Why did J.J. Thomson observe protons in his cathode ray experiment? 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).



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?
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.