In principle, electron energy loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) should be able to detect single atoms of phosphorus in biological macromolecules. Such a capability would provide a direct method for measuring the degree of phosphorylation or nucleotide binding which are important in determining the functional states of protein assemblies. Although it has already been possible to map heavy elements, e.g., uranium, at near single atom sensitivity, this has not yet been achievable for lighter atoms like phosphorus. One difficulty in imaging light atoms in a biological specimen is that there is insufficient contrast to visualize the atoms directly so, in a stationary probe analysis, it is not known where to place the probe. Identifying single phosphorus atoms therefore necessarily involves compositional mapping in which EELS information is collected pixel by pixel, a technique known as spectrum-imaging. Recently, improvements have been made in the acquisition of such images, especially the ability to correct for specimen drift in a robust fashion.