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This data set reports a suite of complementary biogeochemical analyses of peat samples from the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experiment. Results were collected using quantitative molecular analysis of bulk soil carbon to assess the stability of soil organic carbon following whole-ecosystem warming and exposure to elevated carbon dioxide concentrations (eCO2). Targeted soil organic carbon components include solvent-extractable compounds (alkanoic acids, alkanols, alkanes, steroids, and terpenoids), ester-bound hydrolysable biopolymers (cutin and suberin markers), lignin phenols, and pyrogenic carbon. Bulk peat samples were analysed by Soxhlet extraction and solid phase separation for solvent-extractable compounds, alkaline hydrolysis to extract hydrolysable biopolymers, copper (II) oxide oxidation to extract lignin phenols and benzene polycarboxylic acids (BPCAs) as an approximation of pyrogenic carbon. Samples were analysed by gas chromatography (GC) equipped with a flame ionization detector (GC-FID) and compound identification was performed on GC coupled to mass selective detector (MS) for solvent-extractable compounds, ester-bound hydrolysable biopolymers and lignin phenols, and high-performance liquid chromatograph (HPLC) for pyrogenic carbon. Results are presented in Ofiti et al. (accepted). The experimental work was conducted on samples collected in August 2018 at the SPRUCE climate manipulation experiment in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). Samples were collected …