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We have analyzed atom probe tomography reconstructions of disaggregated meteoritic material containing nanodiamonds and disordered carbon to determine whether these phases formed in the solar system or whether they predate the solar system and were formed in supernovae or the interstellar medium. We developed a method to distinguish between these two carbonaceous phases in < 100 nm diameter aggregates using the ratios of various native and contaminant molecular species. We find variations in measured 12C/13C ratios between the two phases that suggest hydrides form more readily during field evaporation of the disordered C than the nanodiamonds.