A novel approach for the localization of X-ray stains in individual cells with ptychographic computed tomography was recently demonstrated. With a basis material decomposition in the image domain the quantitative stain concentration can be retrieved with nanoscopic resolution. So far, the approach was demonstrated for two different staining elements, but it has the potential to be easily applied to other contrast agents. The noise in the resulting basis materials depends on the one hand on the noise in the original data, and is furthermore given by the basis materials and specifically their attenuation properties and electron density. In this work, we theoretically predict the standard deviation in basis material images for several heavy elements. This is done by applying the material decomposition algorithm to an experimental data set. It was found that for more electron dense materials the decomposition should have lower noise in the basis material image of the stain. Furthermore, the energy used for the measurement impacts the standard deviation in the basis material images especially for materials with low atomic number, for which therefore lower X-ray energy should be used for data acquisition.