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In his experiment, Rutherford first shot positively charged alpha particles into a chamber full of nitrogen gas. The sheet of silver foil he placed at the end of the chamber was meant to stop any alpha particles generated from the radiactive source. The particles that did pass through hit a floruescent screen and emitted light. Although the set up was tested with various gasses, nitrogen was the only one to produce the light. The Particles that did pass through the foil to produce light were shown to have a similar range and charge to protons. After further examination, scientists discovered that the alpha particle actually entered the nitrogen nucleus and ejected a hydrogen nuclei This was the first time that one element was changed into another and this process was called nuclear transmutation..
Over the coming years other phycisits conducted a number of experiments transmuting atoms in one another. In every case, hydrogen Nuclei were emitted in the process. As the importance of the hydrogen nuclei became more apparent its nuclear masses and charges were compared. Scientists were then able to deduce that the positive charge of any nucleus could be accounted for by an integer number of hydrogen nuclei. By the late 1920's the hydrogen nuclei were referred to as protons, the term originally coined by Rutherford.
Diagram showing the ejection of a proton from the Nitrogen Nucleus due to the introduction of an alpha particle.