Fractionation of petroleum during migration through sedimentary rock matrices has been observed across lengths of meters to kilometers. Selective adsorption of specific chemical moieties at mineral surfaces and/or the phase behavior of petroleum during pressure changes typically are invoked to explain this behavior. Such phenomena are of interest as they impact both the quality and recoverability of petroleum resources. Given the current emphasis on unconventional (continuous) resources, there is a need to understand petroleum fractionation occurring during expulsion and migration at the nanometer to micrometer scale, due to the fine-grained nature of petroliferous mudrocks. Here, we explore organic matter compositional differences observed within kukersites (petroleum source beds containing acritarch Gloeocapsomorpha prisca) and the overlying carbonate reservoir layer from the Ordovician Stonewall Formation using a suite of spectroscopic methods, primarily through atomic force microscopy-based infrared spectroscopy (AFM-IR). AFM-IR is capable of providing spatial resolution approaching 50 nm and allows for assessment of the molecular fingerprint of kukersite organic matter across transition zones from organic-rich "source" layers into neighboring carbonate "reservoir" layers similar to 150 mu m away. Results indicate that organic matter composition begins to vary immediately following expulsion from source layers, with loss of carbonyl groups and a concomitant decrease in alkyl chain-length, as migration distance increases. These chemical transitions correlate with a decrease in fluorescence intensity, increase in solid bitumen reflectance, and increase in Raman aromaticity proxies (D-G band separation) in the organic matter. Our findings are consistent with the retention of polar compounds onto mineral grains during expulsion and migration, following primary cracking and bituminization of the Gloeocapsomorpha prisca kerogen.