PRIMA: Peptide robust identification from MS/MS spectra

Series on Advances in Bioinformatics and Computational Biology

Volumn 1, Issue , 2005, Pages 181-190

  Liu, Jian ^a   Ma, Bin ^b   Li, Ming ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DATA PRIVACY; LINEAR PROGRAMMING; MASS SPECTROMETRY; MOLECULAR BIOLOGY; NETWORK SECURITY; PEPTIDES; SOFTWARE TESTING;

ION TRAP INSTRUMENTS; LOW QUALITY DATUM; PEPTIDE IDENTIFICATION; PROTEIN IDENTIFICATION; ROBUST IDENTIFICATION; SCORING FUNCTIONS; TANDEM MASS SPECTRA; TANDEM MASS SPECTROMETRY;

BENCHMARKING;

EID: 84863034622     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1142/9781860947322_0018     Document Type: Conference Paper

References (16)

1. V. Bafna and N. Edwards. SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics, 17(2001), S13-S21. (Pubitemid 33793489)
2. C. Bartels. Fast algorithms for peptide sequencing by mass septrometry. Biomedical and Environmental Mass Spectrometry, 19(1990), 363-368. (Pubitemid 20326751)
3. D. Chamrad. Evaluation of algorithms for protein identification form sequence databases using mass spectrometry. Proteomics 4(2004), 619-628. (Pubitemid 38339142)
4. T. Chen, M-Y. Kao, . A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. Journal of Computational Biology 8:3(2001), 325-337. (Pubitemid 32911660)
5. J. Colinge, A. Masselot, et al. Olav: Towards high throughput tandem mass spectrometry data identification. Proteomics, 3(2003), 1454-1463. (Pubitemid 37048071)
6. R. Craig and R. Beavis. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Communications in Mass Spectrometry 17(2003), 2310-2316. (Pubitemid 37243315)
7. V. Danck, T. Addona, K. Clauser, J. Vath, and P. Pevzner. De novo protein sequencing via tandem mass-spectrometry. Journal of Computational Biology 6(1999), 327-341.
8. J.S. Eddes, E.A. Kapp, S.F. Frecklington, ei al. CHOMPER: A bioinformatic tool for rapid validation of tandem mass spectrometry search resutls associated with high-throughput proteomic strategies. Proteomics 2(2002), 1097-1103.
9. 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. Journal of Ammerican Society Mass Spectrometry, 5(1994), 976-989.
10. E. A. Kapp, F. Schutz, . Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Analytical Chemistry 75(2003), 6251-6264. (Pubitemid 37420620)
11. A. Keller, S. Purvine, . Experimental protein mixture for validating tandem mass spectral analysis. OMICS: A Journal of Integrative Biology, 6:2(2002), 207-212. (Pubitemid 35278428)
12. J. Grossmann. Protein identification using mass Spectrometry: development of an approach for automated de novo sequencing, Master thesis, ETH Zurich, Department of Biology, 2003.
13. B. Ma, K. Zhang, C. Liang. An efficient algorithm for peptide de novo sequencing from MS/MS spectrum, Proc. Conference on Combinatorial Pattern Matching 2003,266-278.
14. D.N. Perkins, J.C. Pappin, D.M. Creasy, and J.S. Cottrell. Probability-based protein identification by searching database using mass spectrometry data. Electrophoresis 20(1999), 3551-3567. (Pubitemid 30007252)
15. R. Sadygov, H. Liu, J.R. Yates. Statistical models for protein validation using mass spectral data and protein amino acid sequence databases. Analytical Chemistry, (76)2004, 1664-1671. (Pubitemid 38338411)
16. J.A. Tayor, R.S. Johnson. Sequence database searches via de novo peptide sequencing by mass spectrometry. Rapid Communications Mass Spectrometry, 11(1997), 1067-1075. (Pubitemid 27269545)