Methods and Application of Food Composition Lab, Beltsville Human Nutrition Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, 20705, USA.
U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, Madison, WI, USA.
Anal Bioanal Chem. 2024 Oct;416(25):5527-5555. doi: 10.1007/s00216-024-05528-x. Epub 2024 Sep 17.
The R programming language, RStudio, and open-source software solutions for analysis of liquid chromatography-mass spectrometry (LC-MS) data have been used with user-written R-based custom quantification programs (CQP) for semi-quantification of triacylglycerols (TAGs) in bovine milk lipid extracts. Using the peak-finding capabilities of the package "xcms" in RStudio, peaks were integrated, and retention times aligned, normalized, and then used for semi-quantitative analysis of a custom set of four extraction internal standards (EISs) and 29 TAG regioisomers using the choice of four analytical internal standards (AISs). Alternating stereospecific numbering (sn) 1,3 TAG regioisomers (standards 1, 3, and 5 of six calibration standards) and sn-1,2 TAG regioisomers (standards 2, 4, and 6 of six standards) were used to make a set of six calibration standards, which were used for quantification using a linear fit model, polynomial fit model, power fit model, level-bracketed linear fit, replicate-bracketed polynomial fit, replicate-bracketed power fit, and replicate- and level-bracketed linear fit and response factors. For example, the linear fit for EIS1 gave an unacceptable coefficient of determination (CoD), r = 0.9616, whereas the polynomial fit gave r = 0.9908 and the power fit gave r = 0.9928, while the double-bracketed linear fit gave CoDs of r = 0.9960, 0.9848, and 0.9781 for the three brackets, yet gave the least % difference to known calibration concentrations. For unparalleled transparency, the CQP produced webpages that allowed every step in the data processing and quantification sequence to be verified and reproduced, and contained interactive figures. The data are publicly available using a digital object identifier (DOI). The R code can be downloaded and used with the downloadable data to reproduce the results, to modify the code and further customize the results, or to copy and paste and adapt the code to other quantification applications.
已使用 R 编程语言、RStudio 和用于液相色谱-质谱 (LC-MS) 数据分析的开源软件解决方案，结合用户编写的基于 R 的自定义定量程序 (CQP)，对半定量分析牛脂乳脂质提取物中的三酰基甘油(TAG)。在 RStudio 中的“xcms”软件包的峰查找功能的帮助下，对峰进行积分，调整保留时间，然后使用自定义选择的四套提取内标 (EIS) 和 29 种 TAG 区域异构体进行半定量分析四个分析内标 (AIS)。交替立体特异性编号 (sn)1,3TAG 区域异构体（校准标准 6 个标准中的标准 1、3 和 5）和 sn-1,2TAG 区域异构体（6 个标准中的标准 2、4 和 6）被用于制作一套 6 个校准标准，用于使用线性拟合模型、多项式拟合模型、幂拟合模型、水平括号线性拟合、重复括号多项式拟合、重复括号幂拟合和重复和水平括号线性拟合和响应因子进行定量。例如，EIS1 的线性拟合得到不可接受的决定系数 (CoD)，r=0.9616，而多项式拟合得到 r=0.9908，幂拟合得到 r=0.9928，而双括号线性拟合则给出了三个括号的 CoD 分别为 r=0.9960、0.9848 和 0.9781，但与已知校准浓度的差异最小。为了实现无与伦比的透明度，CQP 生成了网页，允许验证和重现数据处理和定量序列的每一步，并包含交互图形。这些数据可通过数字对象标识符 (DOI) 公开获取。可以下载 R 代码，并结合可下载的数据使用该代码重现结果，修改代码并进一步自定义结果，或复制、粘贴和改编代码以用于其他定量应用。
