An iterative algorithm to quantify factors influencing peptide fragmentation during tandem mass spectrometry

Journal of Bioinformatics and Computational Biology

Volumn 5, Issue 2 A, 2007, Pages 297-311

  Yu, Chungong ^a   Lin, Yu ^a,b   Sun, Shiwei ^a,b   Cai, JinJin ^a,b   Zhang, Jingfen ^a,b   Bu, Dongbo ^a   Zhang, Zhuo ^b,c   Chen, Runsheng ^c  

^a INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

Iterative algorithm; Linear programming; Mass spectrum; Mobile proton hypothesis

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; CHEMICAL BOND; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; FRAGMENTATION REACTION; MATHEMATICAL ANALYSIS; NONLINEAR SYSTEM; PEPTIDE ANALYSIS; PREDICTION; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEOMICS; QUANTITATIVE ANALYSIS; STATISTICAL MODEL; TANDEM MASS SPECTROMETRY; THEORY;

EID: 34347382973     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/s0219720007002643     Document Type: Conference Paper

References (34)

1. Aebersold R, Goodlett DR, Chem Rev 101:269-295, 2001.
2. Bafna V, Edwards N, Bioinformatics 17(Suppl 1):S13-S21, 2001.
3. Bartels C, Biomed Environ Mass Spectrum 19:363-368, 1990.
4. Cannon WR et al., J Proteome Res 4(5):1687-1698, 2005.
5. Chen T, Kao MY, Tepel M, Rush J, Church GM, J Comput Biol 8 325-337, 2001.
6. Dancik V, Addona TA, Clauser KR, Vath JE, Pevzner PA, J Comput Biol 6:327-342, 1999.
7. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP, Nature BioTech 22(2):214-219, 2004.
8. Eng JK, McCormack AL, Yates JR, J Am Soc Mass Spectrom 5 976-989, 1994.
9. Frank A, Pevzner PA, Anal Chem 77:964-973, 2005.
10. Havilio M, Haddad Y, Smilansky Z, Anal Chem 75:435-444, 2003.
11. Hines WM, Falick AM, Burlingame AL, Gibson BW, J Am Sco Mass Spectrom 3:326-336, 1992.
12. Huang Y, Wysocki VH, Tabb DL, Yates JR, J Am Soc Mass Spectrom 219:233-244, 2002.
13. Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E, Omics 6:207-212, 2002.
14. Lu B, Chen T, J Comput Biol 10(1):1-12, 2001.
15. Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G, Rapid Communication in Mass Spectrometry 17(20):2337-2342, 2003.
16. Nold MJ, Cerda BA, Wesdemiotis C, J Am Soc Mass Spectrom 10 1-8, 1999.
17. O'Hair RA, J Mass Spectrom 35:1377-1381, 2000.
18. Paizs B, Suhai S, Mass Spectrom Rev 5:103-113, 2004.
19. Perkins DN, Pappin, DJ, Creasy DM, Cottrell JS, Electrophoresis 20:3551-3567, 1999.
20. Pevzner PA, Mulyukov Z, Dancik V, Tang CL, Genome Res 11 290-299, 2001.
21. Resing KA et al., Anal Chem 76(13):3556-3568, 2004.
22. Sakurai T, Matsuo T, Matsuda H, Katakuse I, Biomed Mass Spectrum 11 (8):396-399, 1984.
23. Schutz F, Kapp EA, Simpson RJ, Speed TP, Biochem Soc Trans 31 1479-1483, 2003.
24. Siegel MM, Bauman N, Biomed Environ Mass Spectrum 15 333-343, 1988.
25. Sonar http://65.219.84.5/ProteinId.html.
26. Tabb DL, Smith LL, Breci LA, Wysocki VH, Lin D, Yates JR, Anal Chem 75:1155-1163, 2003.
27. Wan Y, Chen T, RECOMB 342-356, 2005.
28. Wysocki VH, Tsaprailis G, Smith LL, Breci LA, J Mass Spectrom 35:1399-1406, 2000.
29. Yates JR, J Mass Spectrom 33:1-19, 1998.
30. Zhang N, Aebersold R, Schwikowski B, Proteomics 2:1406-1412, 2002.
31. Zhang ZQ, Anal Chem 76:3908-3922, 2004.
32. Zhang ZQ, Anal Chem 76:6374-6383, 2004.
33. Zhang ZQ, Proc 50th Am So Mass Spectrom Orlando Fl Paper TPE-126, 2002.
34. Zhu H, Bilgin M, Snyder M, Annu Rev Biochem 72:783-812, 2003.