Briefly described, embodiments of this disclosure include methods of calibrating a mass spectrometry system, and the like. One exemplary method of calibrating a mass spectrometry system, among others, includes: acquiring a first mass spectrum of a sample using a first trapping potential, wherein the first mass spectrum are acquired from a low ion population, wherein the first mass spectrum include a first set of mass ion values; and acquiring a second mass spectrum of the sample using a second trapping potential, wherein the second mass spectrum is acquired from a high ion population, wherein the second mass spectrum includes a second set of mass ion values, wherein the first trapping potential is lower than the second trapping potential, wherein the first set of mass ion values are more accurate than the second set of mass ion values, wherein the second set of ion values have a greater signal-to-noise value and a greater detection dynamic range than the first set of mass values, and wherein the first set of mass values are used to calibrate the second set of mass values.