An assessment of computational methods for obtaining structural information of moderately flexible biomolecules from ion mobility spectrometry

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 5, 2012, Pages 792-805

  Zakharova, Natalia L ^a   Crawford, Christina L ^a   Hauck, Brian C ^a   Quinton, Jacob K ^a   Seims, William F ^a   Hill, Herbert H ^a   Clark, Aurora E ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Collision cross section; Density functional theory; Ion mobility mass spectrometry; MOBCAL; Simulated annealing molecular dynamics

Indexed keywords

AMINO ACIDS; BIOMOLECULES; COMPUTATION THEORY; CONFORMATIONS; GASES; IONS; LENNARD-JONES POTENTIAL; MASS SPECTROMETRY; MOLECULAR DYNAMICS; MOLECULES; NUMERICAL METHODS; QUANTUM THEORY; SIMULATED ANNEALING;

ANALYTES; COLLISION CROSS SECTIONS; DENSITY-FUNCTIONAL-THEORY; ENERGY DISTRIBUTIONS; GAS-PHASE STRUCTURES; ION MOBILITY SPECTROMETRY; ION MOBILITY-MASS SPECTROMETRY; MOBCAL; SIMULATED ANNEALING MOLECULAR DYNAMICS; STRUCTURAL INFORMATION;

DENSITY FUNCTIONAL THEORY;

GLYCINE; TRYPTOPHAN; TYROSINE;

ARTICLE; CHEMICAL STRUCTURE; COLLISION CROSS SECTION; COMPUTER PROGRAM; CONFORMATION; CONFORMATIONAL TRANSITION; CORRELATION ANALYSIS; DENSITY FUNCTIONAL THEORY; ELECTROSPRAY MASS SPECTROMETRY; ION MOBILITY SPECTROMETRY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; QUANTUM MECHANICS; REPRODUCIBILITY; SEPARATION TECHNIQUE; SIMULATED ANNEALING MOLECULAR DYNAMICS; TIME OF FLIGHT MASS SPECTROMETRY;

EID: 84862564445     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0339-5     Document Type: Article

References (57)

