Entering the post genomic era, proteomic has become the topic that scientists are interested in. The authentication of protein has been an important item of the topics. Mass spectrometry (MS) has become an important tool for peptide analysis or proteomic authentication. There are many applications of MS such as oncology, ovarian cancer, and prostate cancer. Coombes et al.(2004) proposed a mathematical model of a virtual spectrometer and suggested that the virtual spectrometer can be applied in conducting a MS simulation. In our study, we focus on designing a simulation study of spectrum data from a virtual MS experiment. The virtual experiment includes two stages: pre- and post-virtual spectrometer. Before the sample data are put into the virtual spectrometer, a virtual population of the intensity of all possible proteins should be determined; a virtual sample is randomly drawn; and the generated sample of intensity should be calibrated to abundance, which is the number of molecules ionized and desorbed from the biological sample. The sample data are then put into the virtual spectrometer and the time of flight (TOF) of each ionized molecule is recorded. Another calibration is employed to transfer a TOF to a mass-to-charge ratio (m/z). The spectrometer and the calibration processes produce variation in MS data. In this study, a complete simulation design of mass spectra will be introduced step by step. Moreover, the calibration effects caused from the two calibration procedures will be investigated. A simulation based on a real data set from a prostate cancer study will be also given as an illustration.