An understanding of the chromatographic theory, and operating mechanism of ionisation techniques and mass analysers is essential for method selection, development and optimisation. This is an advanced course in chromatography and mass spectrometry for chemical analysis of organic and inorganic compounds. The course is a natural extension of any basic course in analytical chemistry for everybody who is going to use modern hyphenated techniques such as GC-MS, LC-MS(MS) for analysis of complex mixtures. The course covers chromatographic separation of small molecule organic and inorganic compounds with special emphasize on the molecular mechanism and theory of analyte-column interactions for gas, supercritical fluid and liquid chromatography, and the theory of ionization, fragmentation, mass-to-charge separation, ion detection and data interpretation for all common mass spectrometers and ionization techniques. The theory is taught using lectures, colloquia sessions, and theoretical exercises supplemented with guest-lectures of selected topics.