The development of ProteoRE (Proteomics Research Environment) is an online research service to assist biologists/clinicians in the interpretation of their “Omics” data, including proteomics data. With the increased capabilities to produce MS-based proteomics data, the bottleneck has shifted to the functional analysis of specific proteins to the full exploitation of large protein lists by placing them in their biological context. ProteoRE was concieved to facilitate data mining processes and was built upon the Galaxy framework, a web-based platform for computational biomedical research.