Democratisation of ZooMS: Jena lab protocols published

One of the biggest challenges we faced at the onset of the project in 2016-17 was the lack of transparency in terms of the nitty gritty of ZooMS, the actual analytical protocols, from the wet chemistry laboratory procedures, to equipment settings, data analyses and full data deposition (both reference data as well as analysed unknown samples). I used to jokingly call the method “the best kept secret in archaeological science”.

In FINDER, to ensure that our workflow and results were not only as transparent as possible, but also reproducible and fully accessible by any interested party, we committed early on 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 MPI-SHH were described and deposited in protocols.io. In more detail:

  • The AmBic 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 different 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.

ZooMS methods comparison

 

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 Proteomicshttps://doi.org/10.1016/j.jprot.2020.104078 

 

Proteins are getting older!

One of the most exciting aspects of this work, at least for someone who was previously limited by the radiocarbon limit, is the wider applicability of ZooMS to material covering not only the last 50,000 years but as many as a few million years. Recent publications have pushed the survival of animal proteins in tooth enamel to 1.77 Ma and 1.9 Ma– an exciting pushback in time! A nice write-up with comments from various researchers, including one of us, can be found here.

As for FINDER, we have been hard at work in 2019 both at the lab and travelling to places across Europe, Asia and Australia to access “new” old collections. We’ve hit 10,000 bones from Denisova Cave and analysed material from another 6 sites from northern Asia.

The oldest, protein- and DNA-containing human fossils from Denisova Cave can now be placed, comfortably, to ~200 ka  and possibly beyond this, and we will be reporting more on this as new data come out. For now, here are two pics of the student team (Samantha Brown and Naihui Wang) working at the labs in Jena.

Meeting “Denny” (again)

These have been exciting couple of months.

In early September we’ve reported in Nature, in a article led by our colleagues at the Genetics Department of the MPI-EVA, that Denisova 11, the tiny little bone we found during a pilot study and reported as Neanderthal based on her mtDNA, belonged in fact to a girl whose mother was a Neanderthal AND her father a Denisovan! This is the first