A graph-theoretic approach for the separation of b and y ions in tandem mass spectra

Bioinformatics

Volumn 21, Issue 5, 2005, Pages 563-574

  Yan, Bo ^a,b   Pan, Chongle ^c,d   Olman, Victor N ^a,b   Hettich, Robert L ^d   Xu, Ying ^a,b  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c and Fellow Transcultural Nursing Society Scholars   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOVINE SERUM ALBUMIN; ION; LYSOZYME; MYOGLOBIN;

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; COMPUTER SIMULATION; EXPERIMENTATION; HORSE; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; MATHEMATICAL PARAMETERS; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROBLEM SOLVING; SEPARATION TECHNIQUE; TANDEM MASS SPECTROMETRY; THEORY; YEAST;

EID: 15844407468     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti044     Document Type: Article

References (29)

1. Aebersold,R. and Mann,M. (2003) Mass spectrometry-based proteomics. Nature, 422, 198-207.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Andersen,J.S., Wilkinson,C.J., Mayor,T., Mortensen,P., Nigg,E.A. and Mann,M. (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature, 426, 570-574.
4. Bartels,C. (1990) Fast algorithm for peptide sequencing by mass spectroscopy. Biomed. Environ. Mass Spectrom., 19, 363-368.
5. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I., Pilbout,S. and Schneider,M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365-370.
6. Chen,T., Kao,M.Y., Tepel,M., Rush,J. and Church,G.M. (2001) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol., 8, 325-337.
7. Clauser,K.R., Baker,P. and Burlingame,A.L. (1999) Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71, 2871-2882.
8. Cormen,T.H., Leiserson,C.E., Rivest,R.L. and Stein,C. (2001) Introduction to Algorithms. The MIT Press, Cambridge, MA.
9. Dancik,V., Addona,T.A., Clauser,K.R., Vath,J.E. and Pevzner,P.A. (1999) De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol., 6, 327-342.
10. Eng,J.K., McCormack,A.L. and Yates,J.R.,III (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom., 5, 976-989.
11. Fenyo,D. (2000) Identifying the proteome: software tools. Curr. Opin. Biotechnol., 11, 391-395.
12. Fenyo,D., Qin,J. and Chait,B.T. (1998) Protein identification using mass spectrometric information. Electrophoresis, 19, 998-1005.
13. Gauthier,J.W., Trautman,T.R. and Jacobson,D.B. (1991) Sustained off-resonance irradiation for collision-activated dissociation involving Fourier transform mass spectrometry. Collision-activated dissociation technique that emulates infrared multiphoton dissociation. Anal. Chim. Acta, 246, 211-225.
14. Gooley,A.A. and Packer,N.H. (1997) The importance of co- and post-translational modifications in proteome projects. In Wilkins,W.R., Williams,K.L., Appel,R.D. and Hochstrasser,D.F. (eds), Proteome Research: New Frontiers in Functional Genomics. Springer-Verlag, NY, pp. 65-91.
15. Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
16. Lasonder,E., Ishihama,Y., Andersen,J.S., Vermunt,A.M., Pain,A., Sauerwein,R.W., Eling,W.M., Hall,N., Waters,A.P., Stunnenberg,H.G. and Mann,M. (2002) Analysis of the Plasmodium falciparum, proteome by high-accuracy mass spectrometry. Nature, 419, 537-542.
17. Lu,B. and Chen,T. (2003) A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol., 10, 1-12.
18. Ma,B., Zhang,K., Hendrie,C., Liang,C., Li,M., Doherty-Kirby,A. and Lajoie,G. (2003) PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom., 17, 2337-2342.
19. MacCoss,M.J., McDonald,W.H., Saraf,A., Sadygov,R., Clark,J.M., Tasto,J.J., Gould,K.L., Wolters,D., Washburn,M., Weiss,A., Clark,J.I. and Yates,J.R., III (2002) Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. USA, 99, 7900-7905.
20. Mann,M. and Jensen,O.N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol., 21, 255-261.
21. Mann,M. and Wilm,M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390-4399.
22. Nesvizhskii,A.I. and Aebersold,R. (2004) Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov. Today, 9, 173-181.
23. Perkins,D.N., Pappin,D.J., Creasy,D.M. and Cottrell,J.S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20, 3551-3567.
24. Pevzner,P.A., Dancik,V. and Tang,C.L. (2000) Mutation-tolerant protein identification by mass spectrometry. J. Comput. Biol., 7, 777-787.
25. Tabb,D.L., Smith,L.L., Breci,L.A., Wysocki,V.H., Lin,D. and Yates, J.R.,III (2003) Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal. Chem., 75, 1155-1163.
26. Taylor,J.A. and Johnson,R.S. (1997) Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom., 11, 1067-1075.
27. Taylor,J.A. and Johnson,R.S. (2001) Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal. Chem., 73, 2594-2604.
28. Washburn,M.P., Wolters,D. and Yates,J.R.,III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol., 19, 242-247.
29. Yates,J.R.,III, Eng,J.K., McCormack,A.L. and Schieltz,D. (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem., 67 1426-1436.