In web environments, proteomics data integrationin the life sciences needs to handle the problem of data conflicts arising from the heterogeneity of data resources and from incompatibilities between the inputs and outputs of services used in the analysis of the resources. The integration of complex, fast changing biological data repositories can be potentially supported by Grid computing to enable distributed data analysis. This paper presents an approach addressing the data conflict problems of proteomics data integration. We describe a proposed proteomics data integration architecture, in which a heterogeneous data integration system interoperates with Web Services and query processing tools for the virtual and materialised integration of a number of proteomics resources, either locally or remotely. Finally, we discuss how the architecture can be further used for supporting data maintenance and analysis activities.