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We compare everything to neutral atoms because it gives us a baseline to compare ions and compounds. For example, it helps us understand the differences in ionization energy because it is easier to remove an electron away from a neutral atom instead of a cation.
When we compare to the neutral atom, is it easy to determine if there was a loss or gain in electrons due to the positive or negative charge of the given ion. In the neutral state, the number of electrons equals the number of protons, so if there is a change in the net charge of the atom, it becomes represented with - or +.
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