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The effect of operating conditions on the time-dependent X-ray intensity variation is of great importance for the optimal EPMA conditions for accurate determinations of various elements in carbonate minerals. Beam diameters of 0, 1, 2, 5, 10, 15, and 20 mu m, and beam currents of 3, 5, 10, 20, and 50 nA were tested. Ca, Mg, Zn, and Sr were found to be more sensitive to electron beam irradiation as compared to other elements, and small currents and large beam diameters minimized the time-dependent X-ray intensity variations. We determined the optimal EPMA operating conditions for elements in carbonate: 10 mu m and 5 nA for calcite; 10 mu m and 10 nA for dolomite; 5 mu m and 10 nA or 10 mu m and 20 nA for strontianite; and 20 nA and 5 mu m for other carbonate. Elements sensitive to electron beam irradiation should be determined first. In addition, silicate minerals are preferred as standards rather than carbonate minerals.