Optimized method for computing 18O/16O Ratios of Differentially Stable-isotope labeled peptides in the context of postdigestion 18O exchange/labeling

Analytical Chemistry

Volumn 82, Issue 13, 2010, Pages 5878-5886

  Ye, Xiaoying ^a   Luke, Brian T ^a   Johann, Donald J ^b   Ono, Akira ^c   Prieto, Darue A ^a   Chan, King C ^a   Issaq, Haleem J ^a   Veenstra, Timothy D ^a   Blonder, Josip ^a  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY AND PRECISION; ALGORITHMIC METHODS; APRIORI; BOVINE SERUM ALBUMINS; CARBOXYL TERMINUS; COMPUTATIONAL APPROACH; DETERGENT-RESISTANT MEMBRANES; EVOLUTIONARY PROGRAMMING; ISOTOPIC SPECIES; MATHEMATICAL APPROACH; O INCORPORATION; OPTIMAL VALUES; OXYGEN EXCHANGE; PEAK INTENSITY; PEPTIDE PAIRS; RETENTION TIME; SHOTGUN PROTEOMICS; STABLE-ISOTOPE LABELING; SUBSTRATE AFFINITY; TRAPEZOIDAL RULES; WILD TYPES;

BODY FLUIDS; COMPUTER PROGRAMMING; ENZYMES; ISOTOPES; MOLECULAR BIOLOGY; OPTIMIZATION; OXYGEN; POISSON DISTRIBUTION; PROGRAM INTERPRETERS;

PEPTIDES;

BOVINE SERUM ALBUMIN; GAG PROTEIN; OXYGEN; PEPTIDE; TRYPSIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CATTLE; CELL MEMBRANE; CHEMISTRY; HELA CELL; HUMAN; ISOTOPE LABELING; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; BOVINAE; HELA CELL LINE; PROCEDURES;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; CATTLE; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; HELA CELLS; HUMANS; ISOTOPE LABELING; MEMBRANE MICRODOMAINS; MOLECULAR SEQUENCE DATA; OXYGEN ISOTOPES; PEPTIDES; SERUM ALBUMIN, BOVINE; TRYPSIN;

EID: 77954198163     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac101284c     Document Type: Article

References (36)

