BackgroundDue to the close correlation between choline, L-carnitine, betaine and their intestinal microbial metabolites, including trimethylamine (TMA) and trimethylamine N-oxide (TMAO), and creatinine, there has been an increasing interest in the study of these compounds in vivo. MethodsIn this study, a rapid stable isotope dilution (SID)-UHPLC-MS/MS method was developed for the simultaneous determination of choline, L-carnitine, betaine, TMA, TMAO and creatinine in plasma, liver and feces of rats. The method was validated using quality control (QC) samples spiked at low, medium and high levels. Second, we applied the method to quantify the effects of Rosa Roxburghii Tratt juice (RRTJ) on plasma, liver, and fecal levels of choline, L-carnitine, betaine, TMA, TMAO, and creatinine in high-fat diet-induced hyperlipidemic rats, demonstrating the utility of the method. ResultsThe limits of detection (LOD) were 0.04–0.027 µM and the limits of quantification (LOQ) were 0.009–0.094 µM. The linear ranges for each metabolite in plasma were choline1.50–96 µM; L-carnitine: 2–128 µM; betaine: 3–192 µM; TMA: 0.01–40.96 µM; TMAO: 0.06–61.44 µM and creatinine: 1–64 µM (R2 ≥ 0.9954). The linear ranges for each metabolite in liver were Choline: 12–768 µM; L-carnitine: 1.5–96 µM; betaine: 10–640 µM; TMA: 0.5–32 µM; TMAO: 0.02–81.92 µM and creatinine: 0.2–204.8 µM (R2 ≥ 0.9938). The linear ranges for each metabolite in feces were choline: 1.5–96 µM; L-carnitine: 0.01–40.96 µM; Betaine: 1.5–96 µM; TMA: 1–64 µM; TMAO: 0.02–81.92 µM and Creatinine: 0.02–81.92 µM (R2 ≥ 0.998). The intra-day and inter-day coefficients of variation were < 8 % for all analytes. The samples were stabilized after multiple freeze–thaw cycles (3 freeze–thaw cycles), 24 h at room temperature, 24 h at 4 °C and 20 days at −80 °C. The samples were stable. The average recovery was 89 %-99 %. This method was used to quantify TMAO and its related metabolites and creatinine levels in hyperlipidemic rats. The results showed that high-fat diet led to the disorder of TMAO and its related metabolites and creatinine in rats, which was effectively improved after the intervention of Rosa Roxburghii Tratt juice(RRTJ). ConclusionsA method for the determination of choline, L-carnitine, betaine, TMA, TMAO and creatinine in plasma, liver and feces samples was established, which is simple, time-saving, high precision, accuracy and recovery.