Figure shows UMAP performed for embeddings generated by the best performing IRIS model (Table , Ablation #10). These embeddings cluster similarly to Graphormer-IR, but with lower diversity due to the smaller IRIS dataset. Figure highlights specific node embeddings made for predictions of (E)-hex-2-enoylglycine and exemplifies Graphormer-IRIS's high contextualization of charge. The embedding for the carboxylic acid hydroxyl group oxygen atom for a deprotonated analyte (circled in green, Figure ) exhibits a much larger relative shift compared to the same hydroxyl moiety in sodiated and protonated charge states. This relative shift is also not observed for the deprotonated versions of the other heteroatoms in the same molecule (circled in purple, Figure ). Given this embedding shift, we can conclude that Graphormer-IRIS has likely identified the site of deprotonation in (E)-hex-2-enoylglycine without an explicit annotation of deprotonation (other than the nonspecific global charge node). This identification of charge moiety is impressive given that this information has been learned indirectly from only the IRIS and DFT spectra prediction tasks. We can thus conclude that the global charge embedding succeeds at communicating molecule-wide shifts as a function of charge state (see Figure ) resulting from highly specific and localized embedding shifts associated with the most probable sites of charge.