Page IDMapper: The parameter handling of this tool has been reworked. For greater consistency with other tools, the parameters rt_delta and mz_delta have been renamed to rt_tolerance and mz_tolerance. The possible values of the mz_reference parameter have also been renamed. The default value of mz_tolerance has been increased from 1 ppm to a more realistic 20 ppm.
Most importantly, the use_centroids parameter from previous versions has been split into two parameters, feature:use_centroid_rt and feature:use_centroid_mz. In OpenMS 1.6, peptide identifications would be matched only against monoisotopic mass traces of features if mz_reference was PeptideMass; otherwise, all mass traces would be used. This implicit behaviour has been abandoned, you can now explicitly control it with the feature:use_centroid_mz parameter. feature:use_centroid_mz does not take into account m/z deviations in the monoisotopic mass trace, but this can be compensated by increasing mz_tolerance. The new implementation should work correctly even if the monoisotopic mass trace itself was not detected.
Class MascotInfile: Use MascotGenericFile.h instead, which uses DefaultParamHandler, is more up to date and avoids weird behaviors of this class (especially in terms of MIME boundaries when writing MGF. This class is currently only used by MascotAdapter.cpp.