Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?
E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms ...
To detect the deamidation from Glutamine to Glutamate in a protein, normal practise seems to be a mass spec, where it is claimed there is a change of 1 dalton. EG It is claimed that: Deamidation ...
Once you have your gel with separated proteins can you simple cut out each band and plop it into solution or do you need to take extra steps?