One of the biggest challenges I faced when becoming engaged with the palaeoproteomics/ZooMS community was the lack of transparency in terms of the actual analytical protocols used, from the wet chemistry laboratory procedures, to equipment settings, data analyses and full data deposition in open access. I used to joke and call the method “the best kept secret in archaeological science”. But it was not funny.
To ensure that my lab’s workflow and results were not only as transparent as possible, but also reproducible and fully accessible by any interested party, we (a community of several specialists) committed in 2018 to work towards the “democratisation” of ZooMS.
The first step towards this was to test and publicise in a free and accessible format our analytical protocols. In a series of publications, the 3 main wet chemistry protocols we use at the ZooMS/Palaeoproteomics laboratories of the Max Planck for the Science of Human History (where I was based until 2021) as well as in my lab at the University of Vienna, are described and deposited in protocols.io. In more detail:
- The AmBic-based protocol can be used on samples where destructive analysis cannot be undertaken or where collagen preservation is particularly good hence matrix demineralisation is not necessary.
- Zooarchaeology by Mass Spectrometry (ZooMS) for bone material – AmBiC protocol dx.doi.org/10.17504/protocols.io.bffdjji6
- Two Acid-based protocols are slight variations of a more destructive approach in which the samples are pretreated with hydrocholric acid to demineralize the bone matrix and release inter- and intra-crystalline collagen.
- Zooarchaeology by Mass Spectrometry (ZooMS) for bone material – Acid insoluble protocol dx.doi.org/10.17504/protocols.io.bf43jqyn
- Zooarchaeology by Mass Spectrometry (ZooMS) for bone material – Acid soluble protocol dx.doi.org/10.17504/protocols.io.bf5bjq2n
In a publication in the Journal of Proteomics we test the aforementioned protocols on 400 archaeological bones from different parts of the world. This allowed us to compare how each protocol works depending on collagen preservation. Our results indicate that the least-destructive ZooMS protocol which uses an ammonium bicarbonate buffer as a means of extracting collagen is most suitable for bones with good collagen preservation, whereas the acid-based methodologies can improve success rates for bones with low-to-medium collagen preservation
The full reference and publication can be found here:
Wang, N., Brown, S., Ditchfield, P., Hebestreit, S., Kozilikin, M., Luu, S., Oshan, W., Grimaldi, S., Chazan, M., Horwitz Kolska, L., Spriggs, M. Summerhayes, Gl, Shunkov, M., Korzow Richter, K., Douka, K., Testing the efficacy and comparability of ZooMS protocols on archaeological bone. Journal of Proteomics. https://doi.org/10.1016/j.jprot.2020.104078