The workflow also struggles with overlapping isotope distributions, particularly in cases where there is harmonic overlap or distributions of similar intensity (Figure ). In some cases (Figure ), the charge state is correctly assigned to a minor distribution, but it is not accepted as a match because another distribution has a higher apex intensity. Other problems occur when shared peaks are knocked down on earlier versions of the algorithm, and what is left behind cannot be assigned (Figures and). Future work is exploring ways to limit the focus on the encoding to improve charge assignment when multiple peaks are present and ways to improve peak matching, fitting, and removal after assignment.