This paper explores the applicability of Systems of Systems (SoS) Engineering in the development of large-scale particle accelerator research facilities. Modern particle accelerator facilities, realised by complex constellations of interacting systems, serve a variety of users as research enablers. While the constituent systems exhibit a significant degree of technical and operational independence and distinct life cycles, the performance required to conduct research still needs to emerge from their integration into one overall system, the research facility. This renders a Systems of Systems oriented approach to engineering useful. Furthermore, accelerator based research facilities face increasing availability expectations. Achieving those expectations can be supported through a tailored application of functional safety standards as engineering methodology guideline on an SoS level, as explained in this paper. An SoS-Engineering approach utilising functional safety standards (IEC 61511, IEC 61508) in this way is concretised in a case study on the development of a Machine Protection Systems of Systems in the world-leading neutron science laboratory European Spallation Source ERIC (ESS).