1. Reynolds, K. J. and Fenselau, C. Curr. Protoc. Protein Sci. 2004, DOI: 10.1002/0471140864.ps2304s34, Unit 23.4.
2. Ye, X., Luke, B., Andresson, T., and Blonder, J. Brief. Funct. Genomics Proteomics 2009, 8, 136-144
3. Schnolzer, M., Jedrzejewski, P., and Lehmann, W. D. Electrophoresis 1996, 17, 945-953
4. Reynolds, K. J., Yao, X., and Fenselau, C. J. Proteome Res. 2002, 1, 27-33
5. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. Nat. Biotechnol. 1999, 17, 994-999
6. Back, J. W., Notenboom, V., de Koning, L. J., Muijsers, A. O., Sixma, T. K., de Koster, C. G., and de Jong, L. Anal. Chem. 2002, 74, 4417-4422
7. Qian, W. J., Monroe, M. E., Liu, T., Jacobs, J. M., Anderson, G. A., Shen, Y., Moore, R. J., Anderson, D. J., Zhang, R., Calvano, S. E., Lowry, S. F., Xiao, W., Moldawer, L. L., Davis, R. W., Tompkins, R. G., Camp, D. G., 2nd, and Smith, R. D. Mol. Cell. Proteomics 2005, 4, 700-709
8. Zang, L., Palmer Toy, D., Hancock, W. S., Sgroi, D. C., and Karger, B. L. J. Proteome Res. 2004, 3, 604-612
9. Stockwin, L. H., Blonder, J., Bumke, M. A., Lucas, D. A., Chan, K. C., Conrads, T. P., Issaq, H. J., Veenstra, T. D., Newton, D. L., and Rybak, S. M. J. Proteome Res. 2006, 5, 2996-3007
10. Blonder, J., Yu, L. R., Radeva, G., Chan, K. C., Lucas, D. A., Waybright, T. J., Issaq, H. J., Sharom, F. J., and Veenstra, T. D. J. Proteome Res. 2006, 5, 349-360
11. Hedstrom, L. Chem. Rev. 2002, 102, 4501-4524
12. Heller, M., Mattou, H., Menzel, C., and Yao, X. J. Am. Soc. Mass Spectrom. 2003, 14, 704-718
13. Wang, Y. K., Ma, Z., Quinn, D. F., and Fu, E. W. Anal. Chem. 2001, 73, 3742-3750
14. Hajkova, D., Rao, K. C., and Miyagi, M. J. Proteome Res. 2006, 5, 1667-1673
15. Eckel-Passow, J. E., Oberg, A. L., Therneau, T. M., Mason, C. J., Mahoney, D. W., Johnson, K. L., Olson, J. E., and Bergen, H. R., 3rd Bioinformatics 2006, 22, 2739-2745
16. Halligan, B. D., Slyper, R. Y., Twigger, S. N., Hicks, W., Olivier, M., and Greene, A. S. J. Am. Soc. Mass Spectrom. 2005, 16, 302-306
17. Horn, D. M., Zubarev, R. A., and McLafferty, F. W. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332
18. Mason, C. J., Therneau, T. M., Eckel-Passow, J. E., Johnson, K. L., Oberg, A. L., Olson, J. E., Nair, K. S., Muddiman, D. C., and Bergen, H. R., 3rd. Mol. Cell. Proteomics 2007, 6, 305-318
19. Ramos-Fernandez, A., Lopez-Ferrer, D., and Vazquez, J. Mol. Cell. Proteomics 2007, 6, 1274-1286
20. Shinkawa, T., Taoka, M., Yamauchi, Y., Ichimura, T., Kaji, H., Takahashi, N., and Isobe, T. J. Proteome Res. 2005, 4, 1826-1831
21. Stewart, I. I., Thomson, T., and Figeys, D. Rapid Commun. Mass Spectrom. 2001, 15, 2456-2465
22. Park, S. M., Hwang, I. K., Kim, S. Y., Lee, S. J., Park, K. S., and Lee, S. T. Proteomics 2006, 6, 1192-1199
23. Mueller, L. N., Brusniak, M. Y., Mani, D. R., and Aebersold, R. J. Proteome Res. 2008, 7, 51-61
24. Nguyen, K. L., llano, M., Akari, H., Miyagi, E., Poeschla, E. M., Strebel, K., and Bour, S. Virology 2004, 319, 163-175
25. Ono, A., Waheed, A. A., Joshi, A., and Freed, E. O. J. Virol. 2005, 79, 14131-14140
26. Blonder, J., Hale, M. L., Chan, K. C., Yu, L. R., Lucas, D. A., Conrads, T. P., Zhou, M., Popoff, M. R., Issaq, H. J., Stiles, B. G., and Veenstra, T. D. J. Proteome Res. 2005, 4, 523-531
27. Blonder, J., Chan, K. C., Issaq, H. J., and Veenstra, T. D. Nat. Protoc. 2006, 1, 2784-2790
28. Ono, A. and Freed, E. O. J. Virol. 1999, 73, 4136-4144
29. Lindwasser, O. W. and Resh, M. D. J. Virol. 2001, 75, 7913-7924
30. Yao, X., Afonso, C., and Fenselau, C. J. Proteome Res. 2003, 2, 147-152
31. Jorge, I., Navarro, P., Martinez-Acedo, P., Nunez, E., Serrano, H., Alfranca, A., Redondo, J. M., and Vazquez, J. Mol. Cell. Proteomics 2009, 8, 1130-1149
32. Moulder, R., Filen, J. J., Salmi, J., Katajamaa, M., Nevalainen, O. S., Oresic, M., Aittokallio, T., Lahesmaa, R., and Nyman, T. A. Proteomics 2005, 5, 2748-2760
33. Freed, E. O. Virology 1998, 251, 1-15
34. Takefman, D. M., Spear, G. T., Saifuddin, M., and Wilson, C. A. J. Virol. 2002, 76, 1999-2002
35. Hu, W., Yu, Q., Hu, N., Byrd, D., Amet, T., Shikuma, C., Shiramizu, B., Halperin, J. A., and Qin, X. J. Immunol. 2009, 184, 359-368
36. Brugger, B., Glass, B., Haberkant, P., Leibrecht, I., Wieland, F. T., and Krausslich, H. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 2641-2646