A method of creating characteristic profiles of mass spectra and identification model for analyzing and identifying microorganisms includes collecting m/z data of microorganisms having same features from MALDI-TOF MS; classifying the microorganisms; classifying the collected set of m/z data as a plurality of subsets; creating modified subsets by applying KDE to the subsets; creating first characteristic MS profiles based on the modified subsets; summarizing into a second characteristic MS profile; repeating above six steps to create second characteristic MS profiles; creating a training set comprising first matched vectors; training a machine learning system using the training set to establish a feature classification model; using MALDI-TOF MS to analyze microorganisms having unknown features; comparing m/z of MALDI-TOF MS spectrum of the microorganisms having unknown features with second characteristic MS profiles to obtain second matched vectors; using the feature classification model analyzing the second matched vectors; and identifying the microorganisms.