Target molecules in a sample can be detected at an improved sensitivity by means of a mass spectrometer. A sample with or without a matrix is placed on a substrate and irradiated with a converged and pulsed primary beam selected from an ion beam, a neutral particle beam or a laser beam. Secondary ions and neutral molecules are emitted along with protons from the irradiated point of the sample as an electric field is applied between the substrate and an extraction electrode disposed above the substrate. A proton-control electrode is arranged in axial symmetry with the trajectory of the primary beam. A voltage is applied thereto so that the generated electric field decelerates the flying protons to raise their adhering efficiency to the flying neutral molecules.