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This paper presents a system, PSDiagnosis, designed to automate the analysis of Supervisory, Control and Data Acquisition (SCADA) data for the assessment of power system protection performance. The model-based system exploits the theory of diagnosis through use of the General Diagnostic Engine (GDE). Models of protection devices combined with the GDE provide the ability to diagnose the maloperation of protection equipment: including multiple faults, missing alarms and new or previously unknown faults. The base requirements were determined in conjunction with a transmission system operator within the U.K. with a major task identified in reducing software maintenance while maintaining an accurate diagnostic result. The novel approaches taken in this system include the provision of dynamically configurable protection device models for reuse on a multitude of different network connections and the modification of the GDE to identify the occurrence of missing alarms. The approach taken ensures that the system is easy to update as the network, equipment and data formats evolve. This paper discusses the requirements, development and application of PSDiagnosis to the transmission network and the experience and results gained from the implementation of an online prototype.