1. An ion peak detection method of detecting ion peaks from peaks present in mass spectral data, comprising: acquiring mass spectral data made up of peaks having mass-to-charge ratio and intensity information from a sample using a mass spectrometer; classifying the peaks, by a processor, in the acquired mass spectral data into a plurality of classes according to peak intensity, where the plurality of classes include a low intensity class; determining a noise level, by the processor, from peaks which have been classified into the low intensity class; and detecting ion peaks from peaks present in mass spectral data based on the noise level and identifying ions of the sample by comparing the detected ion peaks with proposed ions in a database, whereby identification of the ions of the sample based on the mass spectral data acquired using the mass spectrometer is improved by detecting ions peaks using the noise level.