Better score function for peptide identification with ETD MS/MS spectra

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Liu, Xiaowen ^a   Shan, Baozhen ^b,c   Xin, Lei ^b,c   Ma, Bin ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b Bioinformatics Solutions Inc   (Canada)

^c UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BASIC PEPTIDES; COLLISION INDUCED DISSOCIATION; DE NOVO SEQUENCING; ELECTRON-TRANSFER DISSOCIATION; PEPTIDE IDENTIFICATION; PROTEIN IDENTIFICATION; SOFTWARE PROGRAM; TANDEM MASS SPECTROMETRY;

DISSOCIATION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; BIOINFORMATICS;

PEPTIDES;

PEPTIDE; PROTEIN;

ARTICLE; CHEMISTRY; METHODOLOGY; PROTEOMICS; TANDEM MASS SPECTROMETRY;

PEPTIDES; PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 76549097437     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S4     Document Type: Article

References (24)

1. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2, 10612281.
2. Eng JK, McCormack AL, John R Yates I. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 1994, 5(11):976-989.
3. Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrum. Rapid Commun Mass Spectrom 2003, 17:2337-2342. 10.1002/rcm.1196, 14558135.
4. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9):1466-1467. 10.1093/bioinformatics/bth092, 14976030.
5. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH. Open mass spectrometry search algorithm. J Proteome Res 2004, 3(5):958-964. 10.1021/pr0499491, 15473683.
6. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Analytical Chemistry 2005, 77(14):4626-4639. 10.1021/ac050102d, 16013882.
7. Mann M, Wilm M. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Analytical Chemistry 1994, 66(24):4390-4399. 10.1021/ac00096a002, 7847635.
8. Clauser KR, Baker P, Burlingame AL. Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Analytical Chemistry 1999, 71(14):2871-2882. 10.1021/ac9810516, 10424174.
9. Bafna V, Edwards N. SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics 2001, 17(Suppl 1):S13-S21.
10. Field HI, Fenyö D, Beavis RC. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2002, 2:36-47. 10.1002/1615-9861(200201)2:1<36::AID-PROT36>3.0.CO;2-W, 11788990.
11. Chen T, Kao MY, Tepel M, Rush J, Church GM. A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. Journal of Computational Biology 2001, 8(3):325-337. 10.1089/10665270152530872, 11535179.
12. Dančík V, Addona TA, Clauser KR, Vath JE, Pevzner PA. De novo peptide sequencing via tandem mass spectrometry. Journal of Computational Biology 1999,
13. Frank A, Pevzner P. PepNovo: de novo peptide sequencing via probabilistic network modeling. Analytical Chemistry 2005, 77:964-973. 10.1021/ac048788h, 15858974.
14. Hines WM, Falick AM, Burlingame AL, Gibson BW. Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra. Journal of the American Society for Mass Spectrometry 1992, 3:326-336.
15. Lu B, Chen T. A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry. Journal of Computational Biology 2003, 10:1-12. 10.1089/106652703763255633, 12676047.
16. Ma B, Zhang K, Liang C. An effective algorithm for the peptide de novo sequencing from MS/MS spectrum. Journal of Computer and System Science 2005, 70:418-430.
17. Taylor JA, Johnson RS. Sequence database searches via de novo peptide sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 1997, 11(9):1067-1075. 10.1002/(SICI)1097-0231(19970615)11:9<1067::AID-RCM953>3.0.CO;2-L, 9204580.
18. Taylor JA, Johnson RS. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Analytical Chemistry 2001, 73(11):2594-2604. 10.1021/ac001196o, 11403305.
19. Little DP, Speir JP, Senko MW, O'Connor PB, McLafferty FW. Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. Analytical Chemistry 1994, 66(18):2809-2815. 10.1021/ac00090a004, 7526742.
20. McLafferty FW, Horn DM, Breuker K, Ge Y, Lewis MA, Cerda B, Zubarev RA, Carpenter BK. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. Journal of the American Society for Mass Spectrometry 2001, 12(3):245-249. 10.1016/S1044-0305(00)00223-3, 11281599.
21. Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. PNAS USA 2004, 101(26):9528-9533. 10.1073/pnas.0402700101, 470779, 15210983.
22. Fu Y, Yang Q, Sun R, Li D, Zeng R, Ling CX, Gao W. Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry. Bioinformatics 2004, 20(12):1948-1954. 10.1093/bioinformatics/bth186, 15044235.
23. Havilio M, Haddad Y, Smilansky Z. Intensity-based statistical scorer for tandem mass spectrometry. Analytical Chemistry 2003, 75(3):435-444. 10.1021/ac0258913, 12585468.
24. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature Biotechnology 2004, 22(2):214-219. 10.1038/nbt930, 14730315.