OpenMS/OpenMS — pull request #1101 by lars20070 (2014-12-07 14:49:26+00:00)
Title: optimisation for knockout searches in FeatureFinderMultiplex

In cases we expect to see knockouts, the FeatureFinderMultiplex tool searches for triplets, doublets and singlets in the same run. This pull request combines three small optimisations.

(1) The knock_out user parameter is by default switched off.
(2) The peak patterns are now correctly ordered. We search for triplets before doublets before singlets. Charge 5+ before 4+ before 3+ before 2+ before 1+. And lastly, small mass shifts first, e.g. 4Da before 8Da.
(3) In knockout searches, the detection of singlets is a special case, since the peptide similarity filter has no effect. In order to compensate for this 'missing filter', we choose a more restrictive averagine similarity parameter p. That is achieved by new (advanced) user parameter averagine_similarity_scaling x.
0 < x < 1 p' = p + x(1-p)
i.e. x = 0 -> p' = p, x = 1 -> p' = 1