1. Karasek, F. W.; Kim, S. H.; Rokushika, S. Plasma Chromatography of Alkyl Amines. Anal. Chem. 197, 50, 2013-2016 (1978).
2. Clemmer, D.E., Hudgins, R.R., Jarrold, M.F.: Naked Protein Conformations: Cytochrome c in the Gas Phase. J. Am. Chem. Soc. 117, 10141-10142 (1995)
3. Dwivedi, P., Wu, C., Matz, L.M., Clowers, B., Siems, W.F., Hill Jr., H. H.: Gas-Phase Chiral Separations by Ion Mobility Spectrometry. Anal. Chem. 78, 8200-8206 (2006) (Pubitemid 44927595)
4. Hudgins, R.R., Mao, Y., Ratner, M.A., Jarrold, M.F.: Conformations of GlynH+ and AlanH+ peptides in the Gas Phase. Biophys. J. 76, 1591-1597 (1999) (Pubitemid 29262637)
5. Shumate, C.B., Hill Jr., H.H.: Coronaspray Nebulization and Ionization of Liquid Samples for Ion Mobility Spectrometry. Anal. Chem. 61, 601-606 (1989)
6. McLean, J.A., Ruotolo, B.T., Gillig, K.J., Russell, D.H.: Ion Mobility-Mass Spectrometry: A New Paradigm for Proteomics. Int. J. Mass Spectrom. 240, 301-315 (2005) (Pubitemid 40093984)
7. Shvartsburg, A.A., Li, F., Tang, K., Smith, R.D.: Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers. Anal. Chem. 78, 3304-3315 (2006)
8. Dwivedi, P., Wu, P., Klopsch, S.J., Puxon, G.J., Xun, L., Hill Jr., H.H.: Metabolic Profiling by Ion Mobility Mass Spectrometry (IMMS). Metabolomics 4, 63-80 (2008) (Pubitemid 351217590)
9. Dwivedi, P., Bendiak, B., Clowers, B.H., Hill Jr., H.H.: Rapid Resolution of Carbohydrate Isomers by Electrospray Ionization Ambient Pressure Ion Mobility Spectrometry-Time-of-Flight Mass Spectrometry (ESI-APIMS-TOFMS). J. Am. Soc.Mass Spectrom. 18, 1163-1175 (2007) (Pubitemid 46963601)
10. Fernandez-Lima, F.A., Becker, C., Gillig, K., Russell, W.K., Nascimento, M.A.C., Russell, D.H.: Experimental and Theoretical Studies of (CsI)nCs+ Cluster Ions Produced by 355 nm Laser Desorption Ionization. J. Phys. Chem. A 112, 11061-11066 (2008)
11. von Helden, G., Wyttenbach, G.T., Bowers, M.T.: Conformations of Macromolecules i the Gas Phase: Use of Matrix-Assisted Laser Desorption Methods in Ion Chromatography. Science 267, 1483-1485 (1995)
12. Myung, S., Lorton, K.P., Merenbloom, S.I., Fioroni, M., Koeniger, S. L., Julian, R.R., Baik, M.-H., Clemmer, D.E.: Chirally Directed Formation of Nanometer-Scale Proline Clusters. J. Am. Chem. Soc. 128, 10833-10839 (2006) (Pubitemid 44277771)
13. Myung, S., Lorton, K.P., Merenbloom, S.I., Fioroni, M., Koeniger, S. L., Julian, R.R., Baik, M.-H., Clemmer, D.E.: Evidence for Spontaneous Resolution of Icosahedral Proline. J. Am. Chem. Soc. 128, 15988-15989 (2006) (Pubitemid 44936563)
14. Jarrold, M.F.: Peptides and Proteins in the Vapor Phase. Ann. Rev. Phys. Chem. 51, 179-207 (2000)
15. Valentine, S.J., Counterman, A.E., Clemmer, D.E.: A Database of 660 Peptide Ion Cross Sections: Use of Intrinsic Size Parameters for Bona Fide Predictions of Cross Sections. J. Am. Soc. Mass Spectrom. 10, 1188-1211 (1999) (Pubitemid 34498675)
16. Tao, L., McLean, J.R., McLean, J.A., Russell, D.H.: A Collision Cross-Section Database of Singly-Charged Peptide Ions. J. Am. Soc. Mass Spectrom. 18, 1232-1238 (2007) (Pubitemid 46963597)
17. Hill Jr., H.H., Hill, C.H., Asbury, G.R., Wu, C., Matz, L.M., Ichiye, T.: Charge location on gas phase peptides. Int. J. Mass Spectrom. 219, 23-27 (2002)
18. Williams, J.P., Bugarcic, T., Habtermariam, A., Giles, K., Campuzano, I., Rodger, P.M., Sadler, P.J.: Isomer Separations andGas-Phase Configurations of Organoruthenium Anticancer Complexes: Ion Mobility Mass Spectrometry and Modeling. J. Am. Soc. Mass Spectrom. 20, 1119-1122 (2009)
19. Fernandez-Lima, F.A., Wei, H., Gao, Y.Q., Russell, D.H.: On the Structure Elucidation Using Ion Mobility Spectrometry and Molecular Dynamics. J. Phys. Chem. A 113, 8221-8234 (2009)
