Lasers are used to couple each ion's internal and external motional degrees of freedom. The Coulomb interaction between the two ions couples their motion. This allows the internal state of one ion to be transferred to the other. An auxiliary "logic ion" provides cooling, state preparation, and state detection for the co-trapped "spectroscopy ion," which has an electronic transition of interest. The logic ion is used to sense and control the internal and external state of the spectroscopy ion.
The logic ion is selected to have a simple energy level structure that can be directly laser cooled, often an alkaline earth ion. The laser cooled logic ion provides sympathetic cooling to the spectroscopy ion, which lacks an efficient laser cooling scheme. Cooling the spectroscopy ion reduces the number of rotational and vibrational states that it can occupy. The remaining states are then accessed by driving stimulated Raman spectroscopy transitions with a laser. The light used for driving these transitions is far off-resonant from any electronic transitions. This enables control over the spectroscopy ion's rotational and vibrational state.
Thus far, QLS is limited to diatomic molecules with a mass within 1 AMU of the laser cooled "logic" ion. This is largely due to poorer coupling of the motional states of the occupants of the ion trap as the mass mismatch becomes larger. Other techniques more tolerant of large mass mismatches are better suited to cases where the ultimate resolution of QLS is not needed, but single-molecule sensitivity is still desired.