The study answers to a question: How are 3D molecular and electronic structures; energetics; thermodynamics, kinetics and diffusion of mass spectrometric (MS) ions correlate quantitatively? Despite, irreplaceable application of the mass spectrometry to many interdisciplinary research fields as a robust analytical instrumentation, due to superior method performances, there is a lacuna in this issue, which as yet is not been unambiguously resolved. Our innovative stochastic dynamic (SD) quantitative MS approach has emerged in recent few years and empirically justified in claiming that exact functions among measurable variable intensity of peaks of ions; their 3D molecular and electronic structures, reaction rates, free Gibbs energy and diffusion exist, and the relations behave as our model formulas say. They treat MS variables highly accurately, precisely, selectively, sensitively, and exactly, respectively. It seems clearly that, we must have reliable empirical facts for such claims, because of many MS ionization phenomena are still far from well understood. However, the SD equations provide reasons to think that they might be warranted in moving toward an exact answer to the question. Herein, we provide new empirical facts and pro-arguments, examining ESI(+)-CID-MSⁿ data (n = 1–4) on apigenin-O-glucoside (1) via the SD formulas. The study argues for that the SD theory provides best quantitative explanation of MS observable subtle electronic effects of complex molecules from perspective of electronic structures, exhibiting a set of tautomers, proton and charge transfer effects, like analyte (1). Ab initio and semi-empirical static methods, molecular dynamics and chemometrics were carried out, as well.