An instrument has been designed and constructed that enables in situ reactivity and time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis of surfaces prepared or modified through soft and reactive landing of mass-selected polyatomic cations and anions. The apparatus employs an electrospray ion source coupled to a high transmission electrodynamic ion funnel, two focusing collision quadrupoles, a large 19 mm diameter quadrupole mass filter, and a quadrupole bender that deflects the ion beam, thereby preventing neutral contaminants from impinging on the deposition surface. The ion soft landing apparatus is coupled to a commercial TOF-SIMS instrument permitting the introduction of surfaces into vacuum and SIMS analysis before and after ion deposition without breaking vacuum. To facilitate a comparison of the current TOF-SIMS instrument with the in situ Fourier transform ion cyclotron resonance (FTICR-SIMS) deposition apparatus constructed previously, dications of the cyclic peptide Gramicidin S (GS) and the photoactive organonometallic complex ruthenium tris-bipyridine (Ru(bpy)(3)) were soft-landed onto fluorinated self-assembled monolayer (FSAM) on gold surfaces. In both cases, similarities and differences were observed in the secondary ion mass spectra, with the TOF-SIMS results, in general, characterized by greater sensitivity, larger dynamic range, less fragmentation, and fewer in-plume reactions than the corresponding FTICR-SIMS spectra. The charge reduction kinetics of both the doubly and singly protonated GS cations on the FSAM surface were also examined as was the influence of the primary gallium ion (Ga(+)) flux on the efficiency of these processes. In addition, we demonstrate that the new instrument enables detailed studies of the reactivity of catalytically active species immobilized by soft and reactive landing toward gaseous reagents.