The problems and advantages of mass-selected ion deposition in matrices are briefly reviewed and discussed, and initial results with our new apparatus are reported. Both laser induced fluorescence, visible and infrared absorption spectra of ions are detected. Using samples with natural abundance, we demonstrate that individual isotopomers of CS+ 2 can be separately deposited and their spectra analyzed. Our studies with halogenated benzene radical cations indicate that deposition from the energetic beam results in matrix damage which in turn leads to site effects and inhomogeneous broadening. The perturbed sites of lower symmetry have a considerable effect on the guest spectroscopy, leading to spectral shifts and change in the spectroscopic selection rules.