The main challenge to direct injection of aqueous sample into GC/MS system is a possible contamination of the column which would shorten the life time of the column and could lead to peak broadening and tailing [13]. In the present study, a glass liner packed with glass wool was inserted into the injection port, which was demonstrated to be good for protecting a column from contamination by non-volatile compounds [4,13,18]. We did not observe any ghost peaks after running samples for more than 1000 injections. In our laboratory, SCFA from biogas digester samples have been routinely quantified with the GC method. We use the same column and similar GC condition as the GC/MS method presented here in. Our experience with the GC method showed that the life time of the polar column is around 4–5 years for the GC that runs almost all the time for the day today measurement of SCFA in a biogas digester samples. In the worst case, when the peak shape starts to broaden and tailing occurs, the gas liner is most probably contaminated and need to be changed in a matter of few minutes. Moreover, glass liner contamination was reduced due to the use of oxalic acid.