OpenMS/OpenMS — pull request #865 by hendrikweisser (2014-06-13 15:36:19+00:00)
Title: Work-around for special modifications in Mascot (fixes #864)

Some modifications are only supported as specificity groups by Mascot (e.g. "Deamidated (NQ)", "Phospho (ST)"), but not by OpenMS. I've added a list of these modifications (taken from Mascot 2.4) to the code and treated them as special cases, in which the OpenMS notation needs to be replaced by the Mascot notation when an MGF file is written.
Tested and found to work with Mascot 2.4.