Pepxmltk—a format converter for peptide identification results obtained from tandem mass spectrometry data using X!Tandem search engine

This is a preview of subscription content, log in to check access.

References

  1. 1.

    Zhang, Y., Fonslow, B.R., Shan, B., Baek, M.-C., and Yates, J.R., Chem. Rev., 2013, vol. 113, no. 4, p. 2343.

    Article  CAS  Google Scholar 

  2. 2.

    Yates, J.R., Electrophoresis, 1998, vol. 19, no. 6, p. 893.

    Article  CAS  Google Scholar 

  3. 3.

    Johnson, R.S., Davis, M.T., Taylor, J.A., and Patterson, S.D., Methods, 2005, vol. 35, no. 3, p. 223.

    Article  CAS  Google Scholar 

  4. 4.

    Perkins, D.N., Pappin, D.J., Creasy, D.M., and Cottrell, J.S., Electrophoresis, 1999, vol. 20, no. 18, p. 3551.

    Article  CAS  Google Scholar 

  5. 5.

    Geer, L.Y., Markey, S.P., Kowalak, J.A., Wagner, L., Xu, M., Maynard, D.M., Yang, X., Shi, W., and Bryant, S.H., J. Proteome Res., 2004, vol. 3, no. 5, p. 958.

    Article  CAS  Google Scholar 

  6. 6.

    Keller, A., Nesvizhskii, A.I., Kolker, E., and Aebersold, R., Anal. Chem., 2002, vol. 74, no. 20, p. 5383.

    Article  CAS  Google Scholar 

  7. 7.

    Käll, L., Canterbury, J.D., Weston, J., Noble, W.S., and MacCoss, M.J., Nat. Methods, 2007, vol. 4, no. 11, p. 923.

    Article  Google Scholar 

  8. 8.

    Ivanov, M.V., Levitsky, L.I., Lobas, A., Panic, T., Laskay, U., Mitulovic, G., Schmid, R., Pridatchenko, M.L., Tsybin, Y.O., and Gorshkov, M.V., J. Proteome Res., 2014, vol. 13, no. 4, p. 1911.

    Article  CAS  Google Scholar 

  9. 9.

    Craig, R. and Beavis, R.C., Bioinformatics, 2004, vol. 20, no. 9, p. 1466.

    Article  CAS  Google Scholar 

  10. 10.

    Keller, A., Eng, J., Zhang, N., Li, X., and Aebersold, R., Mol. Syst. Biol., 2005, vol. 1, no. 1.2005.0017.

  11. 11.

    Laskay, U.A., Lobas, A.A., Srzentic, K., Gorshkov, M.V., and Tsybin, Y.O., J. Proteome Res., 2013, vol. 12, no. 12, p. 5558.

    Article  CAS  Google Scholar 

  12. 12.

    Griffin, N.M., Yu, J., Long, F., Oh, P., Shore, S., Li, Y., Koziol, J.A., and Schnitzer, J.E., Nat. Biotechnol., 2010, vol. 28, no. 1, p. 83.

    Article  CAS  Google Scholar 

  13. 13.

    Goloborodko, A.A., Levitsky, L.I., Ivanov, M.V., and Gorshkov, M.V., J. Am. Soc. Mass Spectrom., 2013, vol. 24, no. 2, p. 301.

    Article  CAS  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to M. V. Ivanov.

Additional information

Published in Russian in Mass-spektrometriya, 2015, Vol. 11, No. 3, pp. 179–180.

The article was translated by the authors.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ivanov, M.V., Levitsky, L.I., Tarasova, I.A. et al. Pepxmltk—a format converter for peptide identification results obtained from tandem mass spectrometry data using X!Tandem search engine. J Anal Chem 70, 1598–1599 (2015). https://doi.org/10.1134/S1061934815130055

Download citation

Keywords

  • proteomics
  • search engine
  • tandem mass spectrometry
  • data mining
  • bioinformatics