The Sample Analysis at Mars (SAM) instrument aboard the Curiosity Rover at Gale crater can characterize organic molecules from scooped and drilled samples via pyrolysis of solid materials. In addition, SAM can conduct wet chemistry experiments which enhance the detection of organic molecules bound in macromolecules and convert polar organic compounds into volatile derivatives amenable to gas chromatography-mass spectrometry analyses. Specifically, N-tert-butyldimethylsilyl-N- methyltrifluoroacetamide (MTBSTFA) is a silylation reagent whereas tetramethylammonium hydroxide (TMAH) is a thermochemolysis methylation reagent. Shortly after arriving at Mars, the SAM team discovered that at least one of the MTBSFTA cups was leaking, contributing to a continuous background inside SAM with the potential to interfere with future TMAH reactions. Therefore, here we characterized possible interactions between the two reagents to determine byproducts and implications for the detection of indigenous organics. SAM-like pyrolysis experiments supplemented with flash pyrolysis were accordingly conducted with fragments of the Murchison meteorite as a reference for exogenous organic matter delivered to Mars. Flash TMAH experiments yielded various aromatic acids, dicarboxylic acids, and amino acids while SAM-like pyrolysis presented mixtures of methylated and non-methylated compounds due to decreased reaction efficiency at slower ramp rates. All experiments in the presence of simulated MTBSTFA vapor produced pervasive silylated byproducts which co-elute and obscure the identification of Murchison-derived compounds. Despite challenges, a significant diversity of pyrolyzates and TMAH derivatives could still be identified in flash pyrolysis in presence of MTBSTFA. However SAM-like experiments with TMAH and MTBSTFA are hindered by both decreased methylation yields and additional co-eluting compounds.