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.