After lots of requests for a more up-to-date MaxQuant tool it finally is there! The European Galaxy server now contains two MaxQuant tools. One features options for SILAC and label free quantification and also the possibility to process fractioned data by uploading an experimental design template. The other one operates on a parameter file uploaded by the user. This enables the usage of all the features of MaxQuant, but might be less convenient to use.
Those tools have been developed by Damian Glaetzer and Friedel Drepper from the University of Freiburg and are available in the Galaxy ToolShed for everyone. Thanks a lot Damian and Friedel!