Objective: To establish a rapid and high-throughput clinical matrix-assisted laser desorption ionisation-time of flight mass spectrometry (CLIN-MALDI-TOF-MS) method for identifying oral microorganisms and to determine the distinct representative species across various oral sites.
Methods: Samples were collected from 54 volunteers from four oral sites: saliva, supragingival plaque, oral mucosa and dorsum of the tongue. Microorganisms were cultured on brain heart infusion (BHI) plates and identified using CLIN-MALDI-TOF-MS after processing with specific reagents for mass spectrometry. 
Results: The method identified 15 species and 12 genera of microorganisms, revealing significant differences in microbial composition among the oral sites, and different oral cavity sites harboured distinct relatively representative species. 
Conclusion: The CLIN-MALDI-TOF-MS method offers a rapid and efficient approach for large-scale microbial identification in the oral cavity, providing a suitable approach for future experimental teaching and highlighting the importance of site-specific microbial communities in oral health research.