Taphonomy and negative results: An integrated approach to ceramic-bound protein residue analysis

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.