In this article we describe the design, construction and implementation of our ion-atom hybrid system incorporating a high resolution time of flight mass spectrometer (TOFMS). Potassium atoms ($^{39}$K) in a Magneto Optical Trap (MOT) and laser cooled calcium ions ($^{40}$Ca$^+$) in a linear Paul trap are spatially overlapped and the combined trap is integrated with a TOFMS for radial extraction and detection of reaction products. We also present some experimental results showing interactions between $^{39}$K$^+$ and $^{39}$K, $^{40}$Ca$^+$ and $^{39}$K$^+$ as well as $^{40}$Ca$^+$ and $^{39}$K pairs. Finally, we discuss prospects for cooling CaH$^+$ molecular ions in the hybrid ion-atom system.
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