Resolution enhancement of metabolomic J-res NMR spectra using deep learning
Author(s)
Type
Journal Article
Abstract
J-Resolved (J-Res) nuclear magnetic resonance (NMR) spectroscopy is pivotal in NMR-based metabolomics, but practitioners face a choice between time-consuming high-resolution (HR) experiments or shorter low-resolution (LR) experiments which exhibit significant peak overlap. Deep learning neural networks have been successfully used in many fields to enhance quality of natural images, especially with regard to resolution, and therefore offer the prospect of improving two-dimensional (2D) NMR data. Here, we introduce the J-RESRGAN, an adapted and modified generative adversarial network (GAN) for image super-resolution (SR), which we trained specifically for metabolomic J-Res spectra to enhance peak resolution. A novel symmetric loss function was introduced, exploiting the inherent vertical symmetry of J-Res NMR spectra. Model training used simulated high-resolution J-Res spectra of complex mixtures, with corresponding low-resolution spectra generated via blurring and down-sampling. Evaluation of peak pair resolvability on J-RESRGAN demonstrated remarkable improvement in resolution across a variety of samples. In simulated plasma data, 100% of peak pairs exhibited enhanced resolution in super-resolution spectra compared to their low-resolution counterparts. Similarly, enhanced resolution was observed in 80.8-100% of peak pairs in experimental plasma, 85.0-96.7% in urine, 94.4-98.9% in full fat milk, and 82.6-91.7% in orange juice. J-RESRGAN is not sample type, spectrometer or field strength dependent and improvements on previously acquired data can be seen in seconds on a standard desktop computer. We believe this demonstrates the promise of deep learning methods to enhance NMR metabolomic data, and in particular, the power of J-RESRGAN to elucidate overlapping peaks, advancing precision in a wide variety of NMR-based metabolomics studies. The model, J-RESRGAN, is openly accessible for download on GitHub at https://github.com/yanyan5420/J-RESRGAN.
Date Issued
2024-07-23
Date Acceptance
2024-06-26
Citation
Analytical Chemistry, 2024, 96 (29), pp.11707-11715
ISSN
0003-2700
Publisher
American Chemical Society
Start Page
11707
End Page
11715
Journal / Book Title
Analytical Chemistry
Volume
96
Issue
29
Copyright Statement
Copyright © 2024 The Authors. Published by American Chemical Society. This publication is licensed under
CC-BY 4.0.
CC-BY 4.0.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/38990576
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2024-07-11