Oxidation processes of a linear and a branched ether, oxymethylene ether 2 (OME₂) and trimethoxymethane, also known as trimethyl orthoformate (TMOF), were investigated in two complementary atmospheric flow reactor setups coupled to electron ionization molecular-beam mass spectrometer (EI-MBMS). One with high mass resolution to measure speciation data and the second with photoionization MBMS (i²PEPICO) to gain isomer distribution. It can be shown that both ethers have different reactivity with trimethoxymethane reacting at lower temperatures. Furthermore, fuel decomposition and intermediate profiles can be analyzed by combining the results of isomer fractionation using i²PEPICO combined with the quantitative species profiles of EI-MBMS. The results show a huge number of oxygenated species. While the obtained species pool is similar, measured mole fractions differ. Isomers, as for example ethanol and dimethyl ether, are separated and quantified. Direct comparison of the oxidation intermediates of the linear and branched ether clarifies the different reactivity due to their given fuel structures.