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In search of fluorinated functional groups which could undergo defluorination, and therefore be included in novel non-polluting fluorinated surfactants, omega-(bis(trifluoromethyl)amino)alkane-1-sulfonates (BTFMA-AS) with a homologue distribution from seven to thirteen methylene groups were synthesized and investigated for aerobic biodegradation applying both a standardized test and a fixed-bed bioreactor (FBBR). These compounds were prepared as part of a screening study for potentially mineralizable fluorinated endgroups.Application of hybrid triple quadrupole-linear ion trap mass spectrometry (QqQ(LIT)-MS) coupled to high-performance liquid chromatography (HPLC) allowed the tracking of primary degradation as well as the detection and structural elucidation of biotransformation intermediates. An understanding of the fragmentation pathway of the test compounds allowed selective precursor ion scans to reveal the presence of stable fluorinated metabolites. Structures were confirmed by enhanced product ion scans and MS(3) scans in the linear ion trap mode.The primary biodegradation rate and the extent of biodegradation were found to be chain-length dependent, with higher homologues being completely primarily degraded within 10 days. For the first time, two simultaneous metabolic pathways for substituted linear alkane-1-sulfonates were discovered: Desulfonation, oxidation to a carboxylic acid and subsequent chain-length shortening by beta-oxidation dominated the metabolism. This pathway resulted in the formation of 3-(bis(trifluoromethyl)amino)propionic acid and bis(trifluoromethyl)aminoacetic acid, which showed recalcitrance in this experiment. Oxidation of the alkyl chain to the respective carbonyl derivative represents the minor pathway. Only the long-chain homologues of these oxidized species were partially degraded; the short-chain homologues were not attacked.