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Extraction of protein residues from archaeological matrices, such as pottery clay, lithics, and grinding stones, has proven to be methodologically challenging. Protein residue analysis is fraught with technical challenges in analytical chemistry. In cooking pottery, protein residues are thought to bind to clay surfaces in vessel walls through a variety of primarily non-covalent interactions. Removal of protein residues requires the disruption of these interactions, and a diverse set of tools has been proposed and applied. Here, we test extraction procedures through varying combinations of physical parameters and solvents to derive an optimal approach yielding efficiencies of recovery from experimental pottery above 60%. The utility of our extraction approach was further validated through liquid chromatography-mass spectrometry analysis of experimental residues. We have identified several hurdles to developing a successful study of protein residues from pottery, each of which is surmountable with additional method development in the realm of archaeological chemistry. [ABSTRACT FROM AUTHOR]

Despite the growing body of evidence demonstrating that proteins can survive for thousands to even millions of years in selected contexts, there are relatively few examples of the successful recovery and identification of archaeological protein residues from ceramic artifacts. Claims of positive results are sometimes contentious and frequently challenged. One source of confusion in the debate is a general lack of consideration for the taphonomic histories of ceramic-bound proteins. To gain insight into this issue, we conducted an integrated, mass spectrometry-based study examining ceramic-bound protein that was experimentally aged over the course of 12 months. Results demonstrate the rapid degradation of proteins, raise questions about the degree to which ceramic-bound proteins can be expected to survive over time, and reveal some of the limitations of non-targeted mass spectrometry-based analyses. Further, by comparing results from our experimentally-aged samples to the those we obtained from a multi-pronged study of archaeological ceramics from the American Southwest, we are able to draw more confident conclusions regarding our lack of meaningful matches in the archaeological samples. [ABSTRACT FROM AUTHOR]