The GlycanBuilder and GlycoWorkbench glycoinformatics tools: Updates and new developments

Biological Chemistry

Volumn 393, Issue 11, 2012, Pages 1357-1362

  Damerell, David ^a   Ceroni, Alessio ^b   Maass, Kai ^c   Ranzinger, Rene ^d   Dell, Anne ^a   Haslam, Stuart M ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b GENEDATA AG   (Switzerland)

^c JUSTUS LIEBIG UNIVERSITY   (Germany)

^d UNIVERSITY OF GEORGIA   (United States)

Author keywords

BioInformatics; Carbohydrate; Glycan; Glycomics; Glycoproteomics; Mass spectrometry

Indexed keywords

GLYCAN; GLYCOLIPID; GLYCOPROTEIN; GLYCOSAMINOGLYCAN; OLIGOSACCHARIDE;

ARTICLE; GLYCANBUILDER GLYCOINFORMATICS TOOL; GLYCOBIOLOGY; GLYCOWORKBENCH GLYCOINFORMATICS TOOL; MASS SPECTROMETRY; MEDICAL INFORMATICS; MEDICAL TECHNOLOGY; PRIORITY JOURNAL; TANDEM MASS SPECTROMETRY;

GLYCOMICS; GLYCOPROTEINS; MASS SPECTROMETRY; POLYSACCHARIDES; SOFTWARE;

EID: 84869475601     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/hsz-2012-0135     Document Type: Article

References (22)

1. Apweiler, R., Hermjakob, H., and Sharon, N. (1999). On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim. Biophys. Acta 1473, 4-8.
2. Bohne-Lang, A., Lang, E., Forster, T., and von der Lieth, C.W. (2001). LINUCS: linear notation for unique description of carbohydrate sequences. Carbohydr. Res. 336, 1-11.
3. Ceroni, A., Dell, A., and Haslam, S.M. (2007). The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures. Source Code Biol. Med. 2, 3.
4. Ceroni, A., Maass, K., Geyer, H., Geyer, R., Dell, A., and Haslam, S.M. (2008). GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. J. Proteome Res. 7, 1650-1659.
5. Domon, B. and Costello, C.E. (1988). A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates. Glycoconj. J. 5, 397-409.
6. Doubet, S. and Albersheim, P. (1992). CarbBank. Glycobiology 2, 505.
7. Hart, G.W. (2011). What do glycans do? Finding the rightful place for carbohydrates in the central dogma of life! Glycobiology 21, 1454.
8. Harvey, D.J., Merry, A.H., Royle, L., Campbell, M.P., Dwek, R.A., and Rudd, P.M. (2009). Proposal for a standard system for drawing structural diagrams of N-and O-linked carbohydrates and related compounds. Proteomics 9, 3796-3801.
9. Harvey, D.J., Merry, A.H., Royle, L., Campbell, M.P., and Rudd, P.M. (2011). Symbol nomenclature for representing glycan structures: extension to cover different carbohydrate types. Proteomics 11, 4291-4295.
10. Herget, S., Toukach, P.V., Ranzinger, R., Hull, W.E., Knirel, Y.A., and von der Lieth, C.W. (2008a). Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. BMC Struct. Biol. 8, 35.
11. Herget, S., Ranzinger, R., Maass, K., and von der Lieth, C.W. (2008b). GlycoCT-a unifying sequence format for carbohydrates. Carbohydr. Res. 343, 2162-2171.
12. Laine, R.A. (1994). A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 10 12 structures for a reducing hexasaccharide: the isomer barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology 4, 759-767.
13. Lutteke, T., Bohne-Lang, A., Loss, A., Goetz, T., Frank, M., and von der Lieth, C.W. (2006). GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 16, 71R-81R.
14. Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W.H., Rompp, A., Neumann, S., Pizarro, A.D., et al. (2011). mzML-A community standard for mass spectrometry data. Mol. Cell Proteomics 10, R110.000133.
15. Marth, J.D. (2008). A unified vision of the building blocks of life. Nat. Cell Biol. 10, 1015-1016.
16. Pedrioli, P.G.A., Eng, J.K., Hubley, R., Vogelzang, M., Deutsch, E.W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R.H., Apweiler, R., et al. (2004). A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22, 1459-1466.
17. Raman, R., Venkataraman, M., Ramakrishnan, S., Lang, W., Raguram, S., and Sasisekharan, R. (2006). Advancing glycomics: implementation strategies at the consortium for functional glycomics. Glycobiology 16, 82R-90R.
18. Ranzinger, R., Herget, S., Wetter, T., and von der Lieth, C.W. (2008). GlycomeDB-integration of open-access carbohydrate structure databases. BMC Bioinform. 9, 384.
19. Ranzinger, R., Frank, M., von der Lieth, C.W., and Herget, S. (2009). Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. Glycobiology 19, 1563-1567.
20. Tissot, B., Ceroni, A., Powell, A.K., Morris, H.R., Yates, E.A., Turnbull, J.E., Gallagher, J.T., Dell, A., and Haslam, S.M. (2008). Software tool for the structural determination of glycosaminoglycans by mass spectrometry. Anal. Chem. 80, 9204-9212.
21. Varki, A., Cummings, R.D., Esko, J.D., Freeze, H.H., Stanley, P., Marth, J.D., Bertozzi, C.R., Hart, G.W., Etzler, M.E. (2009). Symbol nomenclature for glycan representation. Proteomics 9, 5398-5399.
22. von der Lieth, C.W., Freire, A.A., Blank, D., Campbell, M.P., Ceroni, A., Damerell, D.R., Dell, A., Dwek, R.A., Ernst, B., Fogh, R., et al. (2011). EUROCarbDB: an open-access platform for glycoinformatics. Glycobiology 21, 493-502.