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Published

GLIBS workshop in glycobioinformatics 2004

GLIBS workshop in glycobioinformatics 2004

Published in Technology , Education
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Transcript

  • 1. Part 2: Mass spectrometry Structure of glycoproteins/peptides Determination of glycosylation site Determination of glycan structure
  • 2.  
  • 3. GlycoMod www.expasy.org/tools/glycomod/
  • 4. GlycoMod Useful for determining the glycosylation positions in a protein. You enter: protein sequence, type of digest (used to get peptides) and MS-data You get: possible glycopeptides – glycosylation positions – and suggested glycan structures
  • 5.  
  • 6.  
  • 7.  
  • 8. Oligosaccharide
  • 9. Correct structure is Hex 3 Hex N Ac 2
  • 10. … but it takes some deduction to arrive at the solution
  • 11. Glyco-search-MS glycosciences.de A database of calculated MS fragments of oligosaccharides in SweetDB Determination of oligosaccharide structure is easier than in GlycoMod Beware! There are few structures in the database!
  • 12. Fragmentation
  • 13. FAB-MS/MS
  • 14.  
  • 15.  
  • 16.  
  • 17.  
  • 18.  
  • 19.  
  • 20. Conclusion
    • Many of the tools are difficult to use
    • - bad interfaces, lack of manuals
    • Some will/can not give appropriate answers
    • technical limitations
    • sometimes limitations in the experiments
    • They are useful if used the right way
    • they often give useful hints
    • If you can’t get them to solve a problem within ca 30 min you are probably attempting the impossible