This paper derived relation between mass spectrometric variable intensity of analyte peaks and three-dimensional molecular structures of ions toward temperature utilising innovative stochastic dynamics equations, which provide exact analyte quantification and 3D structural analysis and are attractive formulas for modelling of mass spectrometric phenomena. The same equations are opened to develop new relations accounting for temperature; thus, providing argumentation about temperature dependent variables. High-temperature measurement of vapours are important tool, amongst others and use the Arrhenius’s plot. However, there is a variation between experimental and theoretical linear correlation toward temperature; thus, highlighting soft ionisation methods showing significant standard deviations. It could be explained with temperature perturbation of charge values. Descriptive models, so far, provide semi-quantification. This study, first shows validity of new functional model. Straightforwardly, its empirical proof is obtained determining 3D structurally protomers and isotopomers of configurationally locked polyenes via ultra-high resolution electrospray ionization and atmospheric pressure chemical ionization mass spectrometry within the temperature range T=300-450°C. There are used high accuracy quantum chemical static methods, molecular dynamics and chemometrics. There are excellent method performances (|r|=0.99978). The tool could be regarded as an actually honest alternative of available theoretical models.