Efficient power technologies such as high temperature fuel cells demand ultra-low concentrations of contaminants in the fuel feed e.g. < 1 ppm(v), imposing stringent requirements on fuel clean-up technology. Proton transfer reaction-mass spectrometry (PTR-MS), being fast and suitable to measure ultra-low concentrations can be an optimal tool for the characterization of clean-up methods. It is exploited here for the simultaneous measurement of breakthrough curves of biogas filters loaded with a mix of compounds that simulate biogas pollutants. The sorbent materials are able to efficiently remove propanethiol and butanethiol and to a lesser degree methanethiol and hydrogen sulfide. Carbon disulfide and dimethylsulfide were the compounds that elute from the filters. These results support the development of set-ups for the cleaning of real biogas from the Organic Fraction of Municipal Solid Waste (OFMSW) and its use for Solid Oxide Fuel Cell (SOFC) feeding.