A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

Analytical Chemistry

Volumn 83, Issue 16, 2011, Pages 6135-6140

  Stanley, Jeffrey R ^a   Adkins, Joshua N ^b   Slysz, Gordon W ^b   Monroe, Matthew E ^b   Purvine, Samuel O ^b   Karpievitch, Yuliya V ^b   Anderson, Gordon A ^b   Smith, Richard D ^b   Dabney, Alan R ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE MASS; COMMAND LINE; CONFIDENCE MEASURE; FALSE DISCOVERY RATE; GRAPHICAL APPLICATIONS; LC-MS/MS; PEPTIDE IDENTIFICATION; PEPTIDE SEQUENCES; PROTEOMICS; STATISTICAL TOOLS; TAG IDENTIFICATION; TIME TAG;

MOLECULAR BIOLOGY; STATISTICAL MECHANICS;

PEPTIDES;

PEPTIDE;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; LIQUID CHROMATOGRAPHY; METHODOLOGY; PROBABILITY; PROTEIN DATABASE; PROTEOMICS; STANDARD; STATISTICAL MODEL; STATISTICS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; CHROMATOGRAPHY, LIQUID; DATABASES, PROTEIN; MODELS, STATISTICAL; PEPTIDES; PROBABILITY; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 80051746323     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac2009806     Document Type: Article

References (33)

1. Eng, J. K.; McCormack, A. L.; Yates, J. R., I. J. Am. Soc. Mass Spectrom. 1994, 976-989
2. Craig, R.; Beavis, R. C. Bioinformatics 2004, 1466-1467
3. Geer, L. Y.; Markey, S. P.; Kowalak, J. A.; Wagner, L.; Xu, M.; Maynard, D. M.; Yang, X.; Shi, W.; Bryant, S. H. J. Proteome Res. 2004, 958-964
4. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Electrophoresis 1999, 3551-3567
5. Tanner, S.; Shu, H.; Frank, A.; Wang, L.-C.; Zandi, E.; Mumby, M.; Pevzner, P. A.; Bafna, V. Anal. Chem. 2005, 4626-4639
6. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Anal. Chem. 2002, 5383-5392
7. Choi, H.; Ghosh, D.; Nesvizhskii, A. I. J. Proteome Res. 2008, 286-292
8. López-Ferrer, D.; Martìnez-Bartolomè, S.; Villar, M.; Campillos, M.; Martìn-Maroto, F.; Vàzquez, J. Anal. Chem. 2004, 6853-6860
9. Shen, C.; Wang, Z.; Shankar, G.; Zhang, X.; Li, L. Bioinformatics 2008, 202-208
10. Sadygov, R. G.; John R. Yates, I. Anal. Chem. 2003, 3792-3798
11. Kim, S.; Gupta, N.; Pevzner, P. A. J. Proteome Res. 2008, 3354-3363
12. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. Anal. Chem. 2003, 4646-4658
13. Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Paša-Tolic̀, L.; Shen, Y.; Conrads, T. P.; Veenstra, T. D.; Udseth, H. R. Proteomics 2002, 513-523
14. Zimmer, J. S. D.; Monroe, M. E.; Qian, W.-J.; Smith, R. D. Mass Spectrom. Rev. 2006, 450-482
15. Jaffe, J. D.; Mani, D. R.; Leptos, K. C.; Church, G. M.; Gillette, M. A.; Carr, S. A. Mol. Cell. Proteomics 2006, 1927-1941
16. Xu, D.; Suenaga, N.; Edelmann, M. J.; Fridman, R.; Muschel, R. J.; Kessler, B. M. Mol. Cell. Proteomics 2008, 2215-2228
17. Mueller, L. N.; Rinner, O.; Schmidt, A.; Letarte, S.; Bodenmiller, B.; Brusniak, M.-Y.; Vitek, O.; Aebersold, R.; Müller, M. Proteomics 2007, 3470-3480
18. May, D.; Fitzgibbon, M.; Liu, Y.; Holzman, T.; Eng, J.; Kemp, C. J.; Whiteaker, J.; Paulovich, A.; McIntosh, M. J. Proteome Res. 2007, 2685-2694
19. Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Paša-Tolic̀, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y.; Zhao, R.; Smith, R. D. Anal. Chem. 2003, 1039-1048
20. Strittmater, E. F.; Ferguson, P. L.; Tang, K.; Smith, R. D. J. Am. Soc. Mass Spectrom. 2003, 14, 980-991
21. Washburn, M. P.; Wolters, D.; Yates, J. R., I. Nat. Biotechnol. 2001, 242-247
22. Qian, W.-J.; Liu, T.; Monroe, M. E.; Strittmatter, E. F.; Jacobs, J. M.; Kangas, L. J.; Petritis, K.; Camp, D. G., I.; Smith, R. D. J. Proteome Res. 2005, 53-62
23. Keller, A.; Purvine, S.; Nesvizhskii, A. I.; Stolyar, S.; Goodlett, D. R.; Kolker, E. OMICS 2002, 6, 207-212
24. Petyuk, V. A.; Qian, W.-J.; Chin, M. H.; Wang, H.; Livesay, E. A.; Monroe, M. E.; Adkins, J. N.; Jaitly, N.; Anderson, D. J.; Camp, D. G., I.; Smith, D. J.; Smith, R. D. Genome Res. 2007, 328-336
25. Tolmachev, A. V.; Monroe, M. E.; Jaitly, N.; Petyuk, V. A.; Adkins, J. N.; Smith, R. D. Anal. Chem. 2006, 8374-8385
26. Norbeck, A. D.; Monroe, M. E.; Adkins, J. N.; Anderson, K. K.; Daly, D. S.; Smith, R. D. J. Am. Soc. Mass Spectrom. 2005, 1239-1249
27. May, D.; Liu, Y.; Law, W.; Fitzgibbon, M.; Wang, H.; Hanash, S.; McIntosh, M. J. Proteome Res. 2008, 5148-5156
28. Jaitly, N.; Adkins, J. N.; Monroe, M. E.; Norbeck, A. D.; Mottaz, H. M.; Dabney, A. R.; Lipton, M. S.; Anderson, G. A.; Smith, R. D. A Statistical Approach to Quantifying Uncertainties in the AMT Tag Pipeline. In Proceedings of the 55th ASMS Conference on Mass Spectrometry and Allied Topics; American Society for Mass Spectrometry (ASMS): Santa Fe, NM, 2008.
29. Jaitly, N.; Monroe, M. E.; Petyuk, V. A.; Clauss, T. R. W.; Adkins, J. N.; Smith, R. D. Anal. Chem. 2006, 7397-7409
30. Anderson, K. K.; Monroe, M. E.; Daly, D. S. Proteome Sci. 2006, 4, 1 (DOI: 10.1186/1147-5956-4-1).
31. Monroe, M. E.; Tolic̀, N.; Jaitly, N.; Shaw, J. L.; Adkins, J. N.; Smith, R. D. Bioinformatics 2007, 2021-2023
32. Mayampurath, A. M.; Jaitly, N.; Purvine, S. O.; Monroe, M. E.; Auberry, K. J.; Adkins, J. N.; Smith, R. D. Bioinformatics 2008, 24, 1021-1023
33. Elias, J. E.; Gygi, S. P. Nat. Methods 2007, 207-214