OpenMS/OpenMS — pull request #679 by grosenberger (2014-02-11 10:49:47+00:00)
Title: [FIX,TEST] fixed OpenSwathDecoyGenerator / MRMDecoy

This bugfix addresses a problem of the OpenSwathDecoyGenerator / MRMDecoy that didn't properly annotate target product ions and thus generated decoy product ions that didn't correspond to the most likely targets.

The patch includes changes by @hroest for MRMDecoy.cpp as well as some changes in the default behaviour of the TOPP tool. Losses and ion series are now disabled by default and need to be specifically turned on).

We throughly tested the implications of the bug to the mProphet error model and couldn't find differences above variances from other causes (shuffling of the sequences, mProphet semi-supervised learning).