GlycoFragment and GlycoSearchMS: Web tools to support the interpretation of mass spectra of complex carbohydrates

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Lohmann, Klaus Karl ^a   von der Lieth, Claus W ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; GLYCAN; OLIGOSACCHARIDE;

ARTICLE; AUTOMATION; CALCULATION; CARBOHYDRATE ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC DATABASE; MASS SPECTROMETRY; MEASUREMENT; ONLINE SYSTEM; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS;

ALGORITHMS; CARBOHYDRATE SEQUENCE; HUMANS; INTERNET; MASS SPECTROMETRY; POLYSACCHARIDES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 3242890883     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh392     Document Type: Article

References (19)

1. Feizi,T. and Mulloy,B. (2003) Carbohydrates and glycoconjugates. Glycomics: the new era of carbohydrate biology. Curr. Opin. Struct. Biol., 13, 602-604.
2. Rudd,P.M., Colominas,C., Royle,L. Murphy,N., Hart,E., Merry,A.H., Hebestreit,H.F. and Dwek,R.A. (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.
3. Dell,A. and Morris,H.R. (2001) Glycoprotein structure determination by mass spectrometry. Science, 291, 2351-2356.
4. Rudd,P.M., Elliott,T., Cresswell,P., Wilson,I.A. and Dwek,R.A. (2001) Glycosylation and the immune system. Science, 291, 2370-2376.
5. Peracaula,R., Tabares,G., Royle,L. Harvey,D.J., Dwek,R.A., Rudd,P.M. and de Llorens. (2003) Altered glycosylation pattern allows the distinction between prostate-specific antigen (PSA) from normal and tumor origins. Glycobiology, 13, 457-470.
6. Peracaula,R., Royle,L., Tabares,G. Mallorqui-Fernandez,G., Barrabes,S., Harvey,D.J., Dwek,R.A., Rudd,P.M. and de Llorens,R. (2002) Glycosylation of human pancreatic ribonuclease: differences between normal and tumour states. Glycobiology, 13, 227-244.
7. Rudd,P.M., Merry,A.H., Wormald,M.R. and Dwek,R.A. (2002) Glycosylation and prion protein. Curr. Opin. Struct. Biol., 12, 578-586.
8. Butler,M., Quelhas,D., Critchley,AT Carchon,H., Hebestreit,H.F., Hibbert,R.G., Vilarinto,L., Teles,E., Matthijs,G. Scholler,E. et al. (2003) Detailed glycan analysis of serum glycoproteins of patients with congenital disorders of glycosylation indicates the specific defective glycan processing step and provides an insight into pathogenesis. Glycobiology, 13, 601-622.
9. Harvey,D.J. (2001) Identification of protein-bound carbohydrates by mass spectrometry. Proteomics, 1, 311-328.
10. Kuster,B., Krogh,T.N., Mortz,E. and Harvey,D.J. (2001) Glycosylation analysis of gel-separated proteins. Proteomics, 1, 350-61.
11. Sagi,D., Conradt,H.S. Nimtz,M. and Katalinic,J.P. (2002) Sequencing of tri- and tetraantennary N-glycans containing sialic acid by negative mode ESI QTOF tandem MS. Am. Soc. Mass Spectrom., 13, 266-273.
12. Geyer,H., Schmitt,S., Wuhrer,M. and Geyer,R. (1999) Structural analysis of glycoconjugates by on-target enzymatic digestion and MALDI-TOF-MS. Anal. Chem., 71, 476-482.
13. Appel,R.D., Bairoch,A. and Hochstrasser,D.F. (1994) A new generation of information retrieval tools for biologists: the example of the ExPASy www server. Trends Biochem. Sci., 19, 258-260.
14. Cooper,C.A., Gasteiger,E. and Packer,N.H. (2001) GlycoMod - a software tool for determining glycosylation compositions from mass spectrometric data. Proteomics, 1, 340-349.
15. Lohmann,K.K. and von der Lieth,C.-W. (2003)GLYCO-FRAGMENT:a web tool to support the interpretation of mass spectra of complex carbohydrates. Proteomics, 3, 2028-2035.
16. Domon,B. and Costello,C.E. (1988) A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates. Glycoconjugate, 5, 397-409.
17. Bohne,A., Lang,E. and von der Lieth,C. (1998) W3-SWEET: carbohydrate modeling by internet. J. Mol. Model., 4, 33-43.
18. Bohne,A.,Lang,E. and von der Lieth,C.W. (1999)SWEET- www-based rapid 3D construction of oligo- and polysaccharides. Bioinformatics, 15, 767-768.
19. Loss,A., Bunsmann,P., Bohne,A. Loss,A., Schwarzer,E., Lang,E. and von der Lieth,C.W. (2002) SWEET-DB: an attempt to create annotated data collections for carbohydrates. Nucleic Acids Res., 30, 405-408.