Model Performance. Using the datasets described in reference 28 (see Figures ), models (see Figure ) were trained using ten-fold cross validation to determine the optimal transfer learning strategy (see Figure and Table ), encodings (see Tables and), and hyperparameters (see Table ). The best performing model obtained a spectral similarity score of SISμ = 0.6823 ± 0.0343 (ten-fold cross validation, c = 10, Table , Ablation #10). Histograms showing performance for all test splits (c = 10) are depicted in Figure . Detailed results showing all training strategies are shown in Table and are discussed in more detail below. For 195 molecular ions, DFT-computed and experimental IRIS spectra were available; we calculated the SIS score for the DFT-computed spectra using the same preprocessing method as was used for our ML model. This DFT/IRIS comparison yielded 𝑆𝐼𝑆 𝜇 = 0.5616. Although the DFT/IRIS comparison is not perfect due to differences in the composition (e.g. molecular, charge state) and the number of spectra in the two evaluation sets, this benchmark suggests that Graphormer-IRIS (using only a small training dataset) is approximately 21% more accurate than conventional quantum-chemical methods for predicting IRIS spectra. Graphormer-IRIS predictions are also completed in seconds on GPUs, in contrast to the hours-to-days timescale for common DFT workflows (see Supporting Information:Model Training). The best performing transfer learning strategy started with a pretrained Graphormer-IR model, followed by finetuning on DFT-computed spectra, and finally training on the experimental IRIS spectra. For DFT and IRIS finetuning, the first layer of the graph encoder was frozen. This model utilized the novel phase encodings for the global charge node described in the Supporting Information: Charge Encoding section for the IRIS and DFT spectra. As shown in Figure , the best performing model yielded 𝑆𝐼𝑆 𝜇 = 0.6823 ± 0.0343 (c = 10) for spectra of all species, 𝑆𝐼𝑆 𝜇 = 0.6683 (n = 164) for spectra of protonated species, 𝑆𝐼𝑆 𝜇 = 0.6782 (n = 80) for spectra of deprotonated species, and 𝑆𝐼𝑆 𝜇 = 0.7209 (n = 68) for spectra of sodiated species.