A system, method and program product for determining contamination of an ion beam are disclosed. In the event of an isobaric interference, or near isobaric interference between a contaminant ion and an expected ion of an ion beam, which is difficult to detect, it is possible to measure a third ion in the ion beam and estimate, based on the amount of the third ion measured, a relative amount of the contaminant ion compared to the expected ion. The estimated relative amount of the contaminant ion is used together with a measured mass resolution of the ion implantation system to determine whether an ion implantation process needs to be suspended.