox, K. A.; Gaskell, S. J.; Morris, M.; Whiting, A. J. Am. Soc. Mass Spectrom. 1996, 7, 522-531.
80. Summerfield, S. G.; Cox, K. A.; Gaskell, S. J. J. Am. Soc. Mass Spectrom. 1997, 8, 25-31.
81. (a) Gaskell, S. J.; Reilly, M. H. Rapid Commun. Mass Spectrom. 1988, 2, 188-191.
82. (b) Kenny, P. T.; Nomoto, M. K.; Orlando, R. Rapid Commun. Mass Spectrom. 1992, 6, 95-97.
83. (c) Fabris, D.; Kelly M.; Murphy, C.; Wu, Z.; Fenselau, C. J. Am. Soc. Mass Spectrom. 1993, 4, 652-661.
84. Tang, X.-J.; Thiboult, P.; Boyd, R. K. Anal. Chem. 1993, 65, 2824-2834.
85. (a) Summerfield, S. G.; Gaskell, S. J. Int. J. Mass Spectrom. Ion Processes 1997, 166, 509-521.
86. (b) Barinaga, C. J.; Edmonds, C. G.; Udseth, H. R.; Smith, R. D. Rapid Commun. Mass Spectrom. 1989, 3, 160-164.
87. Qin, J.; Chait, B. T. J. Am. Chem. Soc. 1995, 117, 5411-5412.
88. Downard, K. M.; Biemann, K. Int. J. Mass Spectrom. Ion Processes 1995, 148, 191-202.
89. Jones, J. L.; Dongré, A. R.; Nair, H.; Somogyi, Á.; Wysocki, V. H. In Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, Atlanta, GA, 1995; p 1333.
90. (a) Dongré, A. R.; Hayward, M. J.; Wysocki, V. H. In Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, Atlanta, GA, 1995; p 628.
91. (b) Wu, Q.; Van Orden, S.; Cheng, X.; Bakhtiar, R.; Smith, R. D. Anal. Chem. 1995, 67, 2498-2509.
92. Thome, G. C.; Ballard, K. D.; Gaskell, S. J. J. Am. Soc. Mass Spectrom. 1990, 1, 249-257.
93. Nair, H.; Wysocki, V. H.; Summerfield, S. G.; Gaskell, S. J. In Proceedings of the 44th ASMS Conference on Mass Spectrometry and Allied Topics, Portland, OR, 1996; p 464.
94. (a) Tang, X.-J.; Thibault, P.; Boyd, R. K. Anal. Chem. 1993, 65, 2824-2834.
95. (b) Tang, X.-J.; Boyd, R. K. Rapid Commun. Mass Spectrom. 1992, 6, 651-657.
96. (c) Yost, R. A.; Boyd, R. K. In Methods Enzymol. 1990, 193, 154-200.
97. (a) Carr, S. A.; Hemling, M. E.; Bean, M. F.; Roberts, G. D. Anal. Chem. 1991, 63, 2902-2824.
98. (b) Gross, M. L. In Methods Enzymol. 1990, 193, 131-153.
99. (c) Tomer, K. B. Mass Spectrom. Rev. 1989, 8, 445-482, 483-511.
100. (a) Smith, R. D.; Barinaga, C. J.; Udseth, H. R. J. Phys. Chem. 1989, 93, 5019-5022.
101. (b) Loo, J. A.; Edmonds, C. G.; Smith, R. D. Science 1990, 248, 201-204.
102. (c) Loo, J. A.; Edmonds, C. G.; Smith, R. D. Anal. Chem. 1991, 63, 2488-2499.
103. Wysocki, V. H.; Dongré, A. R. In Large Ions: Their Vaporization, Detection and Structural Analysis; Baer, T., Ng, Y., Powis, I., Eds.; John Wiley and Sons Ltd.: New York, 1996; Chapter 6, pp 145-165 and references therein.
104. Wysocki, V. H.; Ding, J.; Jones, J. L.; Callahan J. H.; King, F. L. J. Am. Soc. Mass Spectrom. 1992, 3, 27-32.
105. (a) Meot-Ner, M.; Dongré, A. R.; Somogyi, Á.; Wysocki, V. H. Rapid Commun. Mass Spectrom. 1995, 9, 829-836.
106. (b) Hayward, M. J.; Park, F. D. S.; Phelan, L. M.; Bernasek, S. L.; Somogyi, Á.; Wysocki, V. H. J. Am. Chem. Soc. 1996, 118, 8375-8380.
107. (c) Vékey, K.; Somogyi, Á.; Wysocki, V. H. Rapid Commun. Mass Spectrom. 1996, 10, 911-918.
108. (d) Dongré, A. R.; Wysocki, V. H. Org. Mass Spectrom. 1994, 29, 700-702.
