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The electronic properties of graphene can be modified by the local interaction with a selected metal substrate. To probe this effect, Scanning Tunneling Microscopy is widely employed, particularly by means of local measurement via lock-in amplifier of the differential conductance and of the field emission resonance. In this article we propose an alternative, reliable method of probing the graphene/substrate interaction that is readily available to any STM apparatus. By testing the tunneling current as function of the tip/sample distance on nanostructured graphene on Ni(100) and Ir (100), we demonstrate that I(z) spectroscopy can be quantitatively compared with Density Functional Theory calculations and can be used to assess the nature of the interaction between graphene and substrate. This method can expand the capabilities of standard STM systems to study graphene/substrate complexes, complementing standard topographic probing with spectroscopic information. [Display omitted] [ABSTRACT FROM AUTHOR]