Refinements to label free proteome quantitation: How to deal with peptides shared by multiple proteins

Analytical Chemistry

Volumn 82, Issue 6, 2010, Pages 2272-2281

  Zhang, Ying ^a   Wen, Zhhui ^a   Washburn, Michael P ^a,b   Florens, Laurence ^a  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXHAUSTIVE LISTS; LABEL FREE; PROTEIN SAMPLES; PROTEOMES; QUANTITATIVE ANALYSIS; QUANTITATIVE PROTEOMICS; SHOTGUN PROTEOMICS;

LABELS; MOLECULAR BIOLOGY;

PEPTIDES;

ALBUMINOID; FUNGAL PROTEIN; PEPTIDE; PROTEIN; PROTEOME;

ANIMAL; ARTICLE; CATTLE; CHEMISTRY; EVALUATION; HUMAN; METHODOLOGY; MOUSE; PROTEOMICS; RABBIT; RAT; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SWINE;

ALBUMINS; ANIMALS; CATTLE; FUNGAL PROTEINS; HUMANS; MICE; PEPTIDES; PROTEINS; PROTEOME; PROTEOMICS; RABBITS; RATS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SWINE;

EID: 77949795829     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac9023999     Document Type: Article

References (18)

1. Nesvizhskii, A. I.; Aebersold, R. Mol. Cell. Proteomics 2005, 4,1419-1440.
2. Zhang, B.; Chambers, M. C.; Tabb, D. L.J. Proteome Res. 2007, 6, 3549-3557.
3. Usaite, R.; Wohlschlegel, J.; Venable, J. D.; Park, S. K.; Nielsen, J.; Olsson, L.; Yates, J. R., III J. Proteome Res. 2008, 7, 266-275.
4. Jin, S.; Daly, D. S.; Springer, D. L.; Miller, J. H.J. Proteome Res. 2008, 7, 164-169.
5. Liu, W. L.; Coleman, R. A.; Grob, P.; King, D. S.; Florens, L.; Washburn, M. P.; Geles, K. G.; Yang, J. L.; Ramey, V.; Nogales, E.; Tjian, R. Mol. Cell 2008, 29, 81-91.
6. Zybailov, B.; Rutschow, H.; Friso, G.; Rudella, A.; Emanuelsson, O.; Sun, Q.; van Wijk, K. J. PLoS One 2008, 3, e1994.
7. Florens, L.; Carozza, M. J.; Swanson, S. K.; Fournier, M.; Coleman, M. K.; Workman, J. L.; Washburn, M. P. Methods 2006, 40, 303-311.
8. Paoletti, A. C.; Parmely, T. J.; Tomomori-Sato, C.; Sato, S.; Zhu, D.; Conaway, R. C.; Conaway, J. W.; Florens, L.; Washburn, M. P. Proc. Natl. Acad Sci. U.S.A. 2006, 103, 18928-18933.
9. Zybailov, B.; Mosley, A. L.; Sardiu, M. E.; Coleman, M. K.; Florens, L; Washburn, M. P. J. Proteome Res. 2006, 5, 2339-2347.
10. Florens, L.; Washburn, M. P. Methods Mol. Biol. 2006, 328, 159-175.
11. Eng, J.; McCormack, A. L.; Yates, J. R., III J. Am Soc. Mass Spectrom. 1994, 5, 976-989.
12. Tabb, D. L.; McDonald, W. H.; Yates, J. R.J. Proteome Res. 2002, 1, 2126.
13. Durbin, B. P.; Hardin, J. S.; Hawkins, D. M.; Rocke, D. M. Bioinformatics 2002, 18, S105-110.
14. Lin, S. M.; Du, P.; Huber, W.; Kibbe, W. A. Nucleic Acids Res. 2008, 36, ell.
15. Pavelka, N.; Fournier, M. L.; Swanson, S. K.; Pelizzola, M.; RicdardiCastagnoli, P.; Florens, L.; Washburn, M. P. Mol. Cell. Proteomics 2008, 7, 631-644.
16. Sardiu, M. E.; Cai, Y.; Jin, J.; Swanson, S. K.; Conaway, R. C.; Conaway, J. W.; Florens, L.; Washburn, M. P. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1454-1459.
17. Skaar, J. R.; Florens, L.; Tsutsumi, T.; Arai, T.; Tron, A.; Swanson, S. K.; Washburn, M. P.; DeCaprio, J. A. Cancer Res. 2007, 67, 2006-2014.
18. Sardiu, M. E.; Gilmore, J. M.; Carrozza, M. J.; Li, B.; Workman, J. L; Florens, L.; Washburn, M. P. PLoS One 2009, 4, e7310.