Comprehensive Analysis of Inflammatory Bowel Disease

The Clinical IBD data was obtained from the Inflammatory Bowel Disease Multiomics Database [15 (link)]. A large cohort of IBD patients were included for this study. The stool samples of CD (n = 266), UC (n = 144), and non-IBD (n = 135) were collected. The extraction and purification steps have already been described previously [29 (link)]. The quality control (QC, n = 59) samples were also included. All clinical information from the samples is summarized in Table S2. The data format conversion and initial parameters were identical to the NIST dilution series above. The TICs of the data are shown in Figure S4. Parameter optimization was performed using four QC samples from each group randomly selected from the whole batch. The optimized parameters are provided in Table S1. The data analysis was finished with the whole MetaboAnalystR 3.0 workflow. Functional analysis was performed by integration with Mummichog2 for the comparisons between different groups (cutoff of p value 2.0 × 10⁻⁶).