Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments

Journal of Proteome Research

Volumn 7, Issue 12, 2008, Pages 5148-5156

  May, Damon ^a   Liu, Yan ^a   Law, Wendy ^a   Fitzgibbon, Matt ^a   Wang, Hong ^a   Hanash, Samir ^a   McIntosh, Martin ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

AMT; IPAS; LC MS; msInspect

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; FRACTIONATION; ISOTOPE LABELING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS;

ALGORITHMS; CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; HOT TEMPERATURE; MASS SPECTROMETRY; MODELS, STATISTICAL; PEPTIDE MAPPING; PEPTIDES; PROTEINS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 61349134858     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr8004502     Document Type: Article

References (20)

1. Veltri, P. Briefings Bioinf. 2008, 9, 144-155.
2. Mueller, L. N.; Brusniak, M.; Mani, D. R.; Aebersold, R. J. Proteome Res. 2007, 7, 51-61.
3. Smith, R. D.; erson, G. A.; Lipton, M. S.; Pasa-Tolic, L.; Shen, Y.; Conrads, T. P.; Veenstra, T. D.; Udseth, H. R. Proteomics 2002, 2, 513-23.
4. Norbeck, A. D.; Monroe, M. E.; Adkins, J. N.; erson, K. K.; Daly, D. S.; Smith, R. D. J. Am. Soc. Mass Spectrom. 2005, 16, 1239-49.
5. Petyuk, V.; Qian, W. J:, Chin, M.; Wang, H.; Livesay, E.; Monroe, M. E.; Adkins, J.; Jaitly, N.; erson, D.; Camp, D. G., II; Smith, D. J.; Smith, R. Genome Res. 2007, 17, 328-336.
6. May, D.; Fitzgibbon, M.; Liu, Y.; Holzman, T.; Eng, J.; Kemp, C. J.; Whiteaker, J.; Paulovich, A.; McIntosh, M. J. Proteome Res. 2007, 6, 2685-2694.
7. Elias, J. E.; Gygi, S. P. Nat. Methods 2006, 22, 2830-2832.
8. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Anal. Chem. 2002, 74, 5383-5392.
9. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. Anal. Chem. 2003, 75, 4646-4658.
10. Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Nat. Biotechnol. 2001, 19, 946-951.
11. Li, X. J.; Zhang, H.; Ranish, J. R.; Aebersold, R. Anal. Chem. 2003, 75, 6648-6657.
12. Faca, V.; Coram, M.; Phanstiel, D.; Glukhova, V.; Zhang, Q.; Fitzgibbon, M.; McIntosh, M.; Hanash, S. J. Proteome Res. 2006, 5, 2009-2018.
13. Stewart, I. I.; Thompson, T.; Figeys, D. Rapid Commun. Mass Spectrom. 2001, 15, 2456-2465.
14. Dempster, A. P.; Laird, N. M.; Rubin, D. B. J. R. Stat. Soc., Ser. B 1977, 39, 1-38.
15. Faca, V.; Pitteri, S. J.; Newcomb, L.; Glukhova, V.; Phanstiel, D.; Krasnoselsky, A.; Zhang, Q.; Struthers, J.; Wang, H.; Eng, J.; Fitzgibbon, M.; McIntosh, M.; Hanash, S. J. Proteome Res. 2007, 6, 3558-3565.
16. MacLean, B.; Eng, J.; Beavis, R. C.; McIntosh, M. Bioinformatics 2006, 22, 2830-2832.
17. Krokhin, O. V.; Craig, R.; Spicer, V.; Ens, W.; Standing, K. G.; Beavis, R. C.; Wilkins, J. A. Mol. Cell Proteomics 2004, 3, 908-919.
18. Bellew, M.; Coram, M.; Fitzgibbon, M.; Igra, M.; Randolph, T.; Wang, P.; May, D.; Eng, J.; Fang, R.; Lin, C.; Chen, J.; Goodlett, D.; Whiteaker, J.; Paulovich, A.; McIntosh, M. Bioinformatics 2006, 22, 1902-1909.
19. Jaffe, J. D.; Mani, D. R.; Leptos, K. C.; Church, G. M.; Gillette, M. A.; Carr, S. A. Mol. Cell Proteomics 2006, 5, 1927-1941.
20. Wang, P.; Coram, M.; Tang, H.; Fitzgibbon, M. P.; Zhang, H.; Yi, E.; Aebersold, R.; McIntosh, M. Biostatistics 2006, 8, 357-367.