COLMARq: A Web Server for 2D NMR Peak Picking and Quantitative Comparative Analysis of Cohorts of Metabolomics Samples.
COLMARq: A Web Server for 2D NMR Peak Picking and Quantitative Comparative Analysis of Cohorts of Metabolomics Samples.
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DOI：
10.1021/acs.analchem.2c00891
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发表时间：
2022-06-21
影响因子：
7.4
通讯作者：
Brueschweiler, Rafael
中科院分区：
文献类型：
--
作者：
Li, Da-Wei;Leggett, Abigail;Bruschweiler-Li, Lei;Brueschweiler, Rafael
复杂生物混合物的高定量代谢组学研究通过2D NMR谱（例如2D 13 C-1H HSQC谱）提供的分辨率增强而变得容易。在这里，我们描述了一个新的公共Web服务器，COLMARq，用于半自动分析的2D HSQC光谱的队列的样品集。COLMARq的工作流程包括使用深度神经网络DEEP Picker进行自动峰拾取、使用Voigt Fitter通过数值拟合进行定量交叉峰体积提取、光谱队列中相应交叉峰的匹配、不同光谱之间的峰体积归一化、代谢物鉴定的数据库查询以及结果的基本单变量和多变量统计分析。COLMARq允许分析属于已知和未知代谢物的交叉峰。在用户以其首选格式上传2D 13 C-1H HSQC和可选2D 1H-1H TOCSY光谱的队列后，可以完全自动地执行Web服务器上的所有后续步骤，允许在需要时进行手动编辑，并且可以保存会话以供以后使用。COLMARq的准确性、多功能性和交互性使得能够对广泛的复杂生物混合物进行定量代谢组学分析，包括生物标志物鉴定，如来自铜绿假单胞菌的细菌培养物的样本队列在其生物膜和非渗透状态下所示。
Highly quantitative metabolomics studies of complex biological mixtures are facilitated by the resolution enhancement afforded by 2D NMR spectra such as 2D 13C–1H HSQC spectra. Here, we describe a new public web server, COLMARq, for the semi-automated analysis of sets of 2D HSQC spectra of cohorts of samples. The workflow of COLMARq includes automated peak picking using the deep neural network DEEP Picker, quantitative cross-peak volume extraction by numerical fitting using Voigt Fitter, the matching of corresponding cross-peaks across cohorts of spectra, peak volume normalization between different spectra, database query for metabolite identification, and basic univariate and multivariate statistical analyses of the results. COLMARq allows the analysis of cross-peaks that belong to both known and unknown metabolites. After a user has uploaded cohorts of 2D 13C–1H HSQC and optionally 2D 1H–1H TOCSY spectra in their preferred format, all subsequent steps on the web server can be performed fully automatically, allowing manual editing if needed and the sessions can be saved for later use. The accuracy, versatility, and interactive nature of COLMARq enables quantitative metabolomics analysis, including biomarker identification, of a broad range of complex biological mixtures as is illustrated for cohorts of samples from bacterial cultures of Pseudomonas aeruginosa in both its biofilm and planktonic states.
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影响因子：
3.6
作者：
Kohl, Stefanie M.;Klein, Matthias S.;Hochrein, Jochen;Oefner, Peter J.;Spang, Rainer;Gronwald, Wolfram
通讯作者：
Gronwald, Wolfram
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影响因子：
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作者：
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通讯作者：
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作者：
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通讯作者：
Sussulini, Alessandra
影响因子：
7.4
作者：
Bingol, Kerem;Brueschweiler, Rafael
通讯作者：
Brueschweiler, Rafael
影响因子：
3.6
作者：
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通讯作者：
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