This study compares cross-sectional scanning tunneling microscopy and atom probe tomography. We use epitaxially grown self-assembled InAs quantum dots (QDs) in GaAs as an exemplary material with which to compare these two nanostructural analysis techniques. We studied the composition of the wetting layer and the QDs, and performed quantitative comparisons of the indium concentration profiles measured by each method. We show that computational models of the wetting layer and the QDs, based on experimental data, are consistent with both analytical approaches. This establishes a link between the two techniques and shows their complimentary behavior, an advantage which we exploit in order to highlight unique features of the examined QD material.