Once scientist knew that atoms were made up of a combination of protons neutrons and electrons, and figured out how that combination effected their properties [(Periodic law)](https://en.wikipedia.org/wiki/Periodic_trends), they could say things like “I never had this element to test, but when I find it I know it’ll have these properties.
So whenever they *did* find an element with those properties, they had a good reason to believe they knew it’s number of electrons and protons.
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