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The frequencies of unreliable identification were 1.1% (26/2342) for the Autof MS1000 and 1.5% (34/2342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was 93%, the identification error rate was 3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification. The Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However,