We use an in-house developed web-based sample submission portal for project & data management. Via this interface users can register their projects, submit sample meta data, monitor progress and dowlnoad the results following final data analysis. We offer a standard analysis of the raw data as well as case to case oriented bioinformatics service. For this we use the Perseus framework as well as R and Python for further statistical and bioinformatics analyses, data annotation and visualization. The portal can be accessed via www.proteomics-cologne.de.