20. Tao, L., Dahl, D.B., Perez, L.M., Russell, D.H.: The Contributions of Molecular Framework to IMS Collision Cross-Sections of Gas-Phase Peptide Ions. J. Am. Soc. Mass Spectrom. 20, 1593-1602 (2009)
21. Bleiholder, C., Osburn, S., Williams, T.D., Suahi, S., van Stipdonk, M., Harrison, A.G., Paizs, B.: Sequence-Scrambling Fragmentation Pathways of Protonated Peptides. J. Am. Chem. Soc. 130, 17774-17789 (2008)
22. Spangler, G.E.: Theory and Technique for Measuring Mobility Using Ion Mobility Spectrometry. Anal. Chem. 65, 3010-3014 (1993)
23. Revercomb, H.E., Mason, E.A.: Theory of plasma chromatography/gaseous electrophoresis. Anal. Chem. 47, 970-983 (1975)
24. Spangler, G.E.: Expanded theory for the resolving power of a linear ion mobility spectrometer. Int. J. Mass Spectrom. 220, 399-418 (2002)
25. Kanu, A.B., Gribb, M.M., Hill Jr., H.H.: Predicting Optimal Resolving Power for Ambient Pressure Ion Mobility Spectrometry. Anal. Chem. 80, 6610-6619 (2008)
26. Siems, W.F., Wu, C., Tarver, E.E., Hill Jr., H.H., Larsen, P.R., McMinn, D.G.: Measuring the Resolving Power of Ion Mobility Spectrometers. Anal. Chem. 66, 4195-4201 (1994) (Pubitemid 124006364)
27. Asbury, R.G., Hill Jr., H.H.: Evaluation of ultrahigh resolution ion mobility spectrometry as an analytical separation device in chromatographic terms. J. Microcolumn Sep. 12, 172-178 (2000)
28. Asbury, R.G., Hill Jr., H.H.: Using Different Drift Gases to Change Separation Factors (?) in Ion Mobility Spectrometry. Anal. Chem. 72, 580-584 (2000) (Pubitemid 33595295)
29. Steiner, W.E., Klopsch, S.J., English, W.A., Clowers, B.H., Hill Jr., H. H.: Electrospray Ionization with Ambient Pressure Ion Mobility Separation and Mass Analysis by Orthogonal Time-of-Flight Mass Spectrometry. Rapid Commun. Mass Spectrom. 15, 2221-2226 (2001) (Pubitemid 33140719)
30. Steiner, W.E., Clowers, B.H., Hill Jr., H.H.: Rapid Separation of Phenylthiohydantoin Amino Acids: Ambient Pressure Ion-Mobility Mass Spectrometry (IMMS). Anal. Bioanal. Chem. 375, 99-102 (2003) (Pubitemid 41200848)
31. Steiner, W.E.C., Brian, H., Haigh, P.E., Hill Jr., H.H.: Secondary Ionization of Chemical Warfare Agent Simulants: Atmospheric Pressure Ion Mobility Time-of-Flight Mass Spectrometry. Anal. Chem. 75, 6068-6076 (2003) (Pubitemid 37420596)
32. Beegle, L.W., Kanik, I., Matz, L., Hill Jr., H.H.: Effects of Drift-Gas Polarizability on Glycine Peptides in Ion Mobility Spectrometry. Int. J. Mass Spectrom. 216, 257-268 (2002)
33. Becke, A.D.: Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys 98, 5648-5652 (1993)
34. Lee, C., Yang, W., Parr, R.G.: Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 37, 785-789 (1988)
35. Hehre, W.J., Ditchfield, R., Pople, J.A.: Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules. J. Chem. Phys. 56, 2257-2261 (1972)
36. Frisch, M. J.; Trucks, H. B. S. G. W.; 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 03, Revision D.02., Gaussian, Inc.: Wallingford, CT. (2004)
37. Dunning, T.H.: Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys 90, 1007-1023 (1989)
38. Brooks, B. R.; Brooks C. L. III; Mackerell, A. D. Jr.; Nilsson, L.; Petrella, R. J.; B.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek,M.; Im,W.; Kuczera, K.; Lazaridis, T.;Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM 09 J. Comput. Chem. 1545-1614 (2009)
39. Gao, B., Wyttenbach, T., Bowers, M.T.: Hydration of Protonated Aromatic Amino Acids: Phenylalanine, Tryptophan, and Tyrosine. J. Am. Chem. Soc 131, 4695-4701 (2009)
