We have developed a novel scheme to measure the secular motion of trapped ions. Employing pulsed excitation and analysis of the fluorescence of laser cooled ions, the centre-of-mass mode frequency of single as well as entire ion crystals can be measured with a frequency precision better than 5 10^-4 within an interrogation time on the order of seconds, limited only by the fluorescence collection efficiency and the background noise. We have used this method to measure the mass of ions and observed charge exchange collisions between trapped calcium isotopes.