Gas-phase conformation-specific photofragmentation of proline-containing peptide ions

Journal of the American Society for Mass Spectrometry

Volumn 21, Issue 8, 2010, Pages 1455-1465

  Kim, Tae Young ^a,b   Valentine, Stephen J ^a   Clemmer, David E ^a   Reilly, James P ^a  

^a INDIANA UNIVERSITY   (United States)

^b California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; GASES; PEPTIDES;

AMIDE HYDROGENS; GAS PHASE CONFORMATIONS; GAS PHASE PEPTIDES; HOMOLYTIC CLEAVAGE; LINEAR ION TRAP; PEPTIDE IONS; PHOTOFRAGMENTATION; VACUUM ULTRAVIOLET LIGHT;

IONS;

AMIDE; ARGININE; CARBON; HYDROGEN; ION; PEPTIDE; PROLINE;

AMINO TERMINAL SEQUENCE; ARTICLE; ELECTRON; ELECTROSPRAY MASS SPECTROMETRY; GAS; ION TRAP MASS SPECTROMETRY; LINEAR SYSTEM; PROTEIN CLEAVAGE; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTON TRANSPORT; RESIDUE ANALYSIS; TANDEM MASS SPECTROMETRY; TIME OF FLIGHT MASS SPECTROMETRY; ULTRAVIOLET RADIATION; CHEMISTRY; METHODOLOGY; MOLECULAR DYNAMICS; PHOTOCHEMISTRY;

ARGININE; IONS; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PHOTOCHEMICAL PROCESSES; PROLINE; PROTEIN CONFORMATION; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; ULTRAVIOLET RAYS;

EID: 79955825296     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1016/j.jasms.2010.04.007     Document Type: Article

References (54)

