The authors have developed a parallel imaging MS/MS capability for the PHI nanoTOF II time-of-flight secondary ion mass spectrometry (TOF-SIMS) instrument. The unique design allows a 1 Da wide precursor mass window to be extracted from a stream of mass separated secondary ions while all other secondary ions are detected in the normal manner at the standard TOF-SIMS detector. The selected precursor ions are deflected into an activation cell where they are fragmented using high energy collision induced dissociation and mass analyzed in a separate linear TOF mass spectrometer. This TOF-TOF approach allows MS/MS to be accomplished at a high speed maintaining the primary ion beam repetition rates used in TOF-SIMS. The new MS/MS capability enables molecular identification to be extended to higher mass ions where the mass accuracy of TOF-SIMS is not sufficient to unambiguously identify molecular structure. The ability to acquire TOF-SIMS and MS/MS data simultaneously from the identical analytical volume is a powerful new method for mass spectrometry imaging.