A high performance time-of-flight secondary-ion mass spectrometer equipped with a mass selected pulsed primary ion source, an angle and energy focusing time-of-flight analyzer, and a high efficiency single-ion counting detector is described. The instrument can be applied for trace analysis of organic as well as inorganic material for the detection, identification, and structural analysis of large organic molecules in the pico- and femtomol range, as well as for the undisturbed SIMS investigation of surface structures very sensitive to ion bombardment. Spectra of Teflon, a fully protected tetranucleotide and a nonapeptide are reported.