1. Jarrold, M. F. Unfolding, Refolding, and Hydration of Proteins in the Gas Phase. Acc. Chem. Res. 1999, 32, 360-367.
2. Hoaglund-Hyzer, C. S.; Counterman, A. E.; Clemmer, D. E. Anhydrous Protein Ions. Chem. Rev. 1999, 99, 3037-3079.
3. Karas, M.; Hillenkamp, F. Laser Desorption Ionization of Proteins with Molecular Masses Exceeding 10,000 Daltons. Anal. Chem. 1988, 60, 2299-2301.
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.
5. Wood, T. D.; Chorush, R. A.; Wampler, F. M.; Little, D. P.; O'Connor, P. B.; McLafferty, F. W. Gas-Phase Folding and Unfolding of Cytochrome-c Cations. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 2451-2454.
6. McLafferty, F. W.; Guan, Z. Q.; Haupts, U.; Wood, T. D.; Kelleher, N. L. Gaseous Conformational Structures of Cytochrome c. J. Am. Chem. Soc. 1998, 120, 4732-4740.
7. Valentine, S. J.; Clemmer, D. E. H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase. J. Am. Chem. Soc. 1997, 119, 3558-3566.
8. Valentine, S. J.; Clemmer, D. E. Temperature-Dependent H/D Exchange of Compact and Elongated Cytochrome c Ions in the Gas Phase. J. Am. Soc. Mass Spectrom. 2002, 13, 506-517.
9. Lifshitz, C. A Review of Gas-Phase H/D Exchange Experiments: The Protonated Arginine Dimer and Bradykinin Nonapeptide Systems. Int. J. Mass Spectrom. 2004, 234, 63-70.
10. Mazurek, U.; Engeser, M.; Gas-Phase H/D Exchange of the Protonated Serine Octamer Cluster: "Ion Ping Pong" of Populations A and B. Int. J. Mass Spectrom. 2006, 249, 473-476.
11. Clemmer, D. E.; Jarrold, M. F. Ion Mobility Measurements and Their Applications to Clusters and Biomolecules. J. Mass Spectrom. 1997, 32, 577-592.
12. Liu, Y. S.; Valentine, S. J.; Counterman, A. E.; Hoaglund, C. S.; Clemmer, D. E. Injected-Ion Mobility Analysis of Biomolecules. Anal. Chem. 1997, 69, A728-A735.
13. Horn, D. M.; Breuker, K.; Frank, A. J.; McLafferty, F. W. Kinetic Intermediates in the Folding of Gaseous Protein Ions Characterized by Electron Capture Dissociation Mass Spectrometry. J. Am. Chem. Soc. 2001, 123, 9792-9799.
14. Breuker, K.; Oh, H. B.; Horn, D. M.; Cerda, B. A.; McLafferty, F. W. Detailed Unfolding and Folding of Gaseous Ubiquitin Ions Characterized by Electron Capture Dissociation. J. Am. Chem. Soc. 2002, 124, 6407-6420.
15. Burlet, O.; Yang, C. Y.; Gaskell, S. J. Influence of Cysteine to Cysteic Acid Oxidation on the Collision-Activated Decomposition of Protonated Peptides-Evidence for Intraionic Interactions. J. Am. Soc. Mass Spectrom. 1992, 3, 337-344.
16. Vachet, R. W.; Asam, M. R.; Glish, G. L. Secondary Interactions Affecting the Dissociation Patterns of Arginine-Containing Peptide Ions. J. Am. Chem. Soc. 1996, 118, 6252-6256.
17. Tsaprailis, G.; Nair, H.; Somogyi, A.; Wysocki, V. H.; Zhong, W. Q.; Futrell, J. H.; Summerfield, S. G.; Gaskell, S. J. Influence of Secondary Structure on the Fragmentation of Protonated Peptides. J. Am. Chem. Soc. 1999, 121, 5142-5154.
18. Schnier, P. D.; Price, W. D.; Jockusch, R. A.; Williams, E. R. Blackbody Infrared Radiative Dissociation of Bradykinin and Its Analogues: Energetics, Dynamics, and Evidence for Salt-Bridge Structures in the Gas Phase. J. Am. Chem. Soc. 1996, 118, 7178-7189.
19. Kjeldsen, F.; Silivra, O. A.; Zubarev, R. A. Zwitterionic States in Gas-Phase Polypeptide Ions Revealed by 157-nm Ultra-Violet Photodissociation. Chem. Eur. J. 2006, 12, 7920-7928.
20. MacArthur, M. W.; Thornton, J. M. Influence of Proline Residues on Protein Conformation. J. Mol. Biol. 1991, 218, 397-412.
21. Vanhoof, G.; Goossens, F.; Demeester, I.; Hendriks, D.; Scharpe, S. Proline Motifs in Peptides and Their Biological Processing. FASEB J. 1995, 9, 736-744.
22. Pal, D.; Chakrabarti, P. Cis Peptide Bonds in Proteins: Residues Involved, Their Conformations, Interactions and Locations. J. Mol. Biol. 1999, 294, 271-288.
23. Huang, Y. Y.; Triscari, J. M.; Pasa-Tolic, L.; Anderson, G. A.; Lipton, M. S.; Smith, R. D.; Wysocki, V. H. Dissociation Behavior of Doubly-Charged Tryptic Peptides: Correlation of Gas-Phase Cleavage Abundance with Ramachandran Plots. J. Am. Chem. Soc. 2004, 126, 3034-3035.
24. Harrison, A. G.; Young, A. B. Fragmentation Reactions of Deprotonated Peptides Containing Proline. The Proline Effect. J. Mass Spectrom. 2005, 40, 1173-1186.
25. Hayakawa, S.; Hashimoto, M.; Matsubara, H.; Turecek, F. Dissecting the Proline Effect: Dissociations of Proline Radicals Formed by Electron Transfer to Protonated Pro-Gly and Gly-Pro Dipeptides in the Gas Phase. J. Am. Chem. Soc. 2007, 129, 7936-7949.
26. Counterman, A. E.; Clemmer, D. E. Cis-Trans Signatures of Proline-Containing Tryptic Peptides in the Gas Phase. Anal. Chem. 2002, 74, 1946-1951.
27. Schwartz, B. L.; Bursey, M. M. Some Proline Substituent Effects in the Tandem Mass-Spectrum of Protonated Penta-Alanine. Biol. Mass Spectrom. 1992, 21, 92-96.
