Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics

Journal of Proteome Research

Volumn 5, Issue 4, 2006, Pages 1003-1009

  Xie, Hongwei ^a   Griffin, Timothy J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Database searching; False positive rate; Linear ion trap; Peptide identification; Peptide isoelectric point; Proteomics; Tandem mass spectrometry

Indexed keywords

PROTEIN; SALIVA PROTEIN; TRYPSIN;

ARTICLE; DATA ANALYSIS; FALSE POSITIVE RESULT; FEMALE; FILTRATION; HUMAN; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; ION TRAP MASS SPECTROMETRY; ISOELECTRIC POINT; LINEAR ION TRAP; NORMAL HUMAN; PEPTIDE ANALYSIS; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEOMICS; SEQUENCE HOMOLOGY; SPECTROMETER; TECHNIQUE; TWO DIMENSIONAL LINEAR ION TRAP MASS SPECTROMETRY;

AMINO ACID SEQUENCE; CHEMISTRY, PHYSICAL; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; ELECTROPHORESIS, CAPILLARY; FALSE POSITIVE REACTIONS; FEMALE; FILTRATION; HUMANS; HYDROGEN-ION CONCENTRATION; IONS; MASS SPECTROMETRY; MICROELECTRODES; MOLECULAR WEIGHT; PEPTIDES; PROTEOMICS; SALIVARY PROTEINS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, PROTEIN; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TRYPSIN;

EID: 33645790020     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050472i     Document Type: Article

References (38)

1. Aebersold, R.; Mann, M. Nature 2003, 422, 198-207.
2. Yates, J. R., 3rd Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 297-316.
3. Wolters, D. A.; Washburn, M. P.; Yates, J. R., 3rd Anal. Chem. 2001, 73, 5683-5690.
4. Washburn M. P.; Wolters, D. A.; Yates, J. R., 3rd Nat. Biotechnol. 2001, 19, 242-247.
5. Schwartz, J.C.; Senko, M. W.; Syka, J. E. J. Am. Soc. Mass Spectrom. 2002, 13, 659-669.
6. Mayya V.; Rezaul, K.; Cong, Y. S.; Han, D. Mol. Cell. Proteomics 2005, 4, 214-223.
7. Eng, J.; McCormack, A. L.; Yates, J. R., 3rd J Am. Soc. Mass Spectrom. 1994, 5, 976-989.
8. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Electrophoresis 1999, 20, 3551-3567.
9. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. J. Proteome Res. 2003, 2, 43-50.
10. Cargile, B. J.; Bundy, J. L.; Stephenson, J. L., Jr. J. Proteome Res. 2004, 3, 1082-1085.
11. Sadygov, R. G.; Yates, J. R., 3rd Anal. Chem. 2003, 75, 3792-3798.
12. Sadygov, R. G.; Liu, H.; Yates, J. R., 3rd Anal. Chem. 2004, 76, 1664-1671.
13. Bafna, V.; Edwards, N. Bioinformatics 2001, 17 Suppl 1, S13-21.
14. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Anal. Chem. 2002, 74, 5383-5392.
15. Krivankova L.; Bocek P. Electrophoresis 1998, 19, 1064-1074.
16. Xie H.; Rhodus, N. L.; Griffin, R. J.; Carlis, J. V.; Griffin, T. J. Mol. Cell. Proteomics 2005, 4, 1826-1830.
17. Rhodus, N. L.; Cheng, B.; Myers, S.; Bowels, W.; Ho, V.; Ondrey, F. Clin. Immunol. 2005, 114, 278-283.
18. Xie, H.; Bandhakavi, S.; Griffin, T. J. Anal. Chem. 2005, 77, 3198-3207.
19. Wilmarth, P. A.; Riviere, M. A.; Rustvold D. L.; Lauten, J. D.; Madden, T. E.; David, L. L. J. Proteome Res. 2004, 3, 1017-1134.
20. Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Nat. Biotechnol. 2001, 19, 946-951.
21. Shimura, K.; Kamiya, K.; Matsumoto, H.; Kasai, K. Anal. Chem. 2002, 74, 1046-1053.
22. Yao, Y.; Berg, E. A.; Costello, C. E.; Troxler, R. F.; Oppenheim, F. G. J. Biol. Chem. 2003, 278, 5300-5308.
23. Vitorino, R.; Lobo, M. J.; Ferrer-Correira, A. J.; Dubin, J. R.; Tomer, K. B.; Domingues, P. M.; Amado, F. M. Proteomics 2004, 4, 1109-1115.
24. Ghafouri, B.; Tagesson, C.; Lindahl, M. Proteomics 2003, 3, 1003-1015.
25. Hardt, M.; Thomas, L. R.; Dixon, S. E.; Newport, G.; Agabian, N.; Prakobphol, A.; Hall, S. C.; Witkowska, H. E.; Fisher, S. J. Biochemistry, 2005, 44, 2885-2899.
26. Hu, S.; Xie, Y.; Ramachandran, P.; Ogorzalek Loo, R. R.; Li, Y.; Loo, J. A.; Wong, D. T. Proteomics 2005, 5, 1714-1728.
27. Kapp, E. A.; Schutz, F.; Connolly, L. M.; Chakel, J. A.; Meza, J. E.; Miller, C. A.; Fenyo, D.; Eng, J. K.; Adkins, J. N.; Omenn, G. S.; Simpson, R. J. Proteomics 2005, 5, 3475-3490.
28. Hardt, M.; Witkowska E.; Webb, S.; Thomas, L. R.; Dixon S. E.; Hall, S. C.; Fisher, S. J. Anal. Chem. 2005, 77, 4947-4954.
29. Heller, M.; Ye, M.; Michel, P. E.; Morier, P.; Stalder, D.; Jünger, M. A.; Aebersold, R.; Reymond, F.; Rossier, J. S. J. Proteome Res. 2005, 4, 2273-2282.
30. Qian, W. J.; Camp, D. G., II.; Smith, R. D. Expert Rev. Proteomics 2004, 1, 87-95.
31. Ferguson, P. L.; Smith, R. D. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 399-424.
32. Lipton, M. S.; Pasa-Tolic, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daily, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore R. J.; Romine, M. F.; Shen, Y.; Stritmatter, E.; Tolic, N.; Udseth, H. R.; Venkateswaran, A.; Wong, K. K.; Zhao, R.; Smith, R. D. PNAS 2002, 99, 11049-11054.
33. Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Pasa-Tolic, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y.; Zhao, R.; Smith, R. D. Anal Chem. 2003, 75, 1039-1048.
34. Palmblad, M.; Ramstrom, M.; Markides, K. E.; Hakansson, P.; Bergquist, J. Anal. Chem. 2002, 74, 5826-5850.
35. Shen, Y.; Zhao, R.; Belov, M. E.; Conrads, T. P.; Anderson, G. A.; Tang, K.; Pasa-Tolic, L.; Veenstra, T. D.; Lipton, M. S.; Udseth, H. R.; Smith, R. D. Anal. Chem. 2001, 73, 1766-1775.
36. Cargile, B. J.; Tally, D. L.; Stephenson, J. L., Jr. Electrophoresis 2004, 25, 936-945.
37. Cargile, B. J.; Bundy, J. L.; Freeman, T. W.; Stephenson, J. L., Jr. J. Proteome Res. 2004, 3, 112-119.
38. Carr, S.; Aebersold, R.; Baldwin, M.; Burlingame, A.; Clauser, K.; Nesvizhskii, A. Mol. Cell. Proteomics 2004, 3, 531-533.