Model Released. Scientist injecting a sample into a Mass Spectrometer, an instrument used for protein analysis. Mass spectrometers are used to identify chemical compounds by exploiting the behaviour of their molecular ions in magnetic & electric fields. Samples in liquid form are injected into the machine at right. Inside, the substance is ionised by bombardment from high- energy electrons. Variable electric and magnetic fields are used to accelerate & deflect the ions towards a detector.