An enzyme-stabilized nucleophilic water molecule has been implicated at the transition state of Escherichia coli methylthioadenosine nucleosidase (EcMTAN) by transition state analysis and crystallography. We analyzed the EcMTAN mass in complex with a femtomolar transition state analogue to determine whether the inhibitor and nucleophilic water could be detected in the gas phase. EcMTAN-inhibitor and EcMTAN-inhibitor-nucleophilic water complexes were identified by highresolution mass spectrometry under nondenaturing conditions. The enzyme-inhibitor-water complex is sufficiently stable to exist in the gas phase.