A high resolution time-of-flight mass spectrometer that analyzes secondary ions produced when samples are bombarded with MeV and keV ions and ultraviolet photons is described. The flexibility of the system is demonstrated by showing results from several varied experiments including high resolution mass spectra of molecular ions desorbed from a renin substrate sample by MeV and keV ions, a multiphoton ionization spectrum of gas-phase benzene, and a matrix assisted laser desorption spectrum of a glycoprotein. The keV ion source is useful for secondary ion mass spectrometry work, for imaging, and for micromachining of surfaces. By using the attached electrostatic ion reflector metastable decomposition of various molecular and fragment ions can be studied.