The European Space Agency/Rosetta mission escorted comet 67P/Churyumov-Gerasimenko and witnessed the evolution of its coma from low activity (∼2.5-3.8 au) to rich ion-neutral chemistry (∼1.2-2.0 au). We present an analysis of the ion composition in the coma, focusing on the presence of protonated high proton affinity (HPA) species, in particular. This ion is produced through the protonation of NH3 and is an indicator of the level of ion-neutral chemistry in the coma. We aim to assess the importance of this process compared with other sources, such as the dissociation of ammonium salts embedded in dust grains. The analysis of has been possible thanks to the high mass resolution of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis/Double Focusing Mass Spectrometer (ROSINA/DFMS). In this work, we examine the data set alongside data from the Rosetta Plasma Consortium instruments, and against outputs from our in-house ionospheric model. We show that increased comet outgassing around perihelion yields more detections of and other protonated HPA species, which results from more complex ion-neutral chemistry occurring in the coma. We also reveal a link between the low magnetic field strength associated with the diamagnetic cavity and higher counts. This suggests that transport inside and outside the diamagnetic cavity is very different, which is consistent with 3D hybrid simulations of the coma: non-radial plasma dynamics outside the diamagnetic cavity is an important factor affecting the ion composition.