Indeed, the Pauli Exclusion Principle applies to two or more electrons or two or more protons or two or more of any of the same brand of fermions. Let's work with just electrons -- representative Fermions if you will. The basic stricture of the PEP is: any multiple-electron state must be antisymmetric under the interchange of any two electrons. This necessarily prevents two electrons from being in the same state -- for example, suppose we are interested in the atomic structure of Helium, and we'll use hydrogen wave functions as our basis. A one-electric state is characterized by a complete set of quantum numbers, and for hydrogen we'll use the standard set: orbit number, n, orbital and spin angular momenta L , S =1/2; Lz and Sz, the angular projections on the z-axis. The Helium state with 2 s state electrons (2s for short) with 2Sz=1 or -1. This state is impossible according to the Pauli Principle. It is symmetric under electron interchange.
Why the PEP? The reason is a bit arcane, and is best seen within the context of QFT. In order to guarantee that all non-interacting particles have positive energy (0 is allowed), the particles involved must either obey canonical commutation rules or canonical anti-commutation rules. The proof can be found in many texts, and, probably, in Google, or other internet venues.
And, of course, the major triumph of the PEP is the explanation of why the Periodic Table is as it is.. Atomic shell structures would be otherwise if not for the PEP.
Regards,
Reilly Atkinson
Note: the PEP applies to all electrons. However, if you include all these other electrons, you will find their influence is small, due mainly to distance.