QuanFormer: A Transformer-Based Precise Peak Detection and Quantification Tool in LC-MS-Based Metabolomics

In metabolomic analysis based on liquid chromatography coupled with mass spectrometry, detecting and quantifying intricate objects is a massive job. Current peak picking methods still cause high rates of incorrectly picked peaks to influence the reliability and reproducibility of results. To address these challenges, we developed QuanFormer, a deep learning method based on object detection designed to accurately quantify peak signals. Our algorithm combines the feature extraction capabilities of convolutional neural networks (CNNs) with the global computation capability of Transformer architecture. Data training in QuanFormer by using nearly 20,000 annotated regions-of-interest (ROIs) ensures unique prediction via bipartite matching, achieving 96.5% of the average precision value on the test set. Even without retraining, QuanFormer achieves over 90% accuracy in distinguishing true from false peaks. Performance was further analyzed using visualization techniques applied to the encoder and decoder layers. We also demonstrated that QuanFormer could correct retention time shifts for peak alignment and generally surpass the existing methods, including MZmine 3 and PeakDetective, to obtain a larger number of picked peaks and higher accurate quantification. Finally, we also carried out metabolomic analysis in a clinical cohort of breast cancer patients and utilized QuanFormer to detect and quantify the potential biomarkers. QuanFormer is open-source and available at https://github.com/LinShuhaiLAB/QuanFormer.