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Bivalve shells are extensively used as bioarchives for paleoclimate and paleoenvironmental reconstructions. Proxy calibrations in recent shells are the basis for sclerochronology and the applications of geochemistry data to fossils. Shell geochemical information, however, could be altered with the disappearance of intercrystalline organic matrix components, including those linked to shell growth increments, during early diagenesis. Thus, an evaluation of the chemistry of such organics is needed for the correct use of sclerochronological records in fossil shells. Here, we use atom probe tomography (APT) for in situ geochemical characterization of the insoluble organic matrix in shell growth increments in the Antarctic scallop, Adamussium colbecki. We confirm the presence of carboxylated S-rich proteoglycans, possibly involved in calcite nucleation and growth in these scallops, with significant concentrations of magnesium and calcium. Diagenetic modification of these organic components could impact proxy data based on Mg/Ca ratios, but more importantly the use of the δ15N proxy, since most of the shell nitrogen is likely bound to the amide groups of proteins. Overall, our findings reinforce the idea that shell organics need to be accounted for in the understanding of geochemical proxies.