Abstract
Information about peptides and proteins in urine can be used to search for biomarkers of early stages of various diseases. The main technology currently used for identification of peptides and proteins is tandem mass spectrometry, in which peptides are identified by mass spectra of their fragmentation products. However, the presence of the fragmentation stage decreases sensitivity of analysis and increases its duration. We have developed a method for identification of human urinary proteins and peptides. This method based on the accurate mass and time tag (AMT) method does not use tandem mass spectrometry. The database of AMT tags containing more than 1381 AMT tags of peptides has been constructed. The software for database filling with AMT tags, normalizing the chromatograms, database application for identification of proteins and peptides, and their quantitative estimation has been developed. The new procedures for peptide identification by tandem mass spectra and the AMT tag database are proposed. The paper also lists novel proteins that have been identified in human urine for the first time.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Knorre, D. G., and Myzina, S. D. (2000) Biological Chemistry [in Russian], Vysshaya Shkola, Moscow.
Bogdanov, B., and Smith, R. D. (2005) Mass Spectrometry Reviews, 24, 168–200.
Pappin, D. J., Hojrup, P., and Bleasby, A. J. (1993) Curr. Biol., 3, 327–332.
Perkins, D. N., Pappin, D. J. C., Creasy, D. M., and Cottrell, J. S. (1999) Electrophoresis, 20, 3551–3567.
Kelleher, N. L., Lin, H. Y., Valaskovic, G. A., Aaserud, D. J., Fridriksson, E. K., and McLafferty, F. W. (1999) J. Am. Chem. Soc., 121, 806–812.
Wehofsky, M., and Hoffmann, R. (2002) J. Mass Spectrom., 37, 223–229.
Conrads, T. P., Anderson, G. A., Veenstra, T. D., Pasa-Tolic, L., and Smith, R. D. (2000) Anal. Chem., 72, 3349–3354.
Powell, G. (2005) Beginning Database Design, Wrox, New York.
Adachi, J., Kumar, C., Zhang, Y., Olsen, J. V., and Mann, M. (2006) Genome Biol., 7, R80.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © I. A. Agron, D. M. Avtonomov, A. S. Kononikhin, I. A. Popov, S. A. Moshkovskii, E. N. Nikolaev, 2010, published in Biokhimiya, 2010, Vol. 75, No. 4, pp. 598–605.
Rights and permissions
About this article
Cite this article
Agron, I.A., Avtonomov, D.M., Kononikhin, A.S. et al. Accurate mass tag retention time database for urine proteome analysis by chromatography-mass spectrometry. Biochemistry Moscow 75, 636–641 (2010). https://doi.org/10.1134/S0006297910050147
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297910050147