SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra.
SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra.
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DOI：
10.1093/bioinformatics/btad593
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发表时间：
2023-10-03
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核磁共振光谱（NMR）被广泛用于分析生物样品中的代谢物，但分析需要特定的专业知识，耗时，并且可能不准确。在这里，我们提出了一个强大的自动化工具，空间聚类分析-统计总相关光谱（SPA-STOCSY），它克服了分析NMR数据时面临的挑战，并以高精度识别样品中的代谢物。作为一种数据驱动的方法，SPA-STOCSY从输入数据集估计所有参数。它首先研究数据点之间的协方差模式，然后计算最佳阈值，用于聚类属于相同结构单元（即代谢物）的数据点。生成的聚类然后自动链接到代谢物库以识别候选物。为了评估SPA-STOCSY的效率和准确性，我们将其应用于合成光谱和在果蝇组织和人类胚胎干细胞上获得的光谱。在合成的光谱中，SPA通过捕获更高百分比的信号区域和接近零的噪声区域，优于统计变量再耦合（SRV），这是一种现有的光谱峰聚类方法。在生物数据中，SPA-STOCSY对基于操作员的Chenomx分析进行了改进，同时避免了操作员偏倚，总计算时间<7 min。总的来说，SPA-STOCSY是一种快速，准确，无偏的工具，用于NMR谱中代谢物的非靶向分析。因此，它可以加速NMR在科学发现、医学诊断和患者特定决策中的应用。SPA-STOCSY的代码可在https://github.com/LiuzLab/SPA-STOCSY上获得。
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. 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 required <7 min of total computation time. Overall, 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. The codes of SPA-STOCSY are available at https://github.com/LiuzLab/SPA-STOCSY.
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影响因子：
2.2
作者：
MacKinnon, Neil;Somashekar, Bagganahalli S.;Tripathi, Pratima;Ge, Wencheng;Rajendiran, Thekkelnaycke M.;Chinnaiyan, Arul M.;Ramamoorthy, Ayyalusamy
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