| OpenMS 2.5.0

Deprecated List

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.