Several modules in MZmine offer the option the compare the isotope patterns of peaks and assign a score (percentage) of similarity to them. Until MZmine version 2.2, the CDK (Chemistry Development Kit) library was used to perform this operation. An improved algorithm, introduced in MZmine.3, is described below.
The similarity of two isotope patterns is determined as follows:
A trivial observation is that for two identical isotope patterns the similarity score will be 100%, while for two completely different patterns 0% score is returned. Only a single parameter is required for the evaluation of the algorithm, defining the width of the sliding window. It should be noted, though, that the optimal value of this parameter might be different from the commonly perceived “mass accuracy” of the instrument, because mass resolving power and preprocessing of the data must be considered. For example, even if the mass accuracy of the major isotopes may be less than 0.001 m/z, the mass difference between minor isotopes may be significantly higher.