Abstract
The biological relevance of protein glycosylation has made glycomics, the comprehensive study to identify all glycans in an organism, indispensable in many research fields. Determining the structure and functional relationship of glycoproteins requires the comprehensive characterization of glycan structures by a range of analytical methods. High performance liquid chromatography (HPLC) is a well-established technology commonly used for the complete structural elucidation of N- and O-linked glycans; however, the analysis of data is a major bottleneck and robust bioinformatic solutions are required. This chapter describes the availability of databases and tools, GlycoBase and autoGU developed in conjunction with the EUROCarbDB initiative, to assist the interpretation of HPLC-glycan data collections.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dwek RA (1995) Glycobiology: more functions for oligosaccharides. Science 269:1234–1235
Pang PC, Chiu PC, Lee CL, Chang LY, Panico M, Morris HR, Haslam SM, Khoo KH, Clark GF, Yeung WS, Dell A (2011) Human sperm binding is mediated by the sialyl-Lewis(x) oligosaccharide on the zona pellucida. Science 333:1761–1764
Rudd PM, Elliott T, Cresswell P, Wilson IA, Dwek RA (2001) Glycosylation and the immune system. Science 291:2370–2376
Harvey DJ (2011) Derivatization of carbohydrates for analysis by chromatography; electrophoresis and mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 879:1196–1225
Pabst M, Altmann F (2011) Glycan analysis by modern instrumental methods. Proteomics 11:631–643
Royle L, Radcliffe CM, Dwek RA, Rudd PM (2006) Detailed structural analysis of N-glycans released from glycoproteins in SDS-PAGE gel bands using HPLC combined with exoglycosidase array digestions. Methods Mol Biol 347:125–143
Rudd PM, Guile GR, Kuster B, Harvey DJ, Opdenakker G, Dwek RA (1997) Oligosaccharide sequencing technology. Nature 388:205–207
Guile GR, Rudd PM, Wing DR, Prime SB, Dwek RA (1996) A rapid high-resolution high-performance liquid chromatographic method for separating glycan mixtures and analyzing oligosaccharide profiles. Anal Biochem 240:210–226
Zaia J (2010) Mass spectrometry and glycomics. OMICS J Integr Biol 14:401–418
Harvey DJ (2011) Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005–2006. Mass Spectrom Rev 30:1–100
Royle L, Campbell MP, Radcliffe CM, White DM, Harvey DJ, Abrahams JL, Kim Y-G, Henry GW, Shadick NA, Weinblatt ME, Lee DM, Rudd PM, Dwek RA (2008) HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software. Anal Biochem 376:1–12
Lauc G, Essafi A, Huffman JE, Hayward C, Knezevic A, Kattla JJ, Polasek O, Gornik O, Vitart V, Abrahams JL, Pucic M, Novokmet M, Redzic I, Campbell S, Wild SH, Borovecki F, Wang W, Kolcic I, Zgaga L, Gyllensten U, Wilson JF, Wright AF, Hastie ND, Campbell H, Rudd PM, Rudan I (2010) Genomics meets glycomics-the first GWAS study of human N-glycome identifies HNF1alpha as a master regulator of plasma protein fucosylation. PLoS Genet 6:e1001256
Artemenko NV, Campbell MP, Rudd PM (2010) GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data. J Proteome Res 9:2037–2041
Campbell MP, Royle L, Radcliffe CM, Dwek RA, Rudd PM (2008) GlycoBase and autoGU: tools for HPLC-based glycan analysis. Bioinformatics 24:1214–1216
Ceroni A, Maass K, Geyer H, Geyer R, Dell A, Haslam SM (2008) GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. J Proteome Res 7:1650–1659
von der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lutteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM (2011) EUROCarbDB: an open-access platform for glycoinformatics. Glycobiology 21:493–502
Campbell MP, Hayes CA, Struwe WB, Wilkins MR, Aoki-Kinoshita KF, Harvey DJ, Rudd PM, Kolarich D, Lisacek F, Karlsson NG, Packer NH (2011) UniCarbKB: putting the pieces together for glycomics research. Proteomics 11:4117–4121
Harvey DJ, Merry AH, Royle L, Campbell MP, Rudd PM (2011) Symbol nomenclature for representing glycan structures: extension to cover different carbohydrate types. Proteomics 11:4291–4295
Rudd PM, Colominas C, Royle L, Murphy N, Hart E, Merry AH, Hebestreit HF, Dwek RA (2001) A high-performance liquid chromatography based strategy for rapid, sensitive sequencing of N-linked oligosaccharide modifications to proteins in sodium dodecyl sulphate polyacrylamide electrophoresis gel bands. Proteomics 1:285–294
Harvey DJ, Merry AH, Royle L, Campbell MP, Dwek RA, Rudd PM (2009) Proposal for a standard system for drawing structural diagrams of N- and O-linked carbohydrates and related compounds. Proteomics 9:3796–3801
Acknowledgements
The EUROCarbDB initiative (http://www.eurocarbdb.org, Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases) was funded by the European Union as a Research Infrastructure Design Study implemented as a Specific Support Action under the FP6 Research Framework Program (RIDS Contract number 011952).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Campbell, M.P., Royle, L., Rudd, P.M. (2015). GlycoBase and autoGU: Resources for Interpreting HPLC-Glycan Data. In: Lütteke, T., Frank, M. (eds) Glycoinformatics. Methods in Molecular Biology, vol 1273. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2343-4_2
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2343-4_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2342-7
Online ISBN: 978-1-4939-2343-4
eBook Packages: Springer Protocols