Abstract
Glycosylation is one of the most common post-translational modifications (PTMs) of proteins, the characterization of which is commonly achieved utilizing mass spectrometry (MS). However, its applicability is currently limited by the lack of computational tools capable of autmoated interpretation of high throughput MS experiments which would allow the characterization of glycosylation sites and their microheterogeneities. We present here a computational approach which overcomes this problem and allows the identification and assignment of the microheterogeneities of glycosylation sites of glycoproteins from liquid chromatography ion-trap-based mass spectrometry (LC/MS) data. This method was implemented in a software tool and tested on several model glycoproteins. The results demonstrate the potential of our computational approach in automating the high throughput identification of glycoproteins.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
van den Steen, P., et al.: Crit. Rev. Biochem. Mol. Biol. 33, 151–208 (1998)
Dennis, J.W., Granovsky, M., Warren, C.E.: Protein glycosylation in development and disease. Bioassays 21, 412–421 (1999)
Lowe, J.B., Marth, J.D.: A genetic approach to mammalian glycan function. Ann. Rev. Biochem. 72, 643–691 (2003)
Mechref, Y., Novotny, N.V., Krishnan, C.: Structural characterization of oligosaccharides using MALDI-TOF/TOF tandem mass spectrometry. Anal Chem. 75(18), 4895–4903 (2003)
Zaia, J.: Mass spectrometry of oligosaccharides. Mass Spectrom Rev. 23(3), 161–227 (2004)
Novotny, M.V., Mechref, Y.: New hyphenated methodologies in high-sensitivity glycoprotein analysis. J. Sep. Sci. 28(15), 1956–1968 (2005)
Wuhrer, W., Deelder, A.M., Hokke, C.H.: Protein glycosylation analysis by liquid chromatography-mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 825(2), 124–133 (2005)
Mechref, Y., Klouckova, I., Novotny, M.V.: Ion-trap-based strategy for the mass-spectrometric assignment of glycosylation sites in proteins. Rapid Commun. Mass Spectrom (submitted) (2006)
Hjorth, R., Vretblad.: Group fractionation of human serum glycoproteins using Sepharose bound lectins. In: Lect. Chem. Soc. Int. Symp. Uppsala, Sweden, Ellis Horwood Ltd (1976)
Hage, D.S.: Affinity Chromatography: A Review of Clinical Applications. Clin. Chem. 45(5), 593–615 (1999)
Nawarak, J., Phutrakul, S., Chen, S.-T.: Analysis of Lectin-Bound Glycoproteins in Snake Venom from the Elapidae and Viperidae Families. J. Proteome Res. 3(3), 383–392 (2004)
Xiong, L., Andrews, D., Regnier, F.: Comparative Proteomics of Glycoproteins Based on Lectin Selection and Isotope Coding. J. Proteome Res. 2(6), 618–625 (2003)
Yang, Z., et al.: A study of glycoproteins in human serum and plasma reference standards (HUPO) using multilectin affinity chromatography coupled with RPLC-MS/MS. Proteomics 5, 3353–3366 (2005)
Madera, M., Mechref, Y., Novotny, M.V.: Combining Lectin Microcolumns with High-Resolution Separation Techniques for Enrichment of Glycoproteins and Glycopeptides. Anal. Chem. 77(13), 4081–4090 (2005)
Reinders, J., et al.: Challenges in mass spectrometry-based proteomics. Proteomics 4(12), 3686–3703 (2004)
Lieth, C.W.v.d., Lutteke, T., Frank, M.: The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra. Biochim. Biophys. Acta. Epub in advance (2005)
Tang, H., Mechref, Y., Novotny, M.V.: Automated interpretation of MS/MS spectra of oligosaccharides. Bioinformatics 21(Suppl 1), i431–i439 (2005)
Mechref, Y., Novotny, M.V.: Structural investigations of glycoconjugates at high sensitivity. Chem. Rev. 102(2), 321–369 (2002)
Mann, M., Wilm, M.: Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66(24), 4390–4399 (1994)
Sunyaev, S., et al.: MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry. Anal. Chem. 75(6), 1307–1315 (2003)
Frank, A., et al.: Peptide sequence tags for fast database search in mass-spectrometry. J. Proteome Res. 4(4), 1287–1295 (2005)
Dancik, V., et al.: De novo peptide sequencing via tandem mass spectrometry. J. Comput. Biol. (1999)
Skiena, S.: The Algorithm Design Manual (1998)
Huang, Y., Mechref, Y., Novotny, M.V.: Microscale Nonreductive Release of O-linked Glycans for Subsequent Analysis Through MALDI Mass Spectrometry and Capillary Electrophoresis. Anal. Chem. 73, 6063–6069 (2001)
Peter-Katalinic, J.: O-glycosylation of proteins. Methods Enzymol. 405, 139–171 (2005)
Pevzner, P., et al.: Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res. (February 2001)
Leptos, K.C., et al.: MapQuant: Open-source software for large-scale protein quantification. Proteomics, Epub in advance (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wu, Y., Mechref, Y., Klouckova, I., Novotny, M.V., Tang, H. (2007). A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry. In: Ideker, T., Bafna, V. (eds) Systems Biology and Computational Proteomics. RSB RCP 2006 2006. Lecture Notes in Computer Science(), vol 4532. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73060-6_7
Download citation
DOI: https://doi.org/10.1007/978-3-540-73060-6_7
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73059-0
Online ISBN: 978-3-540-73060-6
eBook Packages: Computer ScienceComputer Science (R0)