The number of protons in an atom is equal to its atomic number. So, if we are given an atom of sodium, using our knowledge of its atomic number (which is 11), we can state that the sodium atom contains 11 protons. Other sub-atomic particles of interest include the neutrons and electrons. The sum of number of protons and neutrons in an atom is known as its mass number. In case of sodium atom, the mass number is 23 and hence we can calculate that the number of neutrons is 23-11= 12.
For an ion (an atom that has lost or gained one or more electrons, such as Cl- or Na+), the atomic number is calculated the same way, i.e. by equating it to the atomic number. In other words, for atoms or ions, the number of protons is same as the atomic number.
Hope this helps.