Cometary studies suggest that the organic composition of the early Solar Nebula was rich in complex nitrile species such a CH$_3$CN. Recent ALMA detections in protoplanetary disks suggest that these species may be common during planet and comet formation, but connecting gas phase measurements to cometary abundances first requires constraints on formation chemistry and distributions of these species. We present here the detection of seven spatially resolved transitions of CH$_3$CN in the protoplanetary disk around the T-Tauri star TW Hya. Using a rotational diagram analysis we find a disk-averaged column density of N$_T$=1.45$^{+0.19}_{-0.15}times10^{12}$ cm$^{-2}$ and a rotational temperature of T$_{rot}$=32.7$^{+3.9}_{-3.4}$ K. A radially resolved rotational diagram shows the rotational temperature to be constant across the disk, suggesting that the CH$_3$CN emission originates from a layer at z/r$sim$0.3. Through comparison of the observations with predictions from a disk chemistry model, we find that grain-surface reactions likely dominate CH$_3$CN formation and that in situ disk chemistry is sufficient to explain the observed CH$_3$CN column density profile without invoking inheritance from the protostellar phase. However, the same model fails to reproduce a Solar System cometary abundance of CH$_3$CN relative to H$_2$O in the midplane, suggesting that either vigorous vertical mixing or some degree of inheritance from interstellar ices occurred in the Solar Nebula.
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