Molecules exhibit their intrinsic properties in their isolated forms. Investigations of isolated large biomolecules require an understanding of the detailed mechanisms for their emergence in the gas phase because these properties may depend on the isolation process. In this study, we apply droplet-beam laser-ablation mass spectrometry to isolate protein molecules in the gas phase by IR-laser ablation of aqueous protein solutions, and we discuss the isolation mechanism. Multiply charged hydrated lysozyme clusters were produced by irradiation of the IR laser onto a droplet beam of aqueous lysozyme solutions with various pH values prepared by addition of sodium hydroxide to the solution. The ions produced in the gas phase show significantly low abundance and have a lower number of charges on them than those in the aqueous solutions, which we explained using a nanodroplet model. This study gives quantitative support for the nanodroplet model, which will serve as a fundamental basis for further studies of biomolecules in the gas phase.