Probe electrospray ionization (PESI), which is an ambient ionization technique, enables us to analyze intact endogenous metabolites without sample preparation. In this study, we applied the newly developed method of PESI coupled to tandem mass spectrometry (PESI/MS/MS) to analyze metabolites in mouse brain, where its lipid composition often interfere with MS-based metabolome analysis. As a result, PESI/MS/MS directly detected 25 metabolites in a mouse frontal cortex, and clearly discriminated the metabolic profiles of mice model with energy metabolism disruption from control mice. PESI/MS/MS also allowed us to perform local distribution analysis of the hippocampus as well as the frontal cortex in each mouse (n = 5), discriminating their subtle metabolic differences. These results showed high potential of PESI/MS/MS for direct metabolome profiling of mouse brain. (C) 2017 Elsevier B.V. All rights reserved.