Our findings highlight noteworthy limitations in current machine-learning-based MS spectral prediction algorithms. This inaccuracy underscores motivation for future research as follows. Given that NEIMS is less accurate for amino acids beyond those used for model training, there is a need to understand better the cause and solution of current limitations. One simple solution for amino acids could be to retrain NEIMS with a larger or targeted training set (e.g. amino acid spectra curated within these analyses).