Alternative methods for verifying the results of the mass spectrometric identification of peptides in shotgun proteomics

Journal of Analytical Chemistry

Volumn 65, Issue 14, 2010, Pages 1462-1468

  Goloborod'ko A A ^a   Mayerhofer, C ^b   Zubarev, A R ^b   Tarasova, I A ^a   Gorshkov, A V ^a   Zubarev, R A ^b   Gorshkov, M V ^a  

^a SEMENOV INSTITUTE OF CHEMICAL PHYSICS   (Russian Federation)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

liquid chromatography; Mascot; mass spectrometry; proteomics; retention time prediction

Indexed keywords

ALGORITHMS; CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETERS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; SEARCH ENGINES; SPECTROMETRY;

CHROMATOGRAPHIC RETENTION; MASCOT; MASS SPECTROMETRIC DATA; MASS SPECTROMETRIC IDENTIFICATION; PEPTIDE IDENTIFICATION; PROTEOMICS; RETENTION TIME PREDICTION; TANDEM MASS SPECTRA;

PROTEINS;

EID: 84973883055     PISSN: 10619348     EISSN: None     Source Type: Journal    
DOI: 10.1134/S1061934810140042     Document Type: Article

References (21)

1. Link, A.J., Eng, J., Schieltz, D.M., Carmack, E., Mize, G.J., Morris, D.R., Garvik, B.M., and Yates, J.R., III, Nat. Biotech., 1999, vol. 17, no. 7, p. 676.
2. Silva, J.C., Denny, R., Dorschel, C., Gorenstein, M.V., Li, G., Richardson, K., Wall, D., and Geromanos, S.J., Mol. Cell. Proteomics, 2006, vol. 5, no. 4, p. 589.
3. Perkins, D.N., Pappin, D.J.C., Creasy, D.M., and Cottrell, J.S., Electrophoresis, 1999, vol. 20, no. 18, p. 3551.
4. Eng, J.K., McCormack, A.L., and Yates, J.R., III, J. Am. Soc. Mass Spectrometry, 1994, vol. 5, no. 11, p. 976.
5. Geer, L.Y., Markey, S.P., Kowalak, J.A., Wagner, L., Xu, M., Maynard, D.M., Shi, W., and Bryant, S.H., J. Proteome Res., 2004, vol. 3, no. 5, p. 958.
6. Feny_, D. and Beavis, R.C., Anal. Chem., 2003, vol. 75, no. 4, p. 768.
7. Colinge, J., Masselot, A., Cusin, I., Mahe, E., Niknejad, A., Argoud-Puy, G., Reffas, S., Bederr, N., Gleizes, A., Rey, P.A., and Bougueleret, L., Proteomics, 2004, vol. 4, no. 7, p. 1977.
8. Zubarev, R.A., Zubarev, A.R., and Savitski, M.M., J. Am. Soc. Mass Spectrometry, 2008, vol. 19, no. 6, p. 753.
9. Creasy, D.M. and Cottrell, J.S., Proteomics, 2004, vol. 4, no. 6, p. 1534.
10. Frank, A.M., Savitski, M.M., Nielsen, M.L., Zubarev, R.A., and Pevzner, P.A., J. Proteome Res., 2007, vol. 6, no. 1, p. 114.
11. Moore, R.E., Young, M.K., and Lee, T.D., J. Am. Soc. Mass Spectrometry, 2002, vol. 13, no. 4, p. 378.
12. Tarasova, I.A., Zubarev, R.A., Goloborod’ko, A.A., Gorshkov, A.V., and Gorshkov, M.V., Mass-spektrometria, 2008, vol. 5, no. 1, p. 7.
13. Tarasova, I.A., Goloborodko, A.A., Zubarev, R.A., and Gorshkov, M.V., Proc. 56th ASMS Conference on Mass Spectrometry and Allied Topic, Denver, 2008.
14. Gorshkov, A.V., Evreinov, V.V., Tarasova, I.A., and Gorshkov, M.V., Polymer Sci. B, 2007, vol. 49, no. 3, p. 93.
15. Tarasova, I.A., Gorshkov, A.V., Evreinov, V.V., Adams, K., Zubarev, R.A., and Gorshkov, M.V., Polymer Sci. A, 2008, vol. 50, no. 3, p. 309.
16. Gorshkov, A.V., Tarasova, I.A., Evreinov, V.V., Savitski, M.M., Nielsen, M.L., Zubarev, R.A., and Gorshkov, M.V., Anal. Chem., 2006, vol. 78, no. 22, p. 7770.
17. Dwivedi, R.C., Spicer, V.L., Harder, M., Antonovici, M., Ens, W., Standing, K.G., Wilkins, J.A., and Krokhin, O.V., Anal. Chem., 2008, vol. 80, no. 18, p. 7036.
18. Krokhin, O.V., Craig, R., Spicer, V., Ens, W., Standing, K.G., Beavis, R.C., and Wilkins, J.A., Mol. Cell. Proteomics, 2004, vol. 3, no. 9, p. 908.
19. Krokhin, O.V., Anal. Chem., 2006, vol. 78, no. 22, p. 7785.
20. Krokhin, O.V., Ying, S., Cortens, J.P., Ghosh, D., Spicer, V., Ens, W., Standing, K.G., Beavis, R.C., and Wilkins, J.A., Anal. Chem., 2006, vol. 78, no. 17, p. 6265.
21. Nesvizhskii, A.I., Keller, A.A., Kolker, E., and Aebersold, R., Anal. Chem., 2003, vol. 75, no. 17, p. 4646.