A leading candidate for the extragalactic source of high energy cosmic rays is the Fermi engine mechanism, in which protons confined by magnetic fields are accelerated to very high energy through repeated scattering by plasma shock fronts. In the process of acceleration, collisions of trapped protons with the ambient plasma produce pions which decay to electromagnetic energy and neutrinos. For optically thin sources, a strong connection between the emerging cosmic rays and secondary neutrinos can be established. In this context, we show the feasibility of using the Glashow resonance as a discriminator between the pp and pγ interactions in Fermi engines as sources of neutrinos. In particular, we demonstrate how three years of observation at the km3 IceCube facility can serve as a filter for the dominance of the pp interaction at the source.