FeatureFinderMultiplex

The FeatureFinderMultiplex TOPP tool can detect peptide features in MS1 data. It is particularly suited for the analysis of labelled experiments, such as SILAC or Dimethyl labelling. The main algorithm was previously submitted in pull requests #868 and #889. - This pull requests contains the user interface, calculation of the fold changes and the export to the final data formats: consensusXML, featureXML and mzQuantML. 
If the knock_out flag is false, I can set the labels, e.g. Dimethyl0, Dimethyl4 and Dimethyl8.
But if knock_out is on, I would leave the labels empty, since this will only be decided during ID mapping.