Mass spectrometry

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GLIBS workshop in glycobioinformatics 2004

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Mass spectrometry

  1. 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/
  3. 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
  4. 8. Oligosaccharide
  5. 9. Correct structure is Hex 3 Hex N Ac 2
  6. 10. … but it takes some deduction to arrive at the solution
  7. 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!
  8. 12. Fragmentation
  9. 13. FAB-MS/MS
  10. 20. Conclusion <ul><li>Many of the tools are difficult to use </li></ul><ul><li>- bad interfaces, lack of manuals </li></ul><ul><li>Some will/can not give appropriate answers </li></ul><ul><li>technical limitations </li></ul><ul><li>sometimes limitations in the experiments </li></ul><ul><li>They are useful if used the right way </li></ul><ul><li>they often give useful hints </li></ul><ul><li>If you can’t get them to solve a problem within ca 30 min you are probably attempting the impossible </li></ul>

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