Upon completion of this module, you should be able to explain how a mass spectrometer works and describe some applications of a mass spectrometer. One of the most beneficial uses of a mass spectrometer is to distinguish the atomic masses and natural abundance of isotopes of an element. Isotopes of an element have the same number of protons but different numbers of neutrons. Therefore, the atomic masses of isotopes of the same element are different. The percentage of an isotope in a sample of an element found in nature is called the relative abundance.