28. Loo, J. A.; Edmonds, C. G.; Smith, R. D. Tandem Mass-Spectrometry of Very Large Molecules. 2. Dissociation of Multiply Charged Proline-Containing Proteins from Electrospray Ionization. Anal. Chem. 1993, 65, 425-438.
29. Vaisar, T.; Urban, J. Probing the Proline Effect in CID of Protonated Peptides. J. Mass Spectrom. 1996, 31, 1185-1187.
30. Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
31. Breci, L. A.; Tabb, D. L.; Yates, J. R.; Wysocki, V. H. Cleavage N-Terminal to Proline: Analysis of a Database of Peptide Tandem Mass Spectra. Anal. Chem. 2003, 75, 1963-1971.
32. Kim, T.-Y.; Thompson, M. S.; Reilly, J. P. Peptide Photodissociation at 157 nm in a Linear Ion Trap Mass Spectrometer. Rapid Commun. Mass Spectrom. 2005, 19, 1657-1665.
33. Kim, T.-Y.; Schwartz, J. C.; Reilly, J. P. Development of a Linear Ion Trap/Orthogonal-Time-of-Flight Mass Spectrometer for Time-Dependent Observation of Product Ions by Ultraviolet Photodissociation of Peptide Ions. Anal. Chem. 2009, 81, 8809-8817.
34. Zhang, L.; Reilly, J. P. Peptide De Novo Sequencing using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer. Anal. Chem. 2010, 82, 898-908.
35. Liu, X. Y.; Valentine, S. J.; Plasencia, M. D.; Trimpin, S.; Naylor, S.; Clemmer, D. E. Mapping the Human Plasma Proteome by SCX-LCIMS-MS. J. Am. Soc. Mass Spectrom. 2007, 18, 1249-1264.
36. Koeniger, S. L.; Merenbloom, S. I.; Valentine, S. J.; Jarrold, M. F.; Udseth, H. R.; Smith, R. D.; Clemmer, D. E. An IMS-IMS Analogue of MS-MS. Anal. Chem. 2006, 78, 4161-4174.
37. Mesleh, M. F.; Hunter, J. M.; Shvartsburg, A. A.; Schatz, G. C.; Jarrold, M. F. Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential. J. Phys. Chem. 1996, 100, 16082-16086.
38. Shvartsburg, A. A.; Jarrold, M. F. An Exact Hard-Spheres Scattering Model for the Mobilities of Polyatomic Ions. Chem. Phys. Lett. 1996, 261, 86-91.
39. Thompson, M. S.; Cui, W.; Reilly, J. P. Fragmentation of Singly Charged Peptide Ions by Photodissociation at λ = 157 nm. Angew. Chem. Int. Ed. 2004, 43, 4791-4794.
40. Cui, W.; Thompson, M. S.; Reilly, J. P. Pathways of Peptide Ion Fragmentation Induced by Vacuum Ultraviolet Light. J. Am. Soc. Mass Spectrom. 2005, 16, 1384-1398.
41. Zhang, L. Y.; Cui, W.; Thompson, M. S.; Reilly, J. P. Structures of α-Type Ions Formed in the 157 nm Photodissociation of Singly-Charged Peptide Ions. J. Am. Soc. Mass Spectrom. 2006, 17, 1315-1321.
42. Zubarev, R. A.; Horn, D. M.; Fridriksson, E. K.; Kelleher, N. L.; Kruger, N. A.; Lewis, M. A.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations. Anal. Chem. 2000, 72, 563-573.
43. Gabelica, V.; Schulz, E.; Karas, M. Internal Energy Build-Up in Matrix-Assisted Laser Desorption/Ionization J. Mass Spectrom. 2004, 39, 579-593.
44. Gabelica, V.; De Pauw, E. Internal Energy and Fragmentation of Ions Produced in Electrospray Sources. Mass Spectrom. Rev. 2005, 24, 566-587.
45. Spengler, B.; Kirsch, D.; Kaufmann, R. Metastable Decay of Peptides and Proteins in Matrix-Assisted Laser-Desorption Mass-Spectrometry. Rapid Commun. Mass Spectrom. 1991, 5, 198-202.
46. Spengler, B. Post-Source Decay Analysis in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry of Biomolecules. J. Mass Spectrom. 1997, 32, 1019-1036.
47. Schimmel, P. R.; Flory, P. J. Conformational Energies and Configurational Statistics of Co-Polypeptides Containing L-Proline. J. Mol. Biol. 1968, 34, 105-120.
48. Ramek, M.; Kelterer, A. M.; Teppen, B. J.; Schafer, L. Theoretical Structure Investigations of N-Acetyl-L-Proline Amide. J. Mol. Struct. 1995, 352, 59-70.
49. Zanni, M. T.; Gnanakaran, S.; Stenger, J.; Hochstrasser, R. M. Heterodyned Two-Dimensional Infrared Spectroscopy of Solvent-Dependent Conformations of Acetylproline-NH2. J. Phys. Chem. B 2001, 105, 6520-6535.
50. Hahn, S.; Lee, H.; Cho, M. Theoretical Calculations of Infrared Absorption, Vibrational Circular Dichroism, and Two-Dimensional Vibrational Spectra of Acetylproline in Liquids Water and Chloroform. J. Chem. Phys. 2004, 121, 1849-1865.
51. Lee, K. K.; Hahn, S.; Oh, K. I.; Choi, J. S.; Joo, C.; Lee, H.; Han, H. Y.; Cho, M. Structure of N-Acetylproline Amide in Liquid Water: Experimentally Measured and Numerically Simulated Infrared and Vibrational Circular Dichroism Spectra. J. Phys. Chem. B 2006, 110, 18834-18843.
52. Sul, S.; Karaiskaj, D.; Jiang, Y.; Ge, N. H. Conformations of N-Acetyl-L-Prolinamide by Two-Dimensional Infrared Spectroscopy. J. Phys. Chem. B 2006, 110, 19891-19905.
53. O'Hair, R. A. J. The Role of Nucleophile-Electrophile Interactions in the Unimolecular and Bimolecular Gas-Phase Ion Chemistry of Peptides and Related Systems. J. Mass Spectrom. 2000, 35, 1377-1381.
54. Wysocki, V. H.; Tsaprailis, G.; Smith, L. L.; Breci, L. A. Special Feature: Commentary-Mobile and Localized Protons: A Framework for Understanding Peptide Dissociation. J. Mass Spectrom. 2000, 35, 1399-1406.