NMR spectroscopy is a technology that is widely used in metabolomic studies. The information that these studies most commonly use from NMR spectra is the metabolite concentration. However, as well as concentration, pH and ionic strength information are also made available by the chemical shift of metabolite signals. This information is typically not used even though it can enhance sample discrimination, since many conditions show pH or ionic imbalance. Here, we demonstrate how chemical shift information can be used to improve the quality of the discrimination between case and control samples in three public datasets of different human matrices. In two of these datasets, chemical shift information helped to provide an AUROC value higher than 0.9 during sample classification. In the other dataset, the chemical shift also showed discriminant potential (AUROC 0.831). These results are consistent with the pH imbalance characteristic of the condition studied in the datasets. In addition, we show that this signal misalignment dependent on sample class can alter the results of fingerprinting approaches in the three datasets. Our results show that it is possible to use chemical shift information to enhance the diagnostic and predictive properties of NMR.