Skip to main content

Software Tools for Glycan Profiling

  • Protocol
  • First Online:
Mass Spectrometry of Glycoproteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 951))

Abstract

We introduce three software tools, Cartoonist, GlycoWorkbench, and MultiGlycan, for N-glycan profiling of complex biological samples. Detailed instructions for using these tools are provided, and their performances are demonstrated by using real glycan profiling data.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Martin-Rendon E, Blake DJ (2003) Protein glycosylation in disease: new insights into the congenital muscular dystrophies. Trends Pharmacol Sci 24(4):178–83

    Article  CAS  PubMed  Google Scholar 

  2. Scanlin TF, Glick MC (2000) Terminal glycosylation and disease: influence on cancer and cystic fibrosis. Glycoconj J 17(7–9):617–26

    Article  CAS  PubMed  Google Scholar 

  3. Turner GA (1992) N-glycosylation of serum proteins in disease and its investigation using lectins. Clin Chim Acta 208(3):149–71

    Article  CAS  PubMed  Google Scholar 

  4. Lapadula AJ et al (2005) Congruent strategies for carbohydrate sequencing. 3. OSCAR: an algorithm for assigning oligosaccharide topology from MSn data. Anal Chem 77(19):6271–9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Goldberg D et al (2005) Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra. Proteomics 5(4):865–75

    Article  CAS  PubMed  Google Scholar 

  6. Ceroni A et al (2008) GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. J Proteome Res 7(4):1650–9

    Article  CAS  PubMed  Google Scholar 

  7. Raman R et al (2006) Advancing glycomics: implementation strategies at the consortium for functional glycomics. Glycobiology 16(5):82R–90R

    Article  CAS  PubMed  Google Scholar 

  8. Doubet S et al (1989) The complex carbohydrate structure database. Trends Biochem Sci 14(12):475–7

    Article  CAS  PubMed  Google Scholar 

  9. Ranzinger R et al (2008) GlycomeDB - integration of open-access carbohydrate structure databases. BMC Bioinformatics 9:384

    Article  PubMed  PubMed Central  Google Scholar 

  10. Lutteke T et al (2006) GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 16(5):71R–81R

    Article  PubMed  Google Scholar 

  11. Yu C-Y et al (2010) Biomarker discovery by automatic annotation of N-glycan species in MALDI-TOF-TOF spectra, in 58th ASMS Conference. Salt Lake City

    Google Scholar 

  12. Krambeck FJ, Betenbaugh MJ (2005) A mathematical model of N-linked glycosylation. Biotechnol Bioeng 92(6):711–28

    Article  CAS  PubMed  Google Scholar 

  13. Hastie T et al (2000) ‘Gene shaving’ as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol 1(2):RESEARCH0003

    Google Scholar 

  14. Kyselova Z et al (2007) Alterations in the serum glycome due to metastatic prostate cancer. J Proteome Res 6(5):1822–32

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Tang Z et al (2010) Identification of N-glycan serum markers associated with hepatocellular carcinoma from mass spectrometry data. J Proteome Res 9(1):104–12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Marshall AG, Hendrickson CL, Jackson GS (1998) Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom Rev 17(1):1–35

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work is partially supported by National Science Foundation (DBI-0642897) and National Cancer Institute (1U01CA128535-01).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Haixu Tang .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Yu, CY., Mayampurath, A., Tang, H. (2013). Software Tools for Glycan Profiling. In: Kohler, J., Patrie, S. (eds) Mass Spectrometry of Glycoproteins. Methods in Molecular Biology, vol 951. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-146-2_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-146-2_18

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-145-5

  • Online ISBN: 978-1-62703-146-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics