Prediction of ion drift times for a proteome-wide peptide set using partial least squares regression, least-squares support vector machine and gaussian process

QSAR and Combinatorial Science

Volumn 28, Issue 11-12, 2009, Pages 1386-1393

  Liu, Xiuhong ^a   Liang, Jun ^a   Fan, Jicai ^a   Shang, Zhicai ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

Bioinformatics; Drift time; Gaussian process; Ion mobility spectrometry; Peptides; Proteome; Quantitative structure property relationship; Statistical modeling method

Indexed keywords

DROSOPHILA PROTEIN; PROTEOME;

ARTICLE; CHEMICAL STRUCTURE; DROSOPHILA MELANOGASTER; GENETIC ALGORITHM; ION MOBILITY SPECTROMETRY; NONHUMAN; NORMAL DISTRIBUTION; PARTIAL LEAST SQUARES REGRESSION; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEOMICS; QUANTITATIVE STRUCTURE PROPERTY RELATION; SUPPORT VECTOR MACHINE;

DROSOPHILA MELANOGASTER;

EID: 76049109467     PISSN: 1611020X     EISSN: 16110218     Source Type: Journal    
DOI: 10.1002/qsar.200910075     Document Type: Article

References (53)

1. G. A. Eiceman, Z. Karpas, Ion Mobility Spectrometry, CRC Press, London 2005.
2. J. I. Baumbach, G. A. Eiceman, Appl. Spectrosc. 1999, 53, 338-355.
3. C. B. Shumate, An Electrospray Nebulization/Ionization Interface for Liquid Introduction into an Ion Mobility Spectrometer. Department of Chemistry, Washington State University, Pullman 1989, p. 158.
4. C.B Shumate, H. H.Jr. Hill, Anal. Chem. 1989, 61, 601-606.
5. K. J. Gillig, B. Ruotolo, E. G. Stone, D. H. Russell, K. Fuhrer, M. Gonin, A. J. Schultz, Anal. Chem. 2000, 72, 3965-3971.
6. D. C. Collins, M. L. Lee, J. Fresenius, Anal. Chem. 2001, 369, 225-233.
7. S. Myung, Y. J. Lee, M. H. Moon, J. Taraszka, R. Sowell, S. Koeniger, A. E. Hilderbrand, S. J. Valentine, L. Cherbas, P. Cherbas, T. C. Kaufmann, D. F. Miller, Y. Mechref, M. V. Novotny, M. A. Ewing, C. R. Sporleder, D. E. Clemmer, Anal. Chem. 2003, 75, 5137-5145.
8. J. A. McLean, D. H. Russell, J. Proteome Res. 2003, 2, 427-430.
9. R. W. Purves, D. A. Barnett, B. Ells, R. Guevremont, J. Am. Soc. Mass Spectrom. 2001, 12, 894-901.
10. J. A. Taraszka, A. E. Counterman, D. E. Clemmer, J. Fresenius, Anal. Chem. 2001, 369, 234-45.
11. L. Jin, P. E. Barran, J. A. Deakin, L M. Yon, D. Uhrin, PhysChemChemPhys. 2005, 7, 3464-3471.
12. C. S. Hoaglund, S. J. Valentine, D. E. Clemmer, Anal. Chem. 1997, 69, 4156-4161.
13. P. Dwivedi, P. Wu, S. J. Klopsch, G. J. Puzon, L. Xun, H. H.Jr. Hill, Metabolomics 2008, 4, 63-80.
14. C. S. Hoaglund, S. J. Valentine, C. R. Sporleder, J. P. Reilly, D. E. Clemmer, Anal. Chem. 1998, 70, 2236-2242.
15. G.W. Griffin, I. Dzidic, D. I. Carroll, R. N. Stillwell, E. C. Horning, Anal. Chem. 1973, 45, 1204-1209.
16. S. N. Lin, G.W. Griffin, E. C. Horning, W. E. Wentworth, J. Chem. Phys. 1974, 60, 4994-4999.
17. M. D. Wessel, P. C. Jurs, Anal. Chem. 1994, 66, 2480-2487.
18. M. D. Wessel, J. M. Sutter, P. C. Jurs, Anal. Chem. 1996, 68, 4237-4243.
19. A. R. Katritzky, V. S. Lobanov, M. Karelson, Chem. Soc. Rev. 1995, 24, 279-287.
20. A. R. Katritzky, U. Maran, V. S. Lobanov, M. Karelson, J. Chem. Inf. Comput. Sci. 2000, 40, 1-18.
21. A. E. Counterman, D. E. Clemmer, J. Am. Chem. Soc. 1999, 121, 4031-4039.
22. S. J. Valentine, A. E. Counterman, C. S. Hoaglund-Hyzer, D. E. Clemmer, J. Phys. Chem. B 1999, 103, 1203-1207.
23. A. A. Shvartsburg, K. W.M. Siu, J. Am. Soc. Mass Spectrom. 2001, 12, 885-888.
24. A. E. Hilderbrand, D. E. Clemmer, J. Phys. Chem. B 2005, 109, 11802-11809.
