The term structural analysis shall be used to refer to innovative stochastic dynamics mass spectrometric equations utilised for determining three-dimensional molecular structures of caffeine metabolites and theoretically predict their mass spectra. The study examines caffeine; uric acid, 1-methyl-, 1,2-, 1,7-, and 3,7-dimethyl-uric acid; xanthine; 1-, 3-, and 7-methyl-xanthine; para- and hydroxy-xanthines; theacrine; theobromine; guanine; thymine; and theophylline, respectively. It employs ultra-high-resolution electrospray ionisation mass spectrometry and ion mobility spectrometry; high accuracy quantum chemical static methods and molecular dynamics based on ab initio and density functional theory. Chemometrics assesses degree of statistical correspondence between observable and theoretical data on these equations and analyte measurands.