Abstract: The present invention provides for systems and methods for automated quantification of individual compounds in a mixture. The invention is generally concerned with quantitative analysis of solid, liquid, or gas samples and relies on a separation instrument and on a mass detector. The separation instrument provide means to separate the individual compounds typically according to certain physicochemical property, and the mass detector provides means to determine the amount or concentration of an arbitrary compound using an instrument-specific calibration curve. The present invention provides automated capability to analyze such mixtures without user intervention by varying pre-determined control parameters on one or more of the instruments so as to achieve a high degree of analytical resolution of some or all of the individual compounds in the mixture.