Comprehensive chemical kinetics models used in the simulation of hydrocarbon and biofuel oxidation rely on accurate prescription of the underlying reaction mechanisms and rate parameters of associated elementary reactions. For practical transportation fuels, such models contain thousands of elementary reactions, which collectively define chain-initiation, -propagation, -branching, and -inhibition pathways. In the low-temperature regime, below approximately 1000 K where R + O₂ reactions dominate, primary oxidation intermediates including cyclic ethers, carbonyls, and conjugate alkenes are formed in abundance via unimolecular decomposition of either chemically activated or thermalized radicals, specifically organic peroxy (ROO) or hydroperoxyalkyl species (QOOH). Experimental results from multiplexed photoionization mass spectrometry (MPIMS) experiments are detailed herein for several intermediates, derived initially from R + O₂ reactions of hydrocarbons and biofuels, and show that intermediate species formed in the initial steps of oxidation undergo similar reactions to those of the parent molecule, including through QOOH-mediated pathways. Products from QOOH decomposition via chain-inhibition and chain-propagation pathways, namely conjugate alkenes, carbonyls, and cyclic ethers, are detected directly. Despite such rich chemistry involving QOOH radicals, most comprehensive chemical kinetics models neglect the complete description of primary oxidation intermediates, and rather consider a restricted number of reaction pathways. It is suggested that exclusion of the details of the oxidation of these intermediate products may affect the interpretation of combustion simulations using such models.