A method of controlling a polishing operation includes receiving a first measurement of a first amount of metal on a substrate made by a first x-ray monitoring system after a first metal layer is deposited on the substrate and before a second metal layer is deposited on the substrate, transferring the substrate to a carrier head of a chemical mechanical polishing apparatus the substrate after the second metal layer is deposited on the substrate, making a second measurement of a second amount of metal on the substrate with a second x-ray monitoring system in the chemical mechanical polishing apparatus, comparing the first measurement to the second measurement to determine a difference, and adjusting a polishing endpoint or a polishing parameter of the polishing apparatus based on the difference.