The development of ambient desorption/ionization mass spectrometry has shown promising applicability for the direct analysis of complex samples in the open, ambient atmosphere. Although numerous plasma-based ambient desorption/ionization sources have been described in the literature, little research has been presented on experimentally validating or determining the desorption and ionization mechanisms that are responsible for their performance. In the present study, established spectrochemical and plasma physics diagnostics in combination with spatially resolved optical emission profiles were applied to reveal a set of reaction mechanisms responsible for afterglow and reagent-ion formation of the Low-Temperature Plasma (LTP) probe, which is a plasma-based ionization source used in the field of ambient mass spectrometry. Within the dielectric-barrier discharge of the LTP probe, He₂⁺ is the dominant positive ion when helium is used as the plasma supporting gas. This helium dimer ion (He₂⁺) has two important roles: First, it serves to carry energy from the discharge into the afterglow region in the open atmosphere. Second, charge transfer between He₂⁺ and atmospheric nitrogen appears to be the primary mechanism in the sampling region for the formation of N₂⁺, which is an important reagent ion as well as the key reaction intermediate for the formation of other reagent ions, such as protonated water clusters, in plasma-based ambient ionization sources. In the afterglow region of the LTP, where the sample is usually placed, a strong mismatch in the rotational temperatures of N₂⁺ (B ²Σ_u⁺) and OH (A ²Σ⁺) was found; the OH rotational temperature was statistically identical to the ambient gas temperature (∼300 K) whereas the N₂⁺ temperature was found to rise to 550 K toward the tail of the afterglow region. This much higher N₂⁺ temperature is due to a charge-transfer reaction between He₂⁺ and N₂, which is known to produce rotationally hot N₂⁺ (B ²Σ_u⁺) ions. Furthermore, it was found that one origin of excited atomic helium in the afterglow region of the LTP is from dielectronic recombination of vibrationally excited He₂⁺ ions.