Database Search Exercises > Exercise MSMS3 > Answers  
 
 

Exercise MSMS3: Answers

 

  1. Try to explain as many as possible of the additional matches found in the second pass search

    Pyro-glu is a very common artefact

    error tolerant   error tolerant

    As are these three for samples separated on a gel. The carbamidomethyl is deliberate alkylation with iodoacetamide. The propionamide is an artefact caused by residual free acrylamide. If you see both, this means that the cysteines were blocked after running the gel.

    error tolerant

    Deamidation and Asn->Asp are the same thing, of course!

    error tolerant   error tolerant

    Could be acetylation or trimethylation

    error tolerant   error tolerant

    Note that X!Tandem provides a summary of modifications that have been discovered.

    error tolerant

  2. Are there any that you cannot explain or do not believe?

    Can anyone come up with a reasonable explanation for this? Its a good score but a very unlikely assignment. Could be a combination of two modifications

    error tolerant

    Probably just an artefact of the mass tolerance. Final match should be another Met-Ox, bringing the delta more into line with the others, but this is outside the tolerance of 0.5 Da.

    error tolerant

  3. Which modifications, if any, should have been selected for the first pass search?
    Oxidation (M) is common, and should be included in the first pass search as a variable modification together with a fixed modification of Carbamidomethylation (C). Other modifications are relatively infrequent and best found by model refinement / error tolerant search.

 

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