1. A method of calibrating ion fragmentation energy used for fragmenting ions in a mass spectrometer, comprising: (a) obtaining data on number of fragment ions produced for each of a plurality of precursor ion populations having respective mass-to-charge ratios at each of a plurality of settings of a fragmentation-energy-related variable, said variable being an instrumental variable used to control applied fragmentation energy; (b) determining, for each mass-to-charge ratio, a respective model curve relating at least a portion of the data on number of fragment ions produced to the fragmentation-energy-related variable, each respective model curve comprising a maximum, and first and second regions in which the value of the model curve continuously decreases as the fragmentation-energy-related variable either increases or decreases away from a point corresponding to the maximum; (c) determining first and second reference features of the model curve determined at each respective value of the mass-to-charge ratio, the first reference feature relating to the respective maximum, the second reference feature relating to either a fragmentation threshold or to a parameter of the respective model curve; (d) locating, for each mass-to-charge ratio, first and second reference values of the fragmentation-energy-related variable, each reference value corresponding to a respective reference feature determined at the respective mass-to-charge ratio; (e) determining, from the plurality of locating steps, the variation, with mass-to-charge-ratio, of each of the reference values of the fragmentation-energy-related variable; (f) associating each of the reference values of the fragmentation-energy-related variable with respective reference values of a dimensionless useable-fragmentation-energy variable; and (g) storing parameters describing the variation of each of the reference values of the fragmentation-energy-related variable with mass-to-charge ratio, wherein the parameters comprise coefficients of at least one non-linear equation.