DeepRT: deep learning for peptide retention time prediction in proteomics

Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Herein, we present DeepRT, a deep learning based software for peptide retention time prediction. DeepRT automatically learns features directly from the peptide sequences using the deep convolutional Neural Network (CNN) and Recurrent Neural Network (RNN) model, which eliminates the need to use hand-crafted features or rules. After the feature learning, principal component analysis (PCA) was used for dimensionality reduction, then three conventional machine learning methods were utilized to perform modeling. Two published datasets were used to evaluate the performance of DeepRT and we demonstrate that DeepRT greatly outperforms previous state-of-the-art approaches ELUDE and GPTime.