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Water is considered a difficult component to analyze. Many think water should not be injected into a GC capillary column; that is a myth.
Water as component or matrix will elute at relative low temperatures, meaning it will do little harm with bonded stationary phases. Water in the carrier gas, or introduced as a leak, is a bigger problem as the column is hot and the phase/surface will hydolize and create active sites. Water as component can be done on several stationary phases, polar and non-polar.
The biggest challenge is to get a reproducible injection. Water as matrix is more challenging. There are several ways to isolate the components from the matrix. It is also possible to inject water, however, one needs to be careful for back flash. Also, adding co-solvents can help to smoothen the injection band.
In this on-demand webinar, Restek's GC Specialst Jaap de Zeeuw discusses different options for measuring water and analysis of analytes in a water matrix.