ZooMS - short for ZooArchaeology by Mass Spectrometry - uses the persistence and slow evolution of collagen as a molecular barcode to read the identity of collagen based materials such as bone, ivory and skin. The method uses a well established approach, peptide mass fingerprinting, allied to high throughput Time of Flight Mass Spectrometry.We routinely run a range of mass spectrometry-based analysis using the comprehensive suite of instrumentation available in the Centre of Excellence in Mass Spectrometry, including a the Ultraflex III MALDI-TOF/TOF and the Bruker maXis HD.
Mass spectrometry (MS) of proteins has been made possible due to the introduction of “soft” ionization methods, most notably MALDI (matrix-assisted laser desorption/ionization) and ESI (electrospray ionization) MS. MALDI achieves ionization of peptides through proton transfer via a solid matrix, where electrospray ionization can be attained directly from the liquid phase. These ionization methods allow molecules to not be degenerated during measurement. Where “harder” ionization would break down a protein in random fragments that are difficult to predict, proteins are instead digested by enzymes into peptides. Restrictive enzymes cut at specific sites (lysine and arginine for trypsin, the most common enzyme used for this purpose), creating consistent and predictable fragments. The resulting peptides can therefore be compared to theoretical fragments based on in silico digestions of known protein sequences.
ZooMS uses MALDI ionization to investigate materials such as bone extracts as these are relatively simple aqueous solutions, containing almost exclusively collagen type I. Collagen type I, the main organic constituent of bone, teeth, antler, and skin (leather and parchment), has a helical structure and consists of three fibrils: two α1 chains and one α2. Some fish collagens also contain a subunit α3 in lieu of one α1 chain. Although collagen is highly conserved through closely related taxa, especially within COLI-α1, there are minor – though significant – changes in primary sequence between genera and in some cases species. The changes in primary sequence cause differences in mass, ultimately producing a fingerprint of masses that may be (partially) characteristic for the animal of origin. Therefore, identification is dependent on the extent of evolutionary divergence (typically to the level of genera). For example, using ZooMS, sheep and goat can be distinguished primarily through a single peptide showing a mass difference between the two species (Buckley et al. 2010).
Fingerprints are matched to either theoretical data based on in silico digestions of sequences obtained through cDNA libraries or comparison to practical data obtained through ZooMS analysis of known standards. In-house collagen databases are currently expanded to animal species other than mammals, including fish (Richter et al. 2011) and birds. Alternatively, indexed peptides of thoroughly investigated taxa can be used to determine animal origin.
Text taken from Van Doorn, N. L. 2014 Zooarchaeology by Mass Spectrometry (ZooMS). In Encyclopedia of Global Archaeology, pp. 7998–8000. Springer New York.