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.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. | OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5 |