## 1 Introduction  
Anaerobic digestion (AD) is a biological process in which microorganisms biodegrade and stabilize complex organic matter in the absence of oxygen, yielding treated effluent and methane for energy recovery [1, 2]. AD has historically been used for waste management and wastewater treatment and has recently emerged as a promising solution for food waste reduction, energy recycling, and nutrient recovery [2, 3]. The process of AD consists of four phases. First, hydrolysis breaks down complex organic matter (proteins, carbohydrates, and fats) into soluble organic molecules (amino acids, sugars, and fatty acids). Second, acidogenesis converts these products into alcohols, carbonic acid, and volatile fatty acids. Third, acetogenesis generates acetic acid, carbon dioxide, and hydrogen. Finally, methanogenesis occurs to produce biogas (typically 60% methane, 40% CO\({}_{2}\)) [1; 2; 3; 4; 5]. Anaerobic bioreactors are complex, multi-variable systems, as during their operation, substrates are consumed and products and intermediate metabolites are formed [6]. The development of volatile fatty acids (VFAs) is a key intermediate in the process of AD; however, the production and accumulation of specific VFA concentrations have shown the ability to be inhibitory, ultimately limiting biogas generation [3; 4; 7]. [PERSON] et al. suggest that only VFAs can be considered reliable for process monitoring; therefore, successful identification of the individual VFAs formed is vital [4], as it can supply valuable information on the different metabolic pathways involved in the process. The typical operation of bioreactors is based on the routine monitoring of several key parameters including: biogas production, biochemical oxygen demand (BOD\({}_{5}\)), chemical oxygen demand (COD), total organic carbon (TOC), pH, and measurements of specific nutrients and by-products, such as carbohydrates, VFAs, amino acids, and ammonium [8; 9]. These traditional methodologies used for monitoring are costly, time-consuming and only provide a narrow snapshot of the process, providing limited information on the chemical composition of the organic matter present [8; 10]. As such, there are benefits to exploring new analytical approaches to characterize anaerobic digestion in order to give an improved analysis of the key chemical parameters governing the system. Microorganisms are the driving force behind the complex biological process of AD [3], with the microbiome being extremely sensitive and heavily dependent upon the environmental conditions present within the bioreactor [11]. The disruption of a digester can be costly and result in heavy losses of biogas production. Quaternary ammonium compounds (QACs) are commonly used industrial disinfectants and are known to interfere with the proper functioning of the AD process. Disinfectants may enter an aerobic digestion system through contamination from the use of disinfectants in other parts of a food processing facility, or by improper cleaning of the digestion system itself. The impact of QACs on the anaerobic microbiome, and in particular their impact on specific metabolic pathways, are not yet fully understood [12; 13]. Benzalkonium chloride (BAC), which is a mixture of alkyl benzyl dimethyl ammonium chlorides with chain lengths C8-C18 [14; 15], is the most frequently found QAC in municipal wastewaters worldwide and is perceived to be recalcitrant under anaerobic conditions [14; 16; 17; 18; 19]. Studies exploring the impact of BAC on anaerobic digestors show this impact primarily through the measured reduction in biogas production and do not explicitly explore the metabolomic profile of the anaerobic digestion process [17; 18; 19; 20]. This limited knowledge of how QACs impact anaerobic microbial processes limits the ability to determine the extent to which QACs have impacted the digestion processes. The measurement of QACs in wastewater is a key step for monitoring potential impacts on AD and have been performed in the past using various technologies, but each with their own limitations.