Machine Learning-based Classification for the Prioritization of Potentially Hazardous Chemicals with Structural Alerts in Nontarget Screening

Nontarget screening (NTS) with liquid chromatography high-resolution mass spectrometry (LC-HRMS) is commonly used to detect unknown organic micropollutants in the environment. One of the main challenges in NTS is the prioritization of relevant LC-HRMS features. A novel prioritization strategy based on structural alerts to select NTS features that correspond to potentially hazardous chemicals is presented here. This strategy leverages raw tandem mass spectra (MS²) and machine learning models to predict the probability that NTS features correspond to chemicals with structural alerts. The models were trained on fragments and neutral losses from the experimental MS² data. The feasibility of this approach is evaluated for two groups: aromatic amines and organophosphorus structural alerts. The neural network classification model for organophosphorus structural alerts achieved an Area Under the Curve of the Receiver Operating Characteristics (AUC-ROC) of 0.97 and a true positive rate of 0.65 on the test set. The random forest model for the classification of aromatic amines achieved an AUC-ROC value of 0.82 and a true positive rate of 0.58 on the test set. The models were successfully applied to prioritize LC-HRMS features in surface water samples, showcasing the high potential to develop and implement this approach further.