Abstract: A screening method for a specific protein in a proteome analysis comprises: (a) obtaining samples containing a protein or protein digest from a cell or tissue in a specific group and a control group; (b) analyzing the samples obtained in the step (a) with a mass spectrometer, thereby obtaining mass spectrometry data; (c) analyzing the mass spectrometry data obtained in the step (b) using an arbitrary database searching software, thereby acquiring a protein list containing items for specifying proteins and indexes for identifying the proteins, for each of the samples; (d) averaging values of the indexes for each of the items in all of the protein lists acquired in the step (c), and acquiring protein list models of the specific group and the control group, containing the average values of the indexes; (e) calculating a difference between the average values for each of the items, between the protein list models of the specific group and the control group obtained in the step (d), and acquiring one protein list i