Metabolic analyses generally fall into two classes: unbiased metabolomic analyses and analyses that are targeted toward specific metabolites. Both techniques have been revolutionized by the advent of mass spectrometers with detectors that afford high mass accuracy and resolution, such as time-of-flights (TOFs) and Orbitraps. One particular area where this technology is key is in the field of metabolic flux analysis because the resolution of these spectrometers allows for discrimination between ¹³C-containing isotopologues and those containing ¹⁵N or other isotopes. While XCMS-based software is freely available for untargeted analysis of mass spectrometric data sets, it does not always identify metabolites of interest in a targeted assay. Furthermore, there is a paucity of vendor-independent software that deals with targeted analyses of metabolites and of isotopologues in particular. Here, we present AssayR, an R package that takes high resolution wide-scan liquid chromatography–mass spectrometry (LC-MS) data sets and tailors peak detection for each metabolite through a simple, iterative user interface. It automatically integrates peak areas for all isotopologues and outputs extracted ion chromatograms (EICs), absolute and relative stacked bar charts for all isotopologues, and a .csv data file. We demonstrate several examples where AssayR provides more accurate and robust quantitation than XCMS, and we propose that tailored peak detection should be the preferred approach for targeted assays. In summary, AssayR provides easy and robust targeted metabolite and stable isotope analyses on wide-scan data sets from high resolution mass spectrometers.

中文翻译：

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AssayR：用于目标代谢物和稳定同位素示踪剂分析的简单质谱软件工具

代谢分析通常分为两类：无偏代谢分析和针对特定代谢物的分析。质谱仪的出现彻底革新了这两种技术，这些质谱仪带有可提供高质量精度和分辨率的检测器，例如飞行时间（TOF）和Orbitraps。该技术至关重要的一个特定领域是代谢通量分析领域，因为这些光谱仪的分辨率可以区分¹³种含C的同位素异源物和^15种含C的同位素异源物N或其他同位素。尽管可以免费使用基于XCMS的软件进行质谱数据集的非目标分析，但它并不总是能在目标分析中识别出感兴趣的代谢产物。此外，缺乏与供应商无关的软件，该软件专门处理代谢物，尤其是同位素异位体的靶向分析。在这里，我们介绍AssayR，这是一种R软件包，它采用高分辨率宽扫描液相色谱-质谱（LC-MS）数据集，并通过简单的迭代用户界面定制每种代谢物的峰检测。它会自动积分所有同位素的峰面积，并输出提取的离子色谱图（EIC），所有同位素的绝对和相对堆积条形图以及一个.csv数据文件。我们展示了几个实例，其中AssayR提供了比XCMS更准确和可靠的定量分析，我们建议定制的峰检测应该是靶向分析的首选方法。总而言之，AssayR在高分辨率质谱仪的宽扫描数据集上提供了简便而强大的目标代谢物和稳定的同位素分析。