Each peak represents a single molecule of graphite.
Molecules are groups of two or more atoms.
Images such as this constitute some of the best experimental evidence that atoms and molecules are the fundamental units of matter. For an electron and a proton the electric charges are equal and opposite, even though the mass of the proton is nearly 2000 times the mass of the electron. Like charges repel. Unlike charges attract. Many objects can become electrically charged when they have an excess of either negative or positive charges.