We show that single alkanethiol-passivated gold nanocrystals can be identified by core size in scanning tunneling microscopy (STM) experiments, through a comparison of the measured STM heights with a direct determination of the gold core sizes by mass spectrometry. We take advantage of the discrete size distribution to correlate the peaks in a histogram of nanocrystal heights with the distinct abundance peaks in a mass spectrum. The correlation establishes a mapping from STM height to core mass or mean core diameter. This is vitally important for the interpretation of size-dependent "single-molecule" tunneling spectra from nanocrystal compounds.