I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere. Consider the following ...
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 ...