A method is provided of measuring the mass thickness of a target sample for use in electron microscopy. Reference data are obtained which is representative of the X-rays (28) generated within a reference sample (12) when a particle beam (7) is caused to impinge upon a region (14) of the reference sample (12). The region (14) is of a predetermined thickness of less than 300 nm and has a predetermined composition. The particle beam (7) is caused to impinge upon a region (18) of the target sample (16). The resulting X-rays (29) generated within the target sample (16) are monitored (27) so as to produce monitored data. Output data are then calculated based upon the monitored data and the reference data, the output data including the mass thickness of the region (18) of the target sample (16).