A regularized method for peptide quantification

Journal of Proteome Research

Volumn 9, Issue 5, 2010, Pages 2705-2712

  Yang, Chao ^a   Yang, Can ^a   Yu, Weichuan ^a  

^a HONG KONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Hong Kong)

Author keywords

Intensity variation; Optimization; Overlapping peptides; Peptide quantification

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; CONTROLLED STUDY; ELUTION; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; RADIOISOTOPE DISTRIBUTION; SIMULATION;

ALGORITHMS; COMPUTER SIMULATION; LEAST-SQUARES ANALYSIS; NORMAL DISTRIBUTION; PEPTIDE FRAGMENTS; PROTEINS; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 77952063827     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr100181g     Document Type: Article

References (26)

1. Aebersold, R.; Mann, M. Nature 2003, 422, 198-207
2. MacCoss, M. J.; Matthews, D. E. Anal. Chem. 2005, 77, 294-302
3. Li, X. J.; Zhang, H.; Ranish, J. A.; Aebersold, R. Anal. Chem. 2003, 75, 6648-6657
4. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Nat. Biotechnol. 1999, 17, 994-999
5. Ross, P. L. Mol. Cell. Proteomics 2004, 3, 1154-1169
6. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Mol. Cell. Proteomics 2002, 1, 376-386
7. Ryu, S.; Gallis, B.; A., G. Y.; Shaffer, S. A.; Radulovic, D.; Goodlett, D. R. Cancer Inform. 2008, 6, 243-255
8. Du, P.; Angeletti, R. H. Anal. Chem. 2006, 78, 3385-3392
9. Leptos, K. C.; Sarracino, D. A.; Jaffe, J. D.; Krastins, B.; Church, G. M. Proteomics 2006, 6, 1770-1782
10. Schulz-Trieglaff, O.; Hussong, R.; Gröpl, C.; Hildebrandt, A.; Reinert, K. Lect. Notes Comput. Sci. 2007, 4453, 473-487
11. Timm, W.; Scherbart, A.; Böcker, S.; Kohlbacher, O.; Nattkemper, T. W. BMC Bioinform. 2008, 9, 443
12. Vandenbogaert, M.; Li-Thiao- Tě, S.; Kaltenbach, H. M.; Zhang, R.; Aittokallio, T.; Schwikowski, B. Proteomics 2008, 8, 650-672
13. Mueller, L. N.; Brusniak, M. Y.; Mani, D. R.; Aebersold, R. J. Proteome Res. 2008, 7, 51-61
14. MacCoss, M. J.; Wu, C. C.; Liu, H.; Sadygov, R.; Yates, J. R., III Anal. Chem. 2003, 75, 6912-6921
15. Park, S. K.; Venable, J. D.; Xu, T.; Yates, J. R., III Nat. Methods 2008, 5, 319-322
16. Wang, P.; Tang, H.; Fitzgibbon, M. P.; Mcintosh, M.; Coram, M.; Zhang, H.; Yi, E.; Aebersold, R. Biostatistics 2007, 8, 357-367
17. Tibshirani, R. J. R. Stat. Soc.: Ser. B 1996, 58, 267-288
18. Rockwood, A. L.; Van Orman, J. R.; Dearden, D. V. J. Am. Soc. Mass Spectrom. 2004, 15, 12-21
19. Rockwood, A. L.; Haimi, P. J. Am. Soc. Mass Spectrom. 2006, 17, 415-419
20. Rockwood, A. L.; Van Orden, S. L. Anal. Chem. 1996, 68, 2027-2030
21. Valkenborg, D.; Jansen, I.; Burzykowski, T. J. Am. Soc. Mass Spectrom. 2008, 19, 703-712
22. Schulz-Trieglaff, O.; Pfeifer, N.; Gröpl, C.; Kohlbacher, O.; Reinert, K. BMC Bioinform. 2008, 9, 423
23. Du, P.; Stolovitzky, G.; Horvatovich, P.; Bischoff, R.; Lim, J.; Suits, F. Bioinformatics 2008, 24, 1070-1077
24. Klimek, J.; Eddes, J. S.; Hohmann, L.; Jackson, J.; Peterson, A.; Letarte, S.; Gafken, P. R.; Katz, J. E.; Mallick, P.; Lee, H.; Schmidt, A.; Ossola, R.; Eng, J. K.; Aebersold, R.; Martin, D. B. J. Proteome Res. 2008, 7, 96-103
25. Eng, J. K.; McCormack, A. L.; Yates, J. R., III J. Am. Soc. Mass Spectrom. 1994, 5, 976-989
26. Lu, B.; Motoyama, A.; Ruse, C.; Venable, J.; Yates, J. R., III Anal. Chem. 2008, 80, 2018-2025