Protein ions of different mass and charge but similar mass-to-charge ratios are shown to undergo significantly different rates of differential neutralization, defined as the rate of change of charge with time, upon initiation of reactions with oppositely charged ions in the quadrupole ion trap. Overlapping charge state distributions arising from mixtures of ions of dissimilar charge are separated on the mass-to-charge scale at short reactions times. It is also demonstrated that the time frame for near total neutralization, defined as charge reduction to the 1+ ion, is relatively insensitive to initial charge state. It is shown, for example, that the (M + 11H)(11+)-(M + 22H)22+ ions derived from horse skeletal muscle apomyoglobin yield the (M + H)+ ion as the major ion/ion reaction product over the same reaction period that largely converts doubly protonated bradykinin to the singly protonated species. Less than 25% of the bradykinin ions are expected to be totally neutralized when roughly 7% of the myoglobin ions are expected to be totally neutralized. The phenomenon of significantly different initial differential neutralization rates for ions of dissimilar charge, and the relative insensitivity to ion charge for total neutralization, can be used to advantage in strategies for protein ion mixture analysis.