This work employs Fourier transform ion cyclotron resonance (FT-ICR) and the Gaussian quantum chemistry composite methods W1 and G2 to experimentally and computationally analyze gas-phase basicities (GB) for a series of weak bases in the basicity region around and below water. The study aims to clarify the long-standing discrepancy between reported GB values for weak bases obtained via high-pressure mass spectrometry (HPMS) and ICR; the ICR scale is observed to be more than 2 times contracted compared to the HPMS scale. The computational results of this work support published HPMS data. This agreement improves with increasing sophistication of the computational method and is excellent at the W1 level. Several equilibria were also re-examined experimentally using FT-ICR. In the experiments with some polyfluorinated weak bases (hexafluoro-2-propanol and nonafluoro-2-methyl-2-propanol), it was found that two protonation processes compete in the gas phase: protonation on oxygen and protonation on fluorine. In these species, protonation on fluorine proceeds faster and is statistically favored over protonation on oxygen but leads to cations that are thermodynamically less stable than oxygen-protonated cations. The process may also lead to the irreversible loss of HF. The rearrangement of fluorine-protonated cations to oxygen-protonated cations is very slow and is further suppressed by the process of HF abstraction. These results at least partially explain the discrepancy between published HPMS data and earlier FT-ICR findings and call for the utmost care in using FT-ICR for gas-phase basicity measurements of heavily fluorinated compounds. The narrower dynamic range of ICR necessitates the measurement of several problematic bases and produces some differences between the ICR results in the present work and the published HPMS data; the wider dynamic range allows HPMS to overcome these difficulties in connecting the ladder.