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Agents have been used to provide qualities of adaptation to the Information Systems (IS) since the Nineties. Apart from agent-based IS, existing IS can benefit from additional services provided by agents. We focus on personalization services, which aim is to give specific and customized responses to individual user requests. This paper describes a methodology to design the adaptation part of an IS with the help of a multi-agent system (MAS). An initial multi-agent architecture with an application-independent organization and interaction protocols is provided. On this base, the methodology proposes a guide into the design of the specific knowledge and skills that allow adaptation of the agents behaviour to the characteristics of the application, and into realization of the integration between IS and MAS. An example taken in the transport information field illustrates our proposition.