The analysis of Mass Spectrometry proteomics data requires the combination of large storage systems, effective preprocessing techniques, and data mining and visualization tools. The collection, storage and analysis of huge mass spectra produced in different laboratories can leverage the services of Computational Grids, that offer efficient data transfer primitives, effective management of large data stores, and large computing power. The paper presents a software platform that uses ontologies and workflows to combine spectra preprocessing tools, efficient spectra management techniques, and off-the-shelf data mining tools to analyze proteomics data on the Grid. Architecture and performance evaluation are presented.