Deep graph convolutional network for small-molecule retention time prediction

The retention time (RT) is a crucial source of data for liquid chromatography-mass spectrometry (LCMS). A model that can accurately predict the RT for each molecule would empower filtering candidates with similar spectra but differing RT in LCMS-based molecule identification. Recent research shows that graph neural networks (GNNs) outperform traditional machine learning algorithms in RT prediction. However, all of these models use relatively shallow GNNs. This study for the first time investigates how depth affects GNNs' performance on RT prediction. The results demonstrate that a notable improvement can be achieved by pushing the depth of GNNs to 16 layers by the adoption of residual connection. Additionally, we also find that graph convolutional network (GCN) model benefits from the edge information. The developed deep graph convolutional network, DeepGCN-RT, significantly outperforms the previous state-of-the-art method and achieves the lowest mean absolute percentage error (MAPE) of 3.3% and the lowest mean absolute error (MAE) of 26.55 s on the SMRT test set. We also finetune DeepGCN-RT on seven datasets with various chromatographic conditions. The mean MAE of the seven datasets largely decreases 30% compared to previous state-of-the-art method. On the RIKEN-PlaSMA dataset, we also test the effectiveness of DeepGCN-RT in assisting molecular structure identification. By 30% lessening the number of potential structures, DeepGCN-RT is able to improve top-1 accuracy by about 11%.