Do you mean that a bottle full of Nitrogen would be Phogiston, in the same way that a Hyrodgen Ion⁺ is a proton(Absence of an electron)?

Acknowledging, of course, that the nomenclature we are considering is among the most ridiculed of historical attempts of scientific explanation I don't think the analogy would call the absence of electron a proton. A proton is a specific particle that has a positive charge but not all positive charges are considered to be protons (even if protons are usually involved somewhere underneath in conventional matter).