40. Liu, D., Seuthe, A.B., Ehrler, O.T., Zhang, X., Wyttenbach, T., Hsu, J. F., Bowers, M.T.: Oxytocin-Receptor Binding: Why Divalent Metals Are Essential. J. Am. Chem. Soc 127, 2024-2025 (2005) (Pubitemid 40270488)
41. Brocker, E.R., Anderson, S.E., Northrop, B.H., Stang, P.J., Bowers, M. T.: Structures of Metallosupramolecular Coordination Assemblies Can Be Obtained by Ion Mobility Spectrometry-Mass Spectrometry. J. Am. Chem. Soc 132, 13486-13494 (2010)
42. Perdew, J.P., Burke, K., Ernzerhof, M.: Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 77, 3865-3868 (1996) (Pubitemid 126631804)
43. Tao, J., Perdew, J.P.: Climbing the Density Functional Ladder: Nonempirical Meta-Generalized Gradient Approximation Designed for Molecules and Solids. Phys. Rev. Lett. 91, 146401-146405 (2003)
44. Voorhis, T.V., Scuseria, G.E.: A novel form for the exchangecorrelation energy functional. J. Chem. Phys. 109, 400-410 (1998) (Pubitemid 128677972)
45. Perdew, J.P., Burke, K., Ernzerhof, M.: Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 77(18), 3865-3868 (1997)
46. Staroverov, V., Scuseria, G.E., Tao, J., Perdew, J.P.: Comparative Assessment of a New Nonempirical Density Functional: Molecules and Hydrogen-Bonded Complexes. J. Chem. Phys. 119, 12129-12137 (2003)
47. Bylaska, E. J.; de Jong, W. A.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Valiev, M.; Wang, D.; Apra, E.; Windus, T. L.; Hammond, J.; Nichols, P.; Hirata, S.; Hackler, M. T.; Zhao, Y.; Fan, P.-D.; Harrison, R. J.; Dupuis, M.; Smith, D. M. A.; Nieplocha, J.; Tipparaju, V.; Krishnan, M.; Wu, Q.; Van Voorhis, T.; Auer, A. A.; Nooijen, M.; Crosby, L. D.; Brown, E.; Cisneros, G.; Fann, G. I.; Fruchtl, H.; Garza, J.; Hirao, K.; Kendall, R.; Nichols, J. A.; Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.; Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.; Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.; Littlefield, R.; Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Pollack, L.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.; Thomas, G.; van Lenthe, J.; Wong, A.; Zhang, Z. NWChem A Computational Chemistry Package for Parallel Computers, Version 5.1.1. , Pacific Northwest National Laboratory: Richland, WA. (2008)
48. 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. A, Erratum, 101, 16082-16086 (1997)
49. Shvartsburg, A.A., Jarrold, M.F.: An Exact Hard Spheres Scattering Model for the Mobilities of Polyatomic Ions. Chem. Phys. Lett. 261, 86-91 (1996) (Pubitemid 126163393)
50. Mack, E.J.: Average Cross-Sectional Areas of Molecules by Gaseous Diffusion Methods. J. Am. Chem. Soc 47, 2468-2482 (1925)
51. Jarrold, M.F., Constant, V.A.: Silicon cluster ions: Evidence for a structural transition. Phys. Rev. Lett. 67, 2994 (1992)
52. Clemmer, D.E., Hunter, J.M., Selimov, K.B., Jarrold, M.F.: Physical and Chemical Evidence for Metallofullerenes with Metal Atoms as Part of the Cage. Nature 372, 248-250 (1994) (Pubitemid 24353331)
53. 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. 100, 16082-16086 (1996) (Pubitemid 126799343)
54. Cuadros, F., Cachadina, I., Ahumada, W.: Determination of Lennard-Jones Interaction Parameters Using a New Procedure. Mol. Eng. 6, 319-325 (1996)
55. Wyttenbach, T., Liu, D., Bowers, M.T.: Interactions of the Hormone Oxytocin with Divalent Metal Ions. J. Am. Chem. Soc. 130, 5993-6000 (2008) (Pubitemid 351620846)
56. Gidden, J., Bowers, M.T.: Gas-Phase Conformations of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling. J. Phys. Chem. B 107, 12829-12837 (2003)
57. Steiner, W.E., English, W.A., Hill Jr., H.H.: Ion-Neutral Potential Models in Atmospheric Pressure Ion Mobility Time-of-Flight Mass Spectrometry IM(TOF)MS. J. Phys. Chem. A, 110, 1836-1844 (2006) (Pubitemid 43348444)