Atom Probe Tomography (APT) analysis is being actively used to provide near-atomic-scale information on the composition of complex materials in three-dimensions. In recent years, there has been a surge of interest in the technique to investigate the distribution of hydrogen in metals. However, the presence of hydrogen in the analysis of almost all specimens from nearly all material systems has caused numerous debates as to its origins and impact on the quantitativeness of the measurement. It is often perceived that most H arises from residual gas ionization, therefore affecting primarily materials with a relatively low evaporation field. In this work, we perform systematic investigations to identify the origin of H residuals in APT experiments by combining density-functional theory (DFT) calculations and APT measurements on an alkali and a noble metal, namely Na and Pt, respectively. We report that no H residual is found in Na metal samples, but in Pt, which has a higher evaporation field, a relatively high signal of H is detected. These results contradict the hypothesis of the H signal being due to direct ionization of residual H2 without much interaction with the specimen's surface. Based on DFT, we demonstrate that alkali metals are thermodynamically less likely to be subject to H contamination under APT-operating conditions compared to transition or noble metals. These insights indicate that the detected H-signal is not only from ionization of residual gaseous H2 alone, but is strongly influenced by material-specific physical properties. The origin of H residuals is elucidated by considering different conditions encountered during APT experiments, specifically, specimen-preparation, transportation, and APT-operating conditions by taking thermodynamic and kinetic aspects into account.