109. (e) Kane, T. E.; Somogyi, Á.; Wysocki, V. H. Org, Mass Spectrom. 1993, 28.1665-1673.
110. (f) Callahan, J. H.; Somogyi, Á., Wysocki, V. H. Rapid Commun. Mass Spectrom. 1993, 7, 693-699.
111. Price, W. D.; Schnier, P. D.; Williams, E. R. Anal. Chem. 1996, 68, 859-866.
112. Senko, M. W.; Speir, J. P.; McLafferty, F. W. Anal. Chem. 1994, 66, 2801-2808.
113. Jockusch, R. A.; Schnier, P. D.; Price, W. D.; Strittmatter, E. F.; Demirev, P. A.; Williams, E. R. Anal. Chem. 1997, 69, 1119-1126.
114. Atherton, E.; Sheppard, R. C. In Solid-Phase Peptide Synthesis: A Practical Approach; Rickwood, D., Hames, B. D., Eds.; IRL Press at Oxford University Press: Oxford, UK, 1989.
115. 2O, and 2.5% anisole.
116. The amino acid residues employed requiring side-chain protection are as follows: Fmoc-L-arginine, 2,2,5,7,8-pentamethlchroman-6-sulfonyl (Pmc); Fmoc-L-cysteine, S-trityl (Trt); Fmoc-L-serine, tert-butyl; Fmoc-L-glutamic acid, tert-butyl; Fmoc-L-aspartic acid, tert-butyl.
117. Chowdhury, S. K.; Katta, V.; Chait, B. T. Rapid Commun. Mass Spectrom. 1990, 4, 81-87.
118. Papac, D. I.; Schey, K. L.; Knapp, D. R. Anal. Chem. 1991, 63, 1658-1660.
119. (a) Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3559-3568.
120. (b) Laibinitis, P. E.; Whitesides, G. M.; Allara, D. L.; Tao, Y.-T.; Parikh, A. N.; Nuzzo, R. G. J. Am. Chem. Soc. 1991, 113, 7152-7167.
121. (c) Bryant, M. A.; Pemberton, J. E. J. Am. Chem. Soc. 1991, 113, 8284-8293.
122. (d) Li, Y.; Huang, J.; Mclver, R. T., Jr.; Hemminger, J. C. J. Am. Chem. Soc. 1992, 114, 2428-2432.
123. (e) Ulman, A. Chem. Rev. 1996, 96, 1533-1554.
124. Morris, M. Riederer, D. E., Jr.; Cooks, R. G.; Ast, T.; Chidsey, C. E. D. Int. J. Mass Spectrom. Ion Processes 1992, 122, 181-217.
125. Winger, B. E.; Julian, R. K., Jr.; Cooks, R. G.; Chidsey, C. E. D. J. Am. Chem. Soc. 1991, 113, 8967-8969.
126. Somogyi, Á.; Kane, T. E.; Ding, J.-M.; Wysocki, V. H. J. Am. Chem. Soc. 1993, 115, 5275-5283.
127. Marshall, A. G.; Grosshans, P. B. Anal. Chem. 1991, 63, 215A-229A.
128. Gauthier, J. W.; Trautman, T. R.; Jacobson, D. B. Anal. Chim. Acta 1991, 246, 211-225.
129. (a) Nikolaev, E.; Somogyi, Á.; Gu, C.; Breci, L.; Finch, J. W.; Martin, C. D.; Samuelson, G. L.; Wysocki, V. H. In Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, 1998; pp 41.
130. (b) Tsaprailis, G.; Nair, H.; Somogyi, Á.; Zhong, W.; Futrell, J. H.; Summerfield, S. G.; Gaskell, S. J. In Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, FL, 1998; p 633.
131. Marzluff, E. M.; Campbell, S.; Rodgers, M. T.; Beauchamp, J. L. J. Am. Chem. Soc. 1994, 116, 7787-7796.
132. Bakhtiar, R.; Wu, Q.; Hofsradler, S. A.; Smith, R. D. Biol. Mass Spectrom. 1994, 65, 707-710.
133. Yu, W.; Vath, J. E.; Huberty, M. C.; Martin, S. A. Anal. Chem. 1993, 65, 3015-3023.
134. Harrison, A.; Tu, Y.-P. J. Mass Spectrom. 1998, 33, 532-542.
135. van Dongen, W. D.; Ruijters, H. F. M.; Luinge, H.-J.; Heerma, W.; Haverkamp, J. J. Mass Spectrom. 1996, 31, 1156-1162.
136. Somogyi, Á.; Wysocki, V. H.; Mayer, I. J. Am. Chem. Soc. 1994, 5, 704-717.
137. Covey, T. R.; Huang, B. C.; Henion, J. D. Anal. Chem. 1991, 63, 1193-1200.
138. Zheng, Y.-J.; Ornstein, R. L. J. Am. Chem. Soc. 1996, 118, 11237-11243.