25. P. Zhou, H. Zeng, F. F. Tian, B. Li, Z. L. Li, QSAR Comb. Sci. 2007, 26, 117-121.
26. P. Zhou, F. F. Tian, Z. L. Li, Anal. Chim. Acta 2007, 597, 214-222.
27. J. A. Taraszka, R. Kurulugama, R. A. Sowell, S. J. Valentine, S. L. Koeniger, R. J. Arnold, D. F. Miller, T. C. Kaufman, D. E. Clemmer, J. Proteome Res. 2005, 4, 1223-1237.
28. M. Baroni, S. Clement, G. Cruciani, N. Kettaneh-Wold, S. Wold, Quant. Struct. Act. Relat. 1993, 12, 225-231.
29. A. R. Katritzky, V. S. Lobanov, M. Karelson, CODESSA Vers. 2.7, Reference Manual, University of Florida, Gainesville, FL 1995-1997.
30. A. R. Katritzky, V. S. Lobanov, M. Karelson, Chem. Soc. Rev. 1995, 24, 279-287.
31. A. R. Katritzky, V. S. Lobanov, M. Karelson, Comprehensive Descriptors for Structural and Statistical Analysis, Reference Manual, Version 2.0, 1994.
32. J. Holland, Adaptation in Natural and Artificial Systems, University of Michigan Press, Ann Arbor, MI 1975.
33. S. Pezeshk, C. V. Camp, State of the art on the use of genetic algorithms in designof steel structures. In Recent Advances in Optimal Structural Design, Burns SA(ed.). American Society of Civil Engineers: New York, 2002.
34. J. R. Koza, Genetic Programming: A Paradigm for Genetically Breeding Populations of Computer Programs to Solve Problems, Stanford University Computer Science Department, Technical Report STAN-CS-90-1314, June, 1990.
35. P. J. Angeline, K. E. Kinnear Jr. (Eds.), Advances in Genetic Programming, MIT Press, Cambridge, MA, 1996.
36. J. R. Koza , Genetic Programming: On the Programming of Computers by Means of Natural Selection, MIT Press, Cambridge, MA 1992.
37. J. R. Koza, Genetic Programming II: Automatic Discovery of Reusable Programs, MIT Press, Cambridge, MA 1994.
38. E. Howard, N. Oakley, Genetic Programming, the Reflection of Chaos, and the Bootstrap: Towards a Useful Test for Chaos, Genetic Programming 96.
39. J. R. Koza, Reverse Engineering and Automatic Synthesis of Metabolic Pathways from Observed Data Using Genetic Programming, Technical Report SMI-2000-0851.
40. P. Zhou, F. F. Tian, X. Chen, Z. C. Shang, Biopolymers (Pept. Sci.) 2008, 90, 772-802.
41. J. M. Luco, J. Chem. Inf. Comput. Sci. 1999, 39, 396-404.
42. M. F. Silva, L. F. Chipre, J. Raba, J. M. Luco, Chromatographia 2001, 53, 392-400.
43. J. M. Luco, A. P. Salinas, A. A.J. Torriero, R. N. Vazquez, J. Raba, E. J. Marchevsky, J. Chem. Inf. Comput. Sci. 2003, 43, 2129-2136.
44. J. M. Luco, E. Marchevsky, Curr. Comput.-Aided Drug Design 2006, 2, 31-55.
45. J. A.K. Suykens, J. Vandewalle, Neural Process. Lett. 1999, 9, 293-300.
46. P. Zhou, X. Chen, Y. Wu, Z. Shang, Amino Acids 2009, DOI 10.1007/s00726-008-0228-1, in press.
47. O. Obrezanova, G. Csányi, J. M.R. Gola, M. D. Segall, J. Chem. Inf. Model 2007, 47, 1847-1857.
48. C. E. Rasmussen, Evaluation of Gaussian Processes and Other Methods for Non-linear Regression. PhD thesis, University of Toronto, Canada 1996.
49. P. Wolfe, SIAM Rev. 1969, 11, 226-235.
50. P. Zhou, F. Tian, F. Lv, Z. Shang, J. Chromatogr. A, 2009, 1216, 3107-3116.
51. J. A. K. Suykens, T. van Gestel, J. de Brabanter, B. de Moor, J. Vandewalle, Least Squares Support Vector Machines, World Scientific, Singapore 2002.
52. C. E. Rasmussen, C. K.I. Williams, Gaussian Processes for Machine Learning, MIT Press, Massachusetts, 2006.
53. ChemoAC Calibration Toolbox, Virtual Institute of Chemometrics and Industrial Metrology, Brussels, Belgium.