New computational approaches for de novo peptide sequencing from MS/MS experiments

Proceedings of the IEEE

Volumn 90, Issue 12, 2002, Pages 1868-1874

  Lubeck, Olaf ^a,b   Sewell, Christopher ^a   Gu, Sheng ^a   Chen, Xian ^a   Cai, D Michael ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b Bioscience Division   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DISSOCIATION; LEARNING SYSTEMS; PROTEINS; SPECTROMETRY;

DISSOCIATION CHEMISTRY; GRAPH THEORETIC FRAMEWORK; PEPTIDE SEQUENCING; PROTEIN IDENTIFICATION;

POLYPEPTIDES;

EID: 0012753946     PISSN: 00189219     EISSN: None     Source Type: Journal    
DOI: 10.1109/JPROC.2002.805301     Document Type: Article

References (14)

1. A. Krogh, Guide to Human Genome Computing. San Diego, CA: Academic, 1998, pp. 261-274.
2. I. Dunham et al., "The DNA sequence of human chromosome 22," Nature, vol. 402, pp. 489-195, 1999.
3. D. Eisenberg et al., "Protein function in the post-genomic era," Nature, vol. 405, pp. 823-826, 2000.
4. A. Pandey et al., "Proteomics to study genes and genomes," Nature, vol. 405, pp. 837-406, 2000.
5. J. Eng et al., "An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database," J. Amer. Soc. Mass Spectrom., vol. 5, pp. 976-989, 1994.
6. V. Dancik et al., "De novo sequencing via tandem mass spectrometry," J. Comput. Biol., vol. 6, pp. 327-342, 1999.
7. T. Chen et al., "A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry," in Proc. 10th SIAM Conf. Discrete Mathematics, 2000.
8. J. Fernandex-de-Cossio et al., "Automated interpretation of low-energy collision-induced dissociation spectra by SEQMS, a software aid for de novo sequencing by tandem mass spectrometry," Electrophoresis, vol. 21, pp. 1694-1699, 2000.
9. T. Chen et al., "A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry," in Proc. 10th SIAM Conf. Discrete Mathematics, 2000.
10. Boost C++ libraries [Online]. Available: www.boost.org.
11. D. Eppstein, "Finding the k shortest paths," SIAM J. Comput., vol. 28, no. 2, pp. 652-673, 1998.
12. S. Gu, S. Pan, E. M. Bradbury, and X. Chen, "The use of deteriumlabeled lysine for efficient protein identification and peptide de novo sequencing," Anal. Chem., to be published.
13. H. Zhu, T. C. Hunter, S. Pan, P. M. Yau, E. M. Bradbury, and X. Chen, "Residue-specific mass signatures for the efficient detection of protein modifications by mass spectrometry," Anal. Chem., vol. 74, pp. 1687-1694, 2002.
14. T. C. Hunter, L. Yang, H. Zhu, V. Majidi, E. M. Bradbury, and X. Chen, "Peptide mass mapping constrained with stable isotope-tagged peptides for identification of protein mixtures," Anal. Chem., vol. 73, pp. 4891-4902, 2001.