Ion/ion proton transfer reactions are shown to be an effective means to facilitate the resolution of ions in electrospray mass spectrometry that differ in mass and charge but are similar in mass-to-charge ratio. Examples are shown in which a minor contaminant protein in a ribonuclease B solution is clearly apparent after ion/ion proton transfer but not in the conventional electrospray mass spectrum. A further example involving a mixture of bovine serum albumin and bovine transferrin also showed the identification of previously unnoticed "contaminant" polymer. The latter mixture also illustrated important issues in the use of the quadrupole ion trap as a reaction vessel and mass analyzer for high mass-to-charge ratio ions. The results suggest that the use of ion trap operating parameters specifically tailored for storage, ejection, detection, and mass-to-charge analysis of high mass-to-charge ratio ions can have attractive analytical figures of merit for determining mixtures of relatively high-mass proteins and, by extension, other types of high-mass biopolymers.