A method for detecting methylated nucleotides within a nucleic acid sample is provided. The method includes the steps of splitting a nucleic acid sample into separate reaction vessels; contacting nucleic acid in one reaction vessel with bisulfite; amplifying the nucleic acid in each reaction vessel; cleaving the nucleic acids in each reaction vessel to produce fragments thereof; and obtaining a mass spectrum of the resulting fragments from one reaction vessel and another mass spectrum of the resulting fragments from another reaction vessel.