Disclose herein is a method for diagnosing virus, comprising the steps of: (a) collecting a sample and lysing virus present in the sample; (b) treating the lysed sample with a specific protease to digest a protein in the sample into peptides; (c) measuring the masses of the peptides in the sample with a mass measurement device; and (d) comparing the masses of the peptides in the sample to the masses of peptides derived from known viral proteins digested with the same protease as used in step (b), thus identifying the protein from which the peptides of the sample were derived. Also disclosed is a system for diagnosing virus which can be used to carry out the above diagnostic method.