2.8. Data Processing, Analysis, and Visualization

The raw data acquired from the LC-MS analysis were processed using the XCMS 3.4.1 R-package for generating a peak list containing the peak area intensity, charge-to-mass ratio (m/z), and retention time. The data pretreatment included normalization to the total ion intensity, the 80% rule, and QC evaluation, as previously described in [16]. The Mann–Whitney’ U nonparametric test was used for the analysis of statistical differences between the two groups (9 BDCT and 9 SDCT). The Mann–Whitney U test, Bartlett’s test of sphericity, and the Kaiser–Meyer–Olkin (KMO) test were performed using SPSS 26.0.0.0 (IBM, New York, NY, USA). The principal component analysis (PCA), partial least-squares analysis (PLS), partial least-squares discriminate analysis (PLS–DA), and the variable importance for the projection (VIP) plot were performed using SIMCA–P 14.1 (Umetrics, Umeå, Sweden). The heatmap analysis was performed using TBtools–Ⅱ (v1.120, Toolbox for Biologists, Guangzhou, China). The graphs of the box plot were visualized using GraphPad Prism (GraphPad Software, San Diego, CA, USA). The pathway analysis was mapped by referring to the MetaboAnalyst (http://www.metaboanalyst.ca (accessed on 14 April 2023)) and KEGG (https://www.kegg.jp/ (accessed on 16 April 2023)) websites.