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In this MIT lecture, at 7:22, the professor says that when J.J. Thomson added a positively charged plate on one side of the cathode ray and a negatively charged plate on the other side, he observed a large deflection towards the positive plate, and a small deflection towards the negative plate (see image below).

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This observation implied that hydrogen gas consists of positively charged particles with lots of mass, and negatively charged particles with a small amount of mass.

However, according to Wikipedia, cathode rays are "streams of electrons observed in vacuum tubes." Thus, my question is: in J.J. Thomson's experiment, where are the protons (positively charged particles) coming from?

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    $\begingroup$ You might need to reverse the polarity of the high voltage source for that to happen. $\endgroup$ – Zhe Jan 23 at 22:20
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Thompson observed more than just cathode rays.

He experimented with different gases and different pressures in his tubes. When there is a significant amount of hydrogen you get ionisation of the gas and more than one type of charged particle can be generated and deflected (though different conditions are needed to see protons than electrons).

Part of the point of this was to distinguish between particles produced by the gas and particles produced when there was little or no gas. The point about cathode rays is that they can still be produced when there is virtually no gas in the tube by thermionic emission from the cathode. They have the same properties as one of the particles produced by ionising hydrogen which established some of the basis for saying that electrons are an important part of atoms.

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In the diagram both the ends of battery group is shown as cathode(small line)(?)

Here a perforated anode is used and so only anions-here electrons- originated from cathode can pass through and so beyond anode only stream of electrons would emerge which registers a high deflection towards positive plate in the external electric field, due to their very small mass and so low momentum.

If the applied high DC voltage is reversed in the discharge tube( not of the external electric field), a stream of protons (hydrogen atom minus electron) would emerge out of perforation in the cathode (they originated from anode) would pass though and in the external field of the same strength as in the earlier experiment, would register less deflection due to heaviness of proton(nearly 1836 times that of electron) and so high momentum.

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