Table of Contents
International Journal of Proteomics
Volume 2012 (2012), Article ID 560391, 7 pages
http://dx.doi.org/10.1155/2012/560391
Research Article

Increasing the Productivity of Glycopeptides Analysis by Using Higher-Energy Collision Dissociation-Accurate Mass-Product-Dependent Electron Transfer Dissociation

Thermo Fisher Scientific, San Jose, CA 95134, USA

Received 6 February 2012; Accepted 15 March 2012

Academic Editor: Qiangwei Xia

Copyright © 2012 Julian Saba et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. Z. Shriver, S. Raguram, and R. Sasisekharan, “Glycomics: a pathway to a class of new and improved therapeutics,” Nature Reviews Drug Discovery, vol. 3, no. 10, pp. 863–873, 2004. View at Publisher · View at Google Scholar · View at Scopus
  2. R. K. T. Kam and T. C. W. Poon, “The potentials of glycomics in biomarker discovery,” Clinical Proteomics, vol. 4, no. 3-4, pp. 67–79, 2008. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Kobata, “Altered glycosylation of surface glycoproteins in tumor cells and its clinical application,” Pigment Cell Research, vol. 2, no. 4, pp. 304–308, 1989. View at Google Scholar · View at Scopus
  4. M. Ono and S. Hakomori, “Glycosylation defining cancer cell motility and invasiveness,” Glycoconjugate Journal, vol. 20, no. 1, pp. 71–78, 2004. View at Publisher · View at Google Scholar · View at Scopus
  5. J. W. Dennis, M. Granovsky, and C. E. Warren, “Glycoprotein glycosylation and cancer progression,” Biochimica et Biophysica Acta, vol. 1473, no. 1, pp. 21–34, 1999. View at Publisher · View at Google Scholar · View at Scopus
  6. A. Kobata and J. Amano, “Altered glycosylation of proteins produced by malignant cells, and application for the diagnosis and immunotherapy of tumours,” Immunology and Cell Biology, vol. 83, no. 4, pp. 429–439, 2005. View at Publisher · View at Google Scholar · View at Scopus
  7. M. Wuhrer, M. I. Catalina, A. M. Deelder et al., “Glycoproteomics based on tandem mass spectrometry of glycopeptides,” Journal of Chromatography B, vol. 849, no. 1-2, pp. 115–128, 2007. View at Google Scholar
  8. J. J. Conboy and J. Henion, “High-performance anion-exchange chromatography coupled with mass spectrometry for the determination of carbohydrates,” Biological Mass Spectrometry, vol. 21, no. 8, pp. 397–407, 1992. View at Publisher · View at Google Scholar · View at Scopus
  9. M. J. Huddleston, M. F. Bean, and S. A. Carr, “Collisional fragmentation of glycopeptides by electrospray ionization LC/MS and LC/MS/MS: methods for selective detection of glycopeptides in protein digests,” Analytical Chemistry, vol. 65, no. 7, pp. 877–884, 1993. View at Google Scholar · View at Scopus
  10. J. Irungu, E. P. Go, Y. Zhang et al., “Comparison of HPLC/ESI-FTICR MS versus MALDI-TOF/TOF MS for glycopeptide analysis of a highly glycosylated HIV envelope glycoprotein,” Journal of the American Society for Mass Spectrometry, vol. 19, no. 8, pp. 1209–1220, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. E. Mirgorodskaya, P. Roepstorff, and R. A. Zubarev, “Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer,” Analytical Chemistry, vol. 71, no. 20, pp. 4431–4436, 1999. View at Publisher · View at Google Scholar · View at Scopus
  12. N. V. Bykova, C. Rampitsch, O. Krokhin, K. G. Standing, and W. Ens, “Determination and characterization of site-specific N-glycosylation using MALDI-Qq-TOF tandem mass spectrometry: case study with a plant protease,” Analytical Chemistry, vol. 78, no. 4, pp. 1093–1103, 2006. View at Publisher · View at Google Scholar · View at Scopus
  13. T. Geiger and S. Clarke, “Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation,” Journal of Biological Chemistry, vol. 262, no. 2, pp. 785–794, 1987. View at Google Scholar · View at Scopus
