Peptide identification by tandem mass spectra: An efficient parallel searching

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 161-168

  Oh, Jung Hun ^a   Gao, Jean ^a  

^a The University of Texas at Arlington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; GRAPH THEORY; MASS SPECTROMETRY; ONLINE SEARCHING; PARALLEL ALGORITHMS; PATTERN RECOGNITION;

AMINO ACID SEQUENCE; MASS SPECTRA; PARALLEL SEARCHING; PEPTIDE SEQUENCING;

POLYPEPTIDES;

EID: 33751187855     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.45     Document Type: Conference Paper

References (15)

1. V. Danick, T.A. Addona, K.R. Clauser, J.E. Vath, P.A. and Pevzner, "De novo peptide sequencing via tandem mass spectrometry", J. Comput. Biol., vol. 6, pp. 327-342. 1999.
2. B. Lu, and T. Chen, "A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry", J. Comput. Biol., vol. 10, pp. 1-12. 2003.
3. B. Ma, K.Z. Zhang, C. Hendrie, C.Z. Liang, M. Li, A. Doherty-Kirby, and G. Lajoie, "PEAKS: powerful software for peptide de novo sequencing by MS/MS", Rapid Communications in Mass Spectrometry, vol. 17, pp. 2337-2342. 2003.
4. N. Zhang, R. Aebersold, and B. Schwikowski, "ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data", Proteomics, vol. 2, pp. 1406-1412. 2003.
5. B. Ma, K. Zhang, and C. Liang, "An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum", CPM'03, pp. 266-278. 2003.
6. Y. Fu, Q. Yang, R. Sun, D. Li, R. Zeng, C.X. Ling, and W. Gao, "Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry", Bioinformatics, vol. 20, pp. 1948-1954. 2004.
7. V. Bafna, and N. Edwards, "SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database", Bioinformatics, vol. 17, pp. S13-S21. 2001.
8. J.K. Eng, A.L. McCormack, and J.R. Yates, "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database", J. Am. Soc. Mass Spectrom., vol. 5, pp.976-989. 1994.
9. B. Lu, and T. Chen, "A suffix tree approach to the interpretation of tandem mass spectra: applications to peptides of non-specific digestion and post-translational modifications", Bioinformatics, vol. 19, pp. ii113-ii121. 2003.
10. J.A. Taylor, and R.S. Johnson, "Sequence database searches via de novo peptide sequencing by tandem mass spectrometry", Rapid Communications in Mass Spectrometry, vol. 11, pp. 1067-1075. 1997.
11. B.T. Clauser, P.R. Baker, and A.L. Burlingame, "Role of accurate mass measurement (+/- 10ppm) in protein identification strategies employing MS or MS/MS", Analytical Chem., vol. 71, pp. 2871-2882. 1999.
12. D.N. Perkins, D.J.C. Pappin, D.M. Creagy, and J.S. Cottrell, "Probability-based protein indentification by searching sequence data-bases using mass spectrometry data", Electrophoresis, vol. 20, pp. 3551-3567. 1999.
13. J.A. Taylor, and R.S. Johnson, "Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry", Anal Chem., vol. 73, pp. 2594-2604. 2001.
14. B. Van, C. Pan, V.N. Olman, R.L. Rettich, and Y. Xu, "A graph-theoretic approach to separation of b and y ions in tandem mass spectra", Bioinformatics, vol. 21, pp. 563-574. 2005.
15. K.D. Jarman, W.R. Cannon, K.H. Jarman, and A. Heredia-Langner, "A model of random sequences for de novo peptide sequencing". Proceedings of IEEE Symposium on Bioinformatics and Bioengineering'03, pp. 206-213. 2003.