Global profiling of gut microbiota-associated lipid metabolites in antibiotic-treated mice by LC-MS/MS- based analyses

We describe a protocol for identifying bacteria-derived lipid metabolites produced in the guts using antibiotic-treated mice, liquid chromatography tandem mass spectrometry-based lipidomics, and feature-based molecular spectrum networking (FBMN). Untargeted lipidomics using the MS-DIAL 4 program provides information on known and unknown complex lipid molecules. The FBMN technique clusters similar MS2 spectra, facilitating the identification of bacterial lipids. Targeted analysis was used as a complementary method to cover oxylipins. Here, we provide details for targeted and untargeted analyses. For complete details on the use and execution of this protocol, please refer to Yasuda et al. (2020).

Automated summary

This protocol involves using liquid chromatography tandem mass spectrometry and FBMN technique for identifying bacteria-derived lipid metabolites in the guts of antibiotic-treated mice. Untargeted lipidomics with MS-DIAL 4 program and clustering similar MS2 spectra are employed for the analysis of bacterial lipids. Targeted analysis is also used to cover oxylipins as a complementary method.