  14. N. E. Robinson and A. B. Robinson, “Prediction of protein deamidation rates from primary and three-dimensional structure,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 8, pp. 4367–4372, 2001. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Tyler-Cross and V. Schirch, “Effects of amino acid sequence, buffers, and ionic strength on the rate and mechanism of deamidation of asparagine residues in small peptides,” Journal of Biological Chemistry, vol. 266, no. 33, pp. 22549–22556, 1991. View at Google Scholar · View at Scopus
  16. H. T. Wright, “Nonenzymatic deamidation of asparaginyl and glutaminyl residues in proteins,” Critical Reviews in Biochemistry and Molecular Biology, vol. 26, no. 1, pp. 1–52, 1991. View at Google Scholar · View at Scopus
  17. G. Palmisano, M. N. Melo-Braga, K. Engholm-Keller et al., “Chemical deamidation: a common pitfall in large-scale N-linked glycoproteomic mass spectrometry-based analyses,” Journal of Proteome Research, vol. 11, no. 3, pp. 1949–1957, 2012. View at Publisher · View at Google Scholar
  18. R. A. Zubarev, “Electron-capture dissociation tandem mass spectrometry,” Current Opinion in Biotechnology, vol. 15, no. 1, pp. 12–16, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. L. M. Mikesh, B. Ueberheide, A. Chi et al., “The utility of ETD mass spectrometry in proteomic analysis,” Biochimica et Biophysica Acta, vol. 1764, no. 12, pp. 1811–1822, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. M. I. Catalina, C. A. M. Koeleman, A. M. Deelder, and M. Wuhrer, “Electron transfer dissociation of N-glycopeptides: loss of the entire N-glycosylated asparagine side chain,” Rapid Communications in Mass Spectrometry, vol. 21, no. 6, pp. 1053–1061, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. W. R. Alley Jr., Y. Mechref, and M. V. Novotny, “Characterization of glycopeptides by combining collision-induced dissociation and electron-transfer dissociation mass spectrometry data,” Rapid Communications in Mass Spectrometry, vol. 23, no. 1, pp. 161–170, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. S. I. Snovida, E. D. Bodnar, R. Viner, J. Saba, and H. Perreault, “A simple cellulose column procedure for selective enrichment of glycopeptides and characterization by nano LC coupled with electron-transfer and high-energy collisional-dissociation tandem mass spectrometry,” Carbohydrate Research, vol. 345, no. 6, pp. 792–801, 2010. View at Publisher · View at Google Scholar · View at Scopus
  23. H. Hahne and B. Kuster, “A novel two-stage tandem mass spectrometry approach and scoring scheme for the identification of O-GlcNAc modified peptidesss,” Journal of the American Society for Mass Spectrometry, vol. 22, no. 5, pp. 931–942, 2011. View at Publisher · View at Google Scholar · View at Scopus
  24. P. Zhao, R. Viner, C. F. Teo et al., “Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment,” Journal of Proteome Research, vol. 10, no. 9, pp. 4088–4104, 2011. View at Google Scholar
  25. S. M. Peterman and J. J. Mulholland, “A novel approach for identification and characterization of glycoproteins using a hybrid linear ion trap/FT-ICR mass spectrometer,” Journal of the American Society for Mass Spectrometry, vol. 17, no. 2, pp. 168–179, 2006. View at Publisher · View at Google Scholar · View at Scopus
  26. J. Jebanathirajah, H. Steen, and P. Roepstorff, “Using optimized collision energies and high resolution, high accuracy fragment ion selection to improve glycopeptide detection by precursor ion scanning,” Journal of the American Society for Mass Spectrometry, vol. 14, no. 7, pp. 777–784, 2003. View at Publisher · View at Google Scholar · View at Scopus