1. An apparatus for of determining an empirical formula of an analyte ion from a mass spectrum that includes a main peak and one or more isotope peak, the system comprising: a processor; and a memory unit coupled to the processor, the memory unit including stored instructions for causing the processor to: a) obtain mass spectrum data; b) determine a relative mass defect of the isotope peak of the mass spectrum relative to the main peak and further isotope peaks; c) calculate a relative mass defect of a corresponding isotopic ion of a proposed empirical formula; d) compare the relative mass defect of the isotope peak of the mass spectrum and the relative mass defect of the isotopic ion of the proposed empirical formula; and e) identify the proposed empirical formula as a potential candidate for the analyte ion based on the comparison.