Spa-Stocsy: An Automated Tool for Identifying Annotated and Non-annotated Metabolites in High-Throughput NMR Spectra

Authors

Xu Han
Wanli Wang
Li-Hua Ma
Ismael Ai-Ramahi
Juan Botas
Kevin MacKenzie
Genevera I Allen
Damian W Young
Zhandong Liu
Mirjana Maletic-Savatic

Publication Date

10-3-2023

Journal

Bioinformatics

DOI

10.1093/bioinformatics/btad593

PMID

37792497

PMCID

PMC10568371

PubMedCentral® Posted Date

10-4-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

no

Keywords

Animals, Humans, Drosophila melanogaster, Magnetic Resonance Spectroscopy, Magnetic Resonance Imaging, Cluster Analysis, Metabolomics

Abstract

MOTIVATION: Nuclear magnetic resonance spectroscopy (NMR) is widely used to analyze metabolites in biological samples, but the analysis requires specific expertise, it is time-consuming, and can be inaccurate. Here, we present a powerful automate tool, SPatial clustering Algorithm-Statistical TOtal Correlation SpectroscopY (SPA-STOCSY), which overcomes challenges faced when analyzing NMR data and identifies metabolites in a sample with high accuracy.

RESULTS: As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset. It first investigates the covariance pattern among datapoints and then calculates the optimal threshold with which to cluster datapoints belonging to the same structural unit, i.e. the metabolite. Generated clusters are then automatically linked to a metabolite library to identify candidates. To assess SPA-STOCSY's efficiency and accuracy, we applied it to synthesized spectra and spectra acquired on Drosophila melanogaster tissue and human embryonic stem cells. In the synthesized spectra, SPA outperformed Statistical Recoupling of Variables (SRV), an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the biological data, SPA-STOCSY performed comparably to the operator-based Chenomx analysis while avoiding operator bias, and it requiredOverall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. It may thus accelerate the use of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making.

Comments

AVAILABILITY AND IMPLEMENTATION: The codes of SPA-STOCSY are available at https://github.com/LiuzLab/SPA-STOCSY.

Associated Data