The Applications and Limitations of a Minimally Destructive Approach to Archaeological Proteomics

Although protein-based studies within archaeology have been applied for many years for bulk analyses, archaeological proteomics is a recent application. Not only can protein mass fingerprinting aid in identification of animal origin, it can reveal new information on the degradation process of proteins.
This study will focus on the MALDI-TOF-MS application ZooMS (Zooarchaeology by Mass Spectrometry) on collagen. Primarily collagen extracted from bone, although other collagenous materials were explored, notably leather. Although most bulk analyses protocols require decalcification prior to collagen extraction, and the first iterations of ZooMS analyses did also, this work presents a minimally destructive method to extract collagen from bone, involving extraction with ammonium bicarbonate buffer. The yield is consequentially lower than with a decalcified sample, however, the current generation of "soft"-ionization mass spectrometers is sufficiently sensitive for peptide fingerprinting these buffer extracts.
This allows us to investigate bone samples without loss of the protective mineral fraction. The contribution of this method is especially relevant to archaeological studies as it allows to (re-)investigate artefacts of worked bone without damaging the object and leaving microscopical features intact. The ability to re-analyze the exact same samples for DNA or other protein-based methods is just as relevant to studies of modern material, such as animal feed quality control. In addition, this study offers a currently unprecedented look at proteomics for animal origin detection in leather, treated with metal and organic tannages.
Aside from method development and exploration of the limits to buffer extraction approach, we investigate how deamidation of individual glutamine sites can give an indication of thermal damage in collagen. We present evidence that suggests that collagen retains its helical structure until nearly all collagen is lost, which offers further insight into the pattern of collagen degradation at a molecular level.