Increased protein identification capabilities through novel tandem MS calibration strategies

Journal of Proteome Research

Volumn 4, Issue 4, 2005, Pages 1434-1441

  Wu, Si ^a   Kaiser, Nathan K ^a   Meng, Da ^a   Anderson, Gordon A ^b   Zhang, Kai ^a   Bruce, James E ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

COFI; FTICR MS; LC MS MS; Multiplexed CID; Protein identification; Proteomics

Indexed keywords

PEPTIDE; PROTEIN;

ACCURACY; ARTICLE; CALIBRATION; FREQUENCY MODULATION; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; ANGIOTENSIN I; ANIMALS; BRADYKININ; MASS SPECTROMETRY; MOLECULAR WEIGHT; PEPTIDE FRAGMENTS; PROTEINS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; SUBSTANCE P;

EID: 23944490667     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0501057     Document Type: Article

References (38)

1. Shevchenko, A.; Jensen, O. N.; Podtelejnikov, A. V.; Sagliocco, F.; Wilm, M.; Vorm, O.; Mortensen, P.; Boucherie, H.; Mann, M. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14440-14445.
2. Wolters, D. A.; Washburn, M. P.; Yates, J. R., 3rd. Anal. Chem. 2001, 73, 5683-5690.
3. Aebersold, R.; Goodlett, D. R. Chem. Rev. 2001, 101, 269-295.
4. Kelleher, N. L. Anal. Chem. 2004, 76, 197A-203A.
5. Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Pasa-Tolic, L.; Smith, R. D. Anal Chem. 2000, 72, 3349-3354.
6. Yates, J. R., 3rd Trends Genet. 2000, 16, 5-8.
7. Clauser, K. R.; Baker, P.; Burlingame, A. L. Anal. Chem. 1999, 71, 2871-2882.
8. He, F.; Emmett, M. R.; Hakansson, K.; Hendrickson, C. L.; Marshall, A. G. J. Proteome Res. 2004, 3, 61-67.
9. Goodlett, D. R.; Bruce, J. E.; Anderson, G. A.; Rist, B.; Pasa-Tolic, L.; Fiehn, O.; Smith, R. D.; Aebersold, R. Anal. Chem. 2000, 72, 1112-1118.
10. Marshall, A. G.; Hendrickson, C. L.; Jackson, G. S. Mass Spectrom. Rev. 1998, 17, 1-35.
11. Bogdanov, B.; Smith, R. D. Mass Spectrom Rev. 2005, 24, 168-200.
12. Ledford, E. B., Jr.; Rempel, D. L.; Gross, M. L. Anal. Chem. 1984, 56, 2744-2748.
13. Ledford, E. B., Jr.; Rempel, D. L.; Gross, M. L. Int. J. Mass Spectrom. Ion Proc. 1984, 55, 143-154.
14. Easterling, M. L.; Mize, T. H.; Amster, I. J. Anal. Chem. 1999, 71, 624-632.
15. Bogdanov, B.; Smith, R. D. Mass Spectrom. Rev. 2004, 24, 168-200.
16. Bruce, J. E.; Anderson, G. A.; Brands, M. D.; Pasa-Tolic, L.; Smith, R. D. J. Am. Soc. Mass Spectrom. 2000, 11, 416-421.
17. Taylor, P. K.; Amster, I. J. Int. J. Mass Spectrom. 2003, 222, 351-361.
18. Flora, J. W.; Hannis, J. C.; Muddiman, D. C. Anal. Chem. 2001, 73, 1247-1251.
19. Lee, S. W.; Berger, S. J.; Martinovic, S.; Pasa-Tolic, L.; Anderson, G. A.; Shen, Y.; Zhao, R.; Smith, R. D. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5942-5947.
20. Meng, F.; Cargile, B. J.; Miller, L. M.; Forbes, A. J.; Johnson, J. R.; Kelleher, N. L. Nat. Biotechnol. 2001, 19, 952-957.
21. Liu, C.; Tolic, L. P.; Hofstadler, S. A.; Harms, A. C.; Smith, R. D.; Rang, C.; Sinha, N. Anal. Biochem. 1998, 262, 67-76.
22. Kaiser, N. K.; Anderson, G. A.; Bruce, J. E. J. Am. Soc. Mass Spectrom 2005, 16, 463-470.
23. Belov, M. E.; Zhang, R.; Strittmatter, E. F.; Prior, D. C.; Tang, K.; Smith, R. D. Anal. Chem. 2003, 75, 4195-4205.
24. Syka, J. E.; Marto, J. A.; Bai, D. L.; Horning, S.; Senko, M. W.; Schwartz, J. C.; Ueberheide, B.; Garcia, B.; Busby, S.; Muratore, T.; Shabanowitz, J.; Hunt, D. F. J. Proteome Res. 2004, 3, 621-626.
25. Senko, M.; Zabrouskov, V.; Lange, O.; Wieghaus, A.; Griep-Raming, J.; S., H. 52nd ASMS Conference on Mass Spectrometry and Allied Topics, Nashville, TN 2004.
26. Polfer, N. C.; Haselmann, K. F.; Zubarev, R. A.; Langridge-Smith, P. R. Rapid Commun. Mass Spectrom. 2002, 16, 936-943.
27. Anderson, G. A.; Bruce, J. E.; Smith, R. D., ICR-2LS, Version 2.18 ed.; Pacific Northwest National Laboratory: Richmond, WA, 1996 released.
28. Mann, M.; Wilm, M. Anal. Chem. 1994, 66, 4390-4399.
29. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Electrophoresis 1999, 20, 3551-3567.
30. Yan, B.; Pan, C.; Olman, V. N.; Hettich, R. L.; Xu, Y. Bioinformatics 2004.
31. Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.
32. Rorabacher, D. B. Anal. Chem. 1991, 63, 139-146.
33. Purvine, S.; Eppel, J. T.; Yi, E. C.; Goodlett, D. R. Proteomics 2003, 3, 847-850.
34. Masselon, C.; Pasa-Tolic, L.; Lee, S. W.; Li, L.; Anderson, G. A.; Harkewicz, R.; Smith, R. D. Proteomics 2003, 3, 1279-1286.
35. Berger, S. J.; Lee, S. W.; Anderson, G. A.; Pasa-Tolic, L.; Tolic, N.; Shen, Y.; Zhao, R.; Smith, R. D. Anal. Chem. 2002, 74, 4994-5000.
36. Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Masselon, C.; Pasa-Tolic, L.; Shen, Y.; Udseth, H. R. Omics 2002, 6, 61-90.
37. Li, L.; Masselon, C. D.; Anderson, G. A.; Pasa-Tolic, L.; Lee, S. W.; Shen, Y.; Zhao, R.; Lipton, M. S.; Conrads, T. P.; Tolic, N.; Smith, R. D. Anal. Chem. 2001, 73, 3312-3322.
38. Masselon, C.; Anderson, G. A.; Harkewicz, R.; Bruce, J. E.; Pasa-Tolic, L.; Smith, R. D. Anal. Chem. 2000, 72, 1918-1924.