Secondary ion mass spectrometry analysis of through-oxide ion implantation in silicon often exhibits strong matrix effects across the SiO2/Si interface. In this study we explored the analytical conditions that required minimal correction for the variation in the relative sensitivity factors and the sputtering rates across the interface. We found that an O-2(+) beam at I keV and 46 degrees provided an equal sputtering erosion rate for SiO2 and Si. Under these sputtering conditions, the SiO2 surface remained smooth, but Si became rough similar to 50 nm below the SiO2/Si interface. A complete depth profile of B implantation through oxide was obtained by utilizing the 1 keV 46 degrees O-2(+) beam in SiO2 and across the SiO2/Si interface and a I keV 60 degrees O-2(+) beam deeper in the Si substrate. The data exhibited an apparent drop in the concentration of the implanted B at the SiO2/Si interface which was attributed to a phase transition in the matrix from amorphous to crystalline. In addition, analyses of an ion-beam synthesized oxide (5 keV O-2(+) at normal incidence) confirmed the occurrence of outdiffusion of B in the altered layer. Also, the results indicated preferential sputtering of B at the surface.