The objective of this work was to explore the capabilities of a field emission gun scanning electron microscope (FEG-SEM) equipped with a transmission scanning electron detector (TSEM) and energy dispersive spectroscopy (EDS) to identify nanoscale chemical heterogeneities in a gas atomization reaction synthesis (GARS) steel sample. The results of this analysis were compared to the same study conducted with scanning transmission electron microscopy (STEM) with EDS mapping. TSEM-EDS was performed using the standard spectral analysis approach, i.e., pixel-by-pixel identification of elements from the spectra, and a new principal component analysis approach to detect regions of similar spectra before identifying elemental contributions to each spectrum. It was determined that features over 200 nm were detectable with the TSEM-EDS standard spectra analysis technique but the PCA analysis approach was necessary for observing smaller features that contained trace elements. Monte Carlo simulations indicated that the spatial resolution expected from a 150 nm thick foil was consistent with those observed in experimental analysis. Simulations also confirm that thinner samples enable higher spatial resolution scans although smaller interaction volumes may require longer acquisition times.