Deep Neural Network Pretrained by Weighted Autoencoders and Transfer Learning for Retention Time Prediction of Small Molecules

Retention time (RT) prediction contributes to identification of small molecules measured by high-performance liquid chromatography coupled with high-resolution mass spectrometry. Deep learning algorithms based on big data can enhance the accuracy of RT prediction. But at different chromatographic conditions, RTs of compounds are different, and the number of compounds with known RTs is small in most cases. Therefore, the transfer of big data is necessary. In this work, a strategy using a deep neural network (DNN) pretrained by weighed autoencoders and transfer learning (DNNpwa-TL) was proposed to efficiently predict RTs of compounds. The loss function in the autoencoders was calculated with features weighted by mutual information. Then, a DNN pretrained by weighted autoencoders (DNNpwa) was produced. For other specific chromatographic methods, the transfer learning model DNNpwa-TLs were built through fine-tuning the DNNpwa with the help of some compounds with known RTs to conduct the RT prediction. With the above strategy, a DNNpwa was first built with the METLIN small molecule retention time data set containing 80 038 small molecule compounds. A median relative error of 3.1% and a mean relative error of 4.9% were achieved. Then, 17 data sets from different chromatographic methods were studied, and the results showed that the performance of DNNpwa-TL was better than those of other deep learning models. Besides, DNNpwa-TL outperformed random forest, gradient boost, least absolute shrinkage and selection operator regression, and DNN for most of the 17 data sets. Therefore, DNNpwa-TL can provide an efficient method to perform RT prediction of small molecule compounds for different chromatographic methods and conditions.