The first example of direct structural characterization of polyaromatic ions by coupling a Fourier transform ion cyclotron resonance mass spectrometer with an infrared free-electron laser is presented. Measurement of the IR spectra of selectively prepared ionic reactive intermediates is allowed by the association of the high peak power and wide tunability of the laser with the flexibility of the spectrometer, where several mass selection and ion reaction steps can be combined, as demonstrated in the case of iron cation complexes of hydrocarbons. The present experimental setup opens the way to understanding chemical reaction paths.