Complex sentence: The gas chromatography stage separates the mixture into its various constituent parts (i.e. substrate and series of active compounds) which are then then passed off to the mass spectrometer for individual characterisation.
Split into simpler sentences: The Gas chromatography stage will separate the mixture into its constituent parts (i.e. substrate and series of active compounds). Each of these stages will then be passed to the mass spectrometer for individual characterisation.