QCQuan is a webtool for automated quality control and statistical analysis of protein expression following labelled mass spectrometry experiments. The tool is focused on differential expression analysis generated by isobaric labelling experiments. Flat text files from maxQuant, Proteome Discoverer or any other tools can be uploaded for a post-identification analysis. In this process, the user is offered very few options to modify the workflow in order to enhance comparable outcomes from different proteomic experiments.
QCQuan is developed at the University of Hasselt in collaboration with VITO, the manuscript published in the Journal of Proteome Research can be accessed here.