In this book we present the structure of stochastic systems theory for formal description of the liquid chromatography - mass spectrometry (LC-MS) measurements. The states of the system are assigned by the chromatographic column elution in so-called retention time. As system variables are considered levels of analytes measured by MS detector. The examining of the behavior leads to the probability distribution functions for deconvolution between the constituents. Related system based approach is introduced for the description of LC-MS measurement data. The abstract model is constructed according to the paradigms of the system theory.