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A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry

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Bioinformatics Research and Applications (ISBRA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9096))

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Abstract

Glycosylation is one of the most important and prevalent post-translational modifications of proteins. Identifying the structures of such protein-linked glycans has become necessary in biochemistry analysis. In the past decade, tandem mass spectrometry (MS/MS) has gradually served as an effective technique in glycoproteomics analysis because of its high throughput and sensitivity. Different approaches have emerged to address the challenges in computational analysis of mass spectrometry based glycoproteomics data. However, there are only a few available software tools characterizing glycans using the spectra produced from intact glycopeptides, which can conserve glycosylation site information. Furthermore, with the development of advanced mass spectrometry techniques, more accurate and complete spectra like HCD spectra can be applied to identify glycopeptides. In this paper, we proposed a heuristic algorithm for glycan de novo sequencing from HCD MS/MS spectra of N-linked glycopeptides. Experiments conducted on a dataset comprising of 46 MS/MS spectra showed that our results were comparable with those identified by GlycoMaster DB, which is designed based on database searching method.

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References

  1. Apweiler, R., Hermjakob, H., Sharon, N.: On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochimica et Biophysica Acta (BBA)-General Subjects 1473(1), 4–8 (1999)

    Article  Google Scholar 

  2. Ohtsubo, K., Marth, J.D.: Glycosylation in cellular mechanisms of health and disease. Cell 126(5), 855–867 (2006)

    Article  Google Scholar 

  3. Dwek, R.A., Butters, T.D., Platt, F.M., Zitzmann, N.: Targeting glycosylation as a therapeutic approach. Nature Reviews Drug Discovery 1(1), 65–75 (2002)

    Article  Google Scholar 

  4. Wuhrer, M., Catalina, M.I., Deelder, A.M., Hokke, C.H.: Glycoproteomics based on tandem mass spectrometry of glycopeptides. Journal of Chromatography B 849(1), 115–128 (2007)

    Article  Google Scholar 

  5. Von Der Lieth, C.W., Bohne-Lang, A., Lohmann, K.K., Frank, M.: Bioinformatics for glycomics: status, methods, requirements and perspectives. Briefings in Bioinformatics 5(2), 164–178 (2004)

    Article  Google Scholar 

  6. Garrett, R., Grisham, C.M.: Biochemistry. Saunders College, Philadelphia (1995)

    Google Scholar 

  7. Gavel, Y., von Heijne, G.: Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering. Protein Engineering 3(5), 433–442 (1990)

    Article  Google Scholar 

  8. Blom, N., Sicheritz-Pontén, T., Gupta, R., Gammeltoft, S., Brunak, S.: Prediction of post translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4(6), 1633–1649 (2004)

    Article  Google Scholar 

  9. Dell, A., Morris, H.R.: Glycoprotein structure determination by mass spectrometry. Science 291(5512), 2351–2356 (2001)

    Article  Google Scholar 

  10. Ma, B.: Challenges in computational analysis of mass spectrometry data for proteomics. Journal of Computer Science and Technology 25(1), 107–123 (2010)

    Article  Google Scholar 

  11. Pan, S., Chen, R., Aebersold, R., Brentnall, T.A.: Mass spectrometry based glycoproteomics from a proteomics perspective. Molecular & Cellular Proteomics 10(1), R110-003251 (2011)

    Google Scholar 

  12. Dalpathado, D.S., Desaire, H.: Glycopeptide analysis by mass spectrometry. Analyst 133(6), 731–738 (2008)

    Article  Google Scholar 

  13. Woodin, C.L., Maxon, M., Desaire, H.: Software for automated interpretation of mass spectrometry data from glycans and glycopeptides. Analyst 138(10), 2793–2803 (2013)

    Article  Google Scholar 

  14. Frese, C.K., Altelaar, A.M., Hennrich, M.L., Nolting, D., Zeller, M., Griep-Raming, J., Mohammed, S., et al.: Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. Journal of Proteome Research 10(5), 2377–2388 (2011)

    Article  Google Scholar 

  15. Alley, W.R., Mechref, Y., Novotny, M.V.: Characterization of glycopeptides by combining collision induced dissociation and electron transfer dissociation mass spectrometry data. Rapid Communications in Mass Spectrometry 23(1), 161–170 (2009)

    Article  Google Scholar 

  16. Lohmann, K.K., von der Lieth, C.W.: GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates. Nucleic Acids Research 32(suppl. 2), W261–W266 (2004)

    Google Scholar 

  17. Go, E.P., Rebecchi, K.R., Dalpathado, D.S., Bandu, M.L., Zhang, Y., Desaire, H.: GlycoPep DB: a tool for glycopeptide analysis using a smart search. Analytical Chemistry 79(4), 1708–1713 (2007)

    Article  Google Scholar 

  18. Pompach, P., Chandler, K.B., Lan, R., Edwards, N., Goldman, R.: Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC MS/MS, and glycan database search. Journal of Proteome Research 11(3), 1728–1740 (2012)

    Article  Google Scholar 

  19. Ren, J.M., Rejtar, T., Li, L., Karger, B.L.: N-Glycan structure annotation of glycopeptides using a linearized glycan structure database (GlyDB). Journal of Proteome Research 6(8), 3162–3173 (2007)

    Article  Google Scholar 

  20. He, L., Xin, L., Shan, B., Lajoie, G.A., Ma, B.: GlycoMaster DB: Software To Assist the Automated Identification of N-Linked Glycopeptides by Tandem Mass Spectrometry. Journal of Proteome Research 13(9), 3881–3895 (2014)

    Article  Google Scholar 

  21. Tang, H., Mechref, Y., Novotny, M.V.: Automated interpretation of MS/MS spectra of oligosaccharides. Bioinformatics 21(suppl. 1), i431–i439 (2005)

    Google Scholar 

  22. Shan, B., Ma, B., Zhang, K., Lajoie, G.: Complexities and algorithms for glycan sequencing using tandem mass spectrometry. Journal of Bioinformatics and Computational Biology 6(01), 77–91 (2008)

    Article  Google Scholar 

  23. Böcker, S., Kehr, B., Rasche, F.: Determination of glycan structure from tandem mass spectra. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 8(4), 976–986 (2011)

    Article  Google Scholar 

  24. Zaia, J.: Mass spectrometry of oligosaccharides. Mass Spectrometry Reviews 23(3), 161–227 (2004)

    Article  Google Scholar 

  25. Ranzinger, R., Herget, S., Wetter, T., Von Der Lieth, C.W.: GlycomeDB-integration of open-access carbohydrate structure databases. BMC Bioinformatics 9(1), 384 (2008)

    Article  Google Scholar 

  26. Aho, A.V., Hopcroft, J.E., Ullman, J.D.: The Design and Analysis of Computer Algorithms. Addison-Wesley, Reading (1974)

    MATH  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computer Science, The University of Western Ontario, London, Ontario, Canada, N6A 5B7

    Weiping Sun & Kaizhong Zhang

  2. Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5C1

    Gilles A. Lajoie

  3. David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada, N2L 3G1

    Bin Ma

Authors
  1. Weiping Sun
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  2. Gilles A. Lajoie
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  3. Bin Ma
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  4. Kaizhong Zhang
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Corresponding author

Correspondence to Weiping Sun .

Editor information

Editors and Affiliations

  1. Georgia State University, Atlanta, USA

    Robert Harrison

  2. Old Dominion University, Norfolk, USA

    Yaohang Li

  3. University of Connecticut, Storrs, Connecticut, USA

    Ion Măndoiu

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© 2015 Springer International Publishing Switzerland

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Sun, W., Lajoie, G.A., Ma, B., Zhang, K. (2015). A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_27

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  • DOI: https://doi.org/10.1007/978-3-319-19048-8_27

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19047-1

  • Online ISBN: 978-3-319-19048-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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