A system for converting product ion mass spectra to product ion mass spectra with higher mass accuracy, comprising: a processor configured to receive at least one product ion mass spectrum produced by a tandem mass spectrometer, receive a chemical structure of a compound that corresponds to the at least one product ion mass spectrum, assign one or more elemental compositions to at least one peak in the at least one product ion spectrum based on the chemical structure, by calculating one or more elemental compositions from the elements of the chemical structure that have masses within a mass tolerance of the mass of the at least one peak and assigning the one or more elemental compositions to the at least one peak, score the one or more assigned elemental compositions, simulate one or more fragmentations of the chemical structure to produce a plurality of substructures (350, 360) of the chemical structure, compare the plurality of substructures to the one or more assigned elemental compositions to find one or more matching substructures, assign the one or more matching substructures to their corresponding assigned elemental compositions, score the one or more matching substructures, combine scores of the one or more assigned elemental compositions and their corresponding one or more matching substructures to produce an overall score for each of the one or more assigned elemental compositions, select at least one elemental composition of the one or more assigned elemental compositions that has the highest overall score, and convert the mass of the at least one peak to the mass of the selected at least one elemental composition, producing a product ion mass spectrum with higher mass accuracy. receive at least one product ion mass spectrum produced by a tandem mass spectrometer, receive a chemical structure of a compound that corresponds to the at least one product ion mass spectrum, assign one or more elemental compositions to at least one peak in the at least one product ion spectrum based on the chemical structure, by calculating one or more elemental compositions from the elements of the chemical structure that have masses within a mass tolerance of the mass of the at least one peak and assigning the one or more elemental compositions to the at least one peak, score the one or more assigned elemental compositions, simulate one or more fragmentations of the chemical structure to produce a plurality of substructures (350, 360) of the chemical structure, compare the plurality of substructures to the one or more assigned elemental compositions to find one or more matching substructures, assign the one or more matching substructures to their corresponding assigned elemental compositions, score the one or more matching substructures, combine scores of the one or more assigned elemental compositions and their corresponding one or more matching substructures to produce an overall score for each of the one or more assigned elemental compositions, select at least one elemental composition of the one or more assigned elemental compositions that has the highest overall score, and convert the mass of the at least one peak to the mass of the selected at least one elemental composition, producing a product ion mass spectrum with higher mass accuracy.