Quartz crystal microbalance (QCM or QCM-D) has become instrumental in life sciences and biosensor research. It is routinely and successfully used for monitoring interfacial processes, such as protein adsorption and conformational changes in the protein-adsorbed films, liposome-surface interactions and supported bilayer formation, and in the development of biosensor platforms. However, quantitative interpretation of QCM data from biological interfaces studied in liquid remains challenging. In vacuum, the so-called Sauerbrey relationship is routinely used to relate QCM frequency shifts due to the adsorbed layer to the mass of the adsorbed layer. Deviations from Sauerbrey relationship are typically observed when studying soft interfaces in liquids; these are interpreted in terms of layer viscoelastic properties. In this study, we develop and use a combined atomic force microscopy (AFM)-QCM setup to investigate the adsorption of protein ferritin on the surface of gold. First, we find that deviations from the Sauerbrey relationship in this system originate almost entirely from the heterogeneity of the protein films caused by the presence of impurities. Second, relying on the ability of AFM to visualize single ferritin molecules adsorbed on the surface, we find that the frequency shifts determined by QCM are not linearly related to the protein surface coverage.