Time-of-flight SIMS is applied to the analysis of single cells and different types of biological tissue samples enabling the generation of images with high spatial resolution and chemical specificity. However, the low yield of secondary ions from this type of sample still remains a challenge. This low yield could potentially be increased by enhancing the protonation of ions with the presence of water. Here, we have explored the application of a prototype water cluster ion beam for the analysis of mouse brain tissue samples. A series of experiments acquired with 20 keV (H2O)3000+ and 20 keV (H2O)4500+ were compared with 20 keV C60+, showing ion yield enhancement when a (H2O)n+ cluster ion is employed in the analysis. The results have demonstrated the potential benefits provided by the use of (H2O)n+ clusters for the analysis of mouse brain tissue samples. © 2014 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.