A method of creating characteristic peak profiles of mass spectra and identification model for analyzing and identifying microorganisms are provided. MALDI-TOF MS data of microorganisms having the same feature are gathered. Discretization of the data is performed. Density-based clustering is used to find m/z values of spectral peaks with high probability of occurrence from the discretized data. A characteristic MS peak profile is created for every specific feature of microorganisms. Every such a characteristic profile forms a feature template. The mass spectrum of each known isolate is matched against all the feature templates and a number of matched vectors are obtained. The matched vectors are then concatenated into a single “integrated vector.” Then, a machine learning method and the integrated vectors generated from all known isolates are used to create a classification model for microorganism identification.