Department of Chinese Medicinal Prescription, China Pharmaceutical University, Nanjing, China.
BMC Bioinformatics. 2011 Aug 12;12:337. doi: 10.1186/1471-2105-12-337.
One of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served as the foundation of metabolomics studies. However, the automated high-throughput identification and quantification of metabolites in NMR spectroscopy is limited by severe spectral overlap. Although numerous software programs have been developed for resolving overlapping resonances, as well as for identifying and quantifying metabolites, most of these programs are frequency-domain methods, considerably influenced by phase shifts and baseline distortions, and effective only in small-scale studies. Almost all these programs require multiple spectra for each application, and do not automatically identify and quantify metabolites in batches.
We created IQMNMR, an R package that integrates a relaxation algorithm, digital filter, and similarity search algorithm. It differs from existing software in that it is a time-domain method; it uses not only frequency to resolve overlapping resonances but also relaxation time constants; it requires only one NMR spectrum per application; is uninfluenced by phase shifts and baseline distortions; and most important, yields a batch of quantified metabolites.
IQMNMR provides a solution that can automatically identify and quantify metabolites by one-dimensional proton NMR spectroscopy. Its time-domain nature, stability against phase shifts and baseline distortions, requirement for only one NMR spectrum, and capability to output a batch of quantified metabolites are of considerable significance to metabolic modeling and simulation.IQMNMR is available at http://cran.r-project.org/web/packages/IQMNMR/.
代谢组学最有前途的方面之一是代谢建模和模拟。此类应用的核心是代谢物的自动化高通量鉴定和定量。NMR 光谱是一种可重复、非破坏性和非选择性的方法，它是代谢组学研究的基础。然而，NMR 光谱中代谢物的自动化高通量鉴定和定量受到严重光谱重叠的限制。尽管已经开发了许多用于解析重叠共振以及鉴定和定量代谢物的软件程序，但这些程序大多数都是频域方法，受到相移和基线扭曲的严重影响，仅在小规模研究中有效。几乎所有这些程序都需要对每个应用程序进行多次光谱处理，并且不能自动批量鉴定和定量代谢物。
我们创建了 IQMNMR，这是一个 R 包，它集成了弛豫算法、数字滤波器和相似性搜索算法。它与现有软件的不同之处在于它是一种时域方法；它不仅使用频率来解析重叠共振，还使用弛豫时间常数；它每个应用程序仅需要一个 NMR 光谱；不受相移和基线扭曲的影响；最重要的是，它可以生成一批定量代谢物。
IQMNMR 提供了一种解决方案，可以通过一维质子 NMR 光谱自动鉴定和定量代谢物。它的时域性质、对相移和基线扭曲的稳定性、仅需要一个 NMR 光谱的要求以及批量输出定量代谢物的能力对代谢建模和模拟具有重要意义。IQMNMR 可在 http://cran.r-project.org/web/packages/IQMNMR/ 获得。
