To be able to predict reversed phase liquid chromatographic (RPLC) retention times of contaminants is an asset in order to solve food contamination issues. The development of quantitative structure–retention relationship models (QSRR) requires selection of the best molecular descriptors and machine-learning algorithms. In the present work, two main approaches have been tested and compared, one based on an extensive literature review to select the best set of molecular descriptors (16), and a second with diverse strategies in order to select among 1545 molecular descriptors (MD), 16 MD. In both cases, a deep neural network (DNN) were optimized through a gridsearch. Pesticides; QSRR; Molecular descriptors; Deep neural network; Reversed-phase liquid chromatography; Selection of inputs.