Photoion mass-selected threshold photoelectron spectroscopy (ms-TPES) is a synchrotron-based, universal, sensitive, and multiplexed detection tool applied in the areas of catalysis, combustion, and gas-phase reactions. Isomer-selective vibrational fingerprints in the ms-TPES of stable and reactive intermediates allow for unequivocal assignment of spectral carriers. Case studies are presented on heterogeneous catalysis, revealing the role of ketenes in the methanol-to-olefins process, the catalytic pyrolysis mechanism of lignin model compounds, and the radical chemistry upon C–H activation in oxyhalogenation. These studies demonstrate the potential of ms-TPES as an analytical technique for elucidating complex reaction mechanisms. We examine the robustness of ms-TPES assignments and address sampling effects, especially the temperature dependence of ms-TPES due to rovibrational broadening. Data acquisition approaches and the Stark shift from the extraction field are also considered to arrive at general recommendations. Finally, the PhotoElectron PhotoIon Spectral Compendium (https://pepisco.psi.ch), a spectral database hosted at Paul Scherrer Institute to support assignment, is introduced.