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 tolerance of course).
I want to know other search algorithms that do include the fragment mass accuracy in the protein identification scores. Also, if the protein scores are not influenced, i would like to know in which way other evaluation values of MASCOT or SEQUEST results are influenced.
Thanks for your time.