Prior to Thomson's experiment, scientists were aware of how charged particles behaved in electric fields. They knew that a charged particle in an electric field would follow a parabolic path. They also knew that the size of the parabola was dependent on the particle's mass, charge, and speed. The speed of a particle in an electric field could be indirectly determined.
The cathode ray in Thomson's experiment behaved exactly like scientists would expect it to behave if it contained particles of negative charge. He was able to conclude that the cathode ray contained particles based on previous knowledge of how known particles behave in an electric field.
Further experiments by Thomson led to the determination of the charge to mass ratio of the particles in the cathode ray. This value indicated that the particles in the cathode ray were much smaller than a hydrogen atom.
Prior to Thomson's experiment, John Dalton had developed several postulates that he thought described atoms. One of his postulates was that atoms are indivisible. Thomson's experiments showed that this postulate was incorrect.
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