SVM-RFE based feature selection for tandem mass spectrum quality assessment

International Journal of Data Mining and Bioinformatics

Volumn 5, Issue 1, 2011, Pages 73-88

  Ding, Jiarui ^a   Shi, Jinhong ^a   Wu, Fang Xiang ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

Feature selection; Proteomics; Quality assessment; SVM RFE; Tandem mass spectra

Indexed keywords

EID: 79951662909     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2011.038578     Document Type: Article

References (29)

1. Aebersold, R. and Mann, M. (2003) 'Mass spectrometry-based proteomics', Nature, Vol. 422 pp.198-207. (Pubitemid 36362757)
2. Baginsky, S., Cieliebak, M., Gruissem, W., Kleffmann, T., Liptak, Z., Muller, M. and Penna, P. (2002) AuDeNS: A Tool for Automatic de novo Peptide Sequencing, Technical Report No. 383, ETH Zurich, Dept. of Computer Science.
3. Bern, M., Goldberg, D., McDonald, W. and Yates, J. (2004) 'Automatic quality assessment
4. Ding, J. (2009) Pre-processing of Tandem Mass Spectra using Machine Learning Methods, Master's Thesis, University of Sasktchewan, Saskatoon, Canada.
5. Duan, K. and Rajapakse, J. (2005) 'SVM-RFE peak selection for cancer classification with
6. Fan, R., Chen, P. and Lin, C. (2005) 'Working set selection using second order information (Pubitemid 41798130)
7. Flikka, K., Martens, L., Vandekerckhove, J., Gevaert, K. and Eidhammer, I. (2006) 'Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering', Proteomics, Vol. 6, No. 7, pp.2086-2094.
8. Guyon, I., Elisseefi, A. and Kaelbling, L. (2003) 'An introduction to variable and feature selection', Journal of Machine Learning Research, Vol. 3, pp.1157-1182.
9. Guyon, I., Weston, J., Barnhill, S. and Vapnik, V. (2002) 'Gene selection for cancer (Pubitemid 34129977)
10. Hua, S. and Sun, Z. (2001) 'Support vector machine approach for protein subcellular (Pubitemid 32851380)
11. Jones, N. and Pevzner, P. (2004) An Introduction to Bioinformatics Algorithms, MIT Press
12. Keller, A., Nesvizhskii, A., Kolker, E. and Aebersold, R. (2002a) 'Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search', Anal. Chem., Vol. 74, No. 20, pp.5383-5392. (Pubitemid 35215372)
13. Keller, A., Purvine, S., Nesvizhskii, A., Stolyar, S., Goodlett, D. and Kolker, E. (2002b) (Pubitemid 35278428)
14. Kinter, M. and Sherman, N. (2000) Protein Sequencing and Identification using Tandem Mass Spectrometry, Wiley, New York.
15. Na, S. and Paek, E. (2006) 'Quality assessment of tandem mass spectra based on cumulative (Pubitemid 44904315)
16. Nesvizhskii, A., Roos, F., Grossmann, J., Vogelzang, M., Eddes, J., Gruissem, W., Baginsky,S. and Aebersold, R. (2006) 'Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides', Molecular and Cellular Proteomics, Vol. 5, No. 4, pp.652-670.
17. Purvine, S., Kolker, N. and Kolker, E. (2004) 'Spectral quality assessment for high-throughput tandem mass spectrometry proteomics', Omics A Journal of Integrative Biology, Vol. 8, No. 3, pp.255-265. (Pubitemid 39425675)
18. Rakotomamonjy, A., Guyon, I. and Elisseeff, A. (2003) 'Variable selection using SVM-based
19. Saeys, Y., Inza, I. and Larranaga, P. (2007) 'A review of feature selection techniques in (Pubitemid 350048351)
20. Salmi, J., Moulder, R., Filen, J., Nevalainen, O., Nyman, T., Lahesmaa, R. and Aittokallio,T. (2006) 'Quality classification of tandem mass spectrometry data', Bioinformatics, Vol. 22, No. 4, pp.400-406. (Pubitemid 43231413)
21. Tabb, D., Eng, J. and Yates III, J. (2001) 'Protein identification by SEQUEST', in Peter, J. (Ed.): Proteome Research: Mass Spectrometry, Springer, Berlin, pp.125-142.
22. Tang, Y., Zhang, Y. and Huang, Z. (2007) 'Development of two-stage SVM-RFE gene selection strategy for microarray expression data analysis', IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 4, No. 3, pp.365-381. (Pubitemid 47274713)
23. Tanner, S., Shu, H., Frank, A., Wang, L., Zandi, E., Mumby, M., Pevzner, P. and Bafna, V. (2005) 'Inspect: fast and accurate identification of post-translationally modified peptides from tandem mass spectra', Anal. Chem., Vol. 77, No. 14, pp.4626-4639. (Pubitemid 41542287)
24. Wang, J. and Wu, X. (2006) 'Kernel design for RNA classification using support vector machines', International Journal of Data Mining and Bioinformatics, Vol. 1, No. 1, pp.57-76.
25. Wong, J., Sullivan, M., Cartwright, H. and Cagney, G. (2007) 'msmsEval: tandem mass spectral quality assignment for high-throughput proteomics', BMC Bioinformatics, Vol. 8, No. 1, p.S11.
26. Wu, F.X., Ding, J. and Poirier, G. (2008) 'An approach to assessing peptide mass spectral quality without prior information', International Journal of Functional Informatics and Personalised Medicine, Vol. 1, No. 2, pp.140-155.
27. Wu, F.X., Gagne, P., Droit, A. and Poirier, G. (2008) 'Quality assessment of peptide tandem
28. Xu, M., Geer, L., Bryant, S., Roth, J., Kowalak, J., Maynard, D. and Markey, S. (2005) 'Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry', J.Proteome Res., Vol. 4, No. 2, pp.300-305. (Pubitemid 40548133)
29. Zhang, X., Lu, X., Shi, Q., Xu, X., Leung, H., Harris, L., Iglehart, J., Miron, A., Liu, J.