MetaboScope: a statistical toolbox for analyzing 1 H nuclear magnetic resonance spectra from human clinical studies

• Published in: Bioinformatics advances 2024, Vol.4 (1), p.vbae142
• Main Authors: Loo, Ruey Leng, Mosquera, Javier Osorio, Zasso, Michael, Mathews, Jacqueline, Johnston, Desmond G, Nicholson, Jeremy K, Patiny, Luc, Holmes, Elaine, Wist, Julien
• Format: Article
• Language: English
• ISSN: 2635-0041

Metabolic phenotyping, using high-resolution spectroscopic molecular fingerprints of biological samples, has demonstrated diagnostic, prognostic, and mechanistic value in clinical studies. However, clinical translation is hindered by the lack of viable workflows and challenges in converting spectral data into usable information. MetaboScope is an analytical and statistical workflow for learning, designing and analyzing clinically relevant H nuclear magnetic resonance data. It features modular preprocessing pipelines, multivariate modeling tools including Principal Components Analysis (PCA), Orthogonal-Projection to Latent Structure Discriminant Analysis (OPLS-DA), and biomarker discovery tools (multiblock PCA and statistical spectroscopy). A simulation tool is also provided, allowing users to create synthetic spectra for hypothesis testing and power calculations. MetaboScope is built as a pipeline where each module accepts the output generated by the previous one. This provides flexibility and simplicity of use, while being straightforward to maintain. The system and its libraries were developed in JavaScript and run as a web app; therefore, all the operations are performed on the local computer, circumventing the need to upload data. The MetaboScope tool is available at https://www.cheminfo.org/flavor/metabolomics/index.html. The code is open-source and can be deployed locally if necessary. Module notes, video tutorials, and clinical spectral datasets are provided for modeling.