Advertisement

Biochemistry (Moscow)

, 74:1195 | Cite as

Use of models of biomacromolecule separation in AMT database generation for shotgun proteomics

  • M. L. Pridatchenko
  • I. A. Tarasova
  • V. Guryca
  • A. S. Kononikhin
  • C. Adams
  • D. A. Tolmachev
  • A. Yu. Agapov
  • V. V. Evreinov
  • I. A. Popov
  • E. N. Nikolaev
  • R. A. Zubarev
  • A. V. Gorshkov
  • C. D. Masselon
  • M. V. GorshkovEmail author
Article

Abstract

Generation of a complex proteome database requires use of powerful analytical methods capable of following rapid changes in the proteome due to changing physiological and pathological states of the organism under study. One of the promising technologies with this regard is the use of so-called Accurate Mass and Time (AMT) tag peptide databases. Generation of an AMT database for a complex proteome requires combined efforts by many research groups and laboratories, but the chromatography data resulting from these efforts are tied to the particular experimental conditions and, in general, are not transferable from one platform to another. In this work, we consider an approach to solve this problem that is based on the generation of a universal scale for the chromatography data using a multiple-point normalization method. The method follows from the concept of linear correlation between chromatography data obtained over a wide range of separation parameters. The method is further tested for tryptic peptide mixtures with experimental data collected from mutual studies by different independent research groups using different separation protocols and mass spectrometry data processing tools.

Key words

high performance liquid chromatography proteomics mass spectrometry 

Abbreviations

AMT

accurate mass and time

BioLCCC

liquid chromatography of biomacromolecules under critical conditions

LSS

Linear Solvent Strength theory proposed by Snyder

MPN

multi-point normalization

MS/MS

tandem mass spectrometry

SSRCalc

Sequence Specific Retention Calculator

References

  1. 1.
    Conrads, T. P., Anderson, G. A., Veenstra, T. D., Pasa-Tolic, L., and Smith, R. D. (2000) Anal. Chem., 72, 3349–3354.CrossRefPubMedGoogle Scholar
  2. 2.
    Norbek, A. D., Monroe, M. E., Adkins, J. N., Anderson, K. K., Daly, D. S., and Smith, R. D. (2005) Am. Soc. Mass Spectrom., 16, 1239–1249.CrossRefGoogle Scholar
  3. 3.
    May, D., Fitzgibbon, M., Liu, Y., Holzman, T., Eng, J., Kemp, C. J., Whiteaker, J., Paulovich, A., and McIntosh, M. (2007) J. Proteome Res., 6, 2685–2694.CrossRefPubMedGoogle Scholar
  4. 4.
    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., and Smith, R. D. (2003) Anal. Chem., 75, 1039–1048.CrossRefPubMedGoogle Scholar
  5. 5.
    Sapirstein, H. D., Scanlon, M. G., and Bushuk, W. (1989) J. Chromatogr. A, 469, 127–135.CrossRefGoogle Scholar
  6. 6.
    Krokhin, O. V., Craig, R., Spicer, V., Ens, V., Standing, K. G., Beavis, R. C., and Wilkins, J. A. (2004) Mol. Cell. Proteom., 3, 908–919.CrossRefGoogle Scholar
  7. 7.
    Spiser, V., Yamchuk, A., Cortens, J., Sousa, S., Ens, W., Standing, K. G., Wilkins, J. A., and Krokhin, O. V. (2007) Anal. Chem., 79, 8762–8768.CrossRefGoogle Scholar
  8. 8.
    Shinoda, K., Tomita, M., and Ishihama, Y. (2008) Bioinformatics, 24, 1590–1595.CrossRefPubMedGoogle Scholar
  9. 9.
    Snyder, L. R. (1983) J. Chromatogr., 255, 3–26.CrossRefGoogle Scholar
  10. 10.
    Tarasova, I. A., Guryca, V., Pridatchenko, M. L., Gorshkov, A. V., Kieffer-Jaquinod, S., Evreinov, V. V., Masselon, C. D., and Gorshkov, M. V. (2009) J. Chromatogr. B, 877, 433–440.CrossRefGoogle Scholar
  11. 11.
    Gorshkov, A. V., Tarasova, I. A., Evreinov, V. V., Savitski, M. M., Nielsen, M. L., Zubarev, R. A., and Gorshkov, M. V. (2006) Anal. Chem., 78, 7770–7778.CrossRefPubMedGoogle Scholar
  12. 12.
    Gorshkov, A. V., Evreinov, V. V., Tarasova, I. A., and Gorshkov, M. V. (2007) Polymer Sci. Ser. B, 49, 93–107.CrossRefGoogle Scholar
  13. 13.
    Tarasova, I. A., Gorshkov, A. V., Evreinov, V. V., Zubarev, R. A., and Gorshkov, M. V. (2008) Polymer Sci. Ser. B, 50, 1–15.CrossRefGoogle Scholar
  14. 14.
    Casal, V., Martin-Alvarez, P. J., and Herraiz, T. (1996) Analyt. Chim. Acta, 326, 77–84.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2009

Authors and Affiliations

  • M. L. Pridatchenko
    • 1
  • I. A. Tarasova
    • 1
  • V. Guryca
    • 2
  • A. S. Kononikhin
    • 1
  • C. Adams
    • 3
  • D. A. Tolmachev
    • 1
  • A. Yu. Agapov
    • 1
  • V. V. Evreinov
    • 4
  • I. A. Popov
    • 5
  • E. N. Nikolaev
    • 5
  • R. A. Zubarev
    • 3
  • A. V. Gorshkov
    • 4
  • C. D. Masselon
    • 2
  • M. V. Gorshkov
    • 1
    Email author
  1. 1.Institute for Energy Problems of Chemical PhysicsRussian Academy of SciencesMoscowRussia
  2. 2.CEAUniversite Joseph FourierGrenoble Cedex 9France
  3. 3.Institute for Cell and Molecular BiologyUppsala UniversityUppsalaSweden
  4. 4.Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscowRussia
  5. 5.Emmanuel Institute of Biochemical PhysicsRussian Academy of SciencesMoscowRussia

Personalised recommendations