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Despite increasing interest by organisations in deploying SoS (Systems of Systems) to manage complexity, and promote agility within their businesses, there are a number of research areas that are currently underdeveloped. One of these is the role of standards within organisations which develop, operate and share systems within SoS. The paper is not about what standards should be chosen, or indeed developed. Instead, it explores the information that needs to be elicited and modelled, to reason about the standards that member systems of a SoS adhere to, and to provide a structure within which to promote discussion of the incompatibilities that inevitably arise within large SoS. The paper evaluates the approach taken using a running example based on the supply chain SoS for RAF Nimrod aircraft, in light of the recent investigations into the explosion of an aircraft in 2006. The paper concludes that the interaction of standards within SoS is a complex issue, but that a methodology to discover, model and analyse problems can be developed to further best practice in this area.