X-ray acquisition time must be short enough to ensure that spatial resolution is not degraded by specimen drift and contamination and to ensure that artifact is not generated by beam damage.

In many cases, elements are partially removed from the EM specimens (especially when TEM thin films are used) during EDS measurements. For instance, it is very common that the sulfur (S) content determined from EDS analysis is slightly lower (up to 20%) than the real sulfur content due to the unavoidable sublimation of sulfur in the high vacuum environment during the measurement. Therefore, the measured S concentration is lowered, but the concentrations of other elements are raised. It is important to note that the contents of some elements are lowered more, but some are lowered less. This makes the quantification very complicated.