Prediction of Retention Time by Combining Multiple Data Sets with Chromatographic Parameter Vectorization and Transfer Learning

Retention time (RT) can provide orthogonal information to mass spectra, supporting the qualitative identification. However, RT is influenced by experimental conditions and column parameters, and it is difficult to have a large amount of RT data in the user’s experimental conditions. Hence, various machine learning methods, including advanced deep learning approaches, have been developed for RT prediction. However, most of them were limited to a given column and operational conditions. In the meantime, data sparsity often hinders the prediction performance. In this study, we propose an MDL-TL method that combines multiple data sets to jointly train the base model. MDL-TL vectorizes the column and conditions (chromatographic parameters, CPs) using word2vec and autoencoders, and distinguishes the data sets from different chromatographic experiments by including the CPs in the compound representation. This not only augments the data but also introduces the CPs into the RT prediction, allowing the pretrained model to be efficiently transferred to different target systems by fine-tuning. MDL-TL was evaluated against five popular deep learning approaches and four machine learning approaches on 14 reversed-phase liquid chromatography data sets and 14 hydrophilic interaction liquid chromatography data sets, respectively. The results show that our method surpassed the compared methods, including transfer learning methods based on the METLIN small molecule retention time (SMRT) data set, in mean absolute error, median absolute error, mean relative error, and R2 in most cases, demonstrating that MDL-TL is a promising approach for predicting RTs for various chromatographic systems and operational conditions.