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Proteomics is a science to which all of the previous discussion applies. It is relying heavily on computational data analysis. There are many portals providing access to various tools to analyze proteomics data, but most of them are focussed on a very specific use case. Proteomics depends heavily on reliable, reproducible, high-throughput analysis methods and pipelines. The Swiss Proteomics Portal provides then possibility to define simple and complex workflows, combining the available tools to improve the data analysis or to create new analysis pipelines. It serves both the end-user community who just wants to get their data analyzed in the best-possible way, as well as to the expert community developing new tools and methods to improve the data analysis pipelines. The expert user community can create workflows through the portal's workflow editor and link together existing tools (power-users). In addition, we also define a category of super-users who can also deploy new tools and algorithms that can be used as new building blocks by the power-users to build new workflows. They can control the software execution and parameters completely.