Described are techniques for performing automated maintenance evaluations on a gas chromatograph (GC) or a gas chromatograph-mass spectrometer (GC-MS). Systems and methods are described for directing an injector 106 of a GC or GC-MS instrument system 100 to autonomously inject a diagnostic material sample 114 into a material analysis chamber and initiate a scientific analysis to formulate a set of results. The systems and methods further include the instrument system analyzing the set of results generating one or more output reports.