Exercise MSMS1: answers
- Try to explain as many as possible of the additional error tolerant matches
Pyro-glu is a very common artefact
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.
These are the same thing, of course!
- Are there any that you cannot explain or do not believe?
Can anyone come up with a reasonable explanation for this? Could be a combination of two modifications
Ignore this, there’s a better match to ROAA_HUMAN with a more likely explanation
Probably just an artefact of the wide mass tolerance. Delta should really be -0.5 Da
Same again. Final match should be another Met-Ox
No reason to accept this unlikely match when the score for a match to an unmodified peptide is almost the same. Setting require bold red would remove this hit from the report.
- Which modifications, if any, should have been selected for the first pass search?
May be worth repeating the search with the following variable modifications:
- Oxidised Methionine
- Pyro-Glu
This may find additional peptide matches that are doubly modified.