A system for X-ray analysis, includes: (a) an X-ray analysis assembly configured to (i) direct an X-ray beam to impinge on a surface of a sample, and (ii) receive fluorescence radiation excited from the sample in response to the impinged X-ray beam, (b) a target assembly including measurement targets: placed in an optical path between the X-ray analysis assembly and the sample, and configured to move between (i) one or more first positions in which one or more of the measurement targets are positioned in the X-ray beam, and (ii) one or more second positions in which the optical path is unobstructed by the target assembly, and (c) a processor, configured to control movement of the target assembly between the first and second positions, for alternately, (i) monitoring properties of the X-ray beam using the measurement targets, and (ii) performing the X-ray analysis at a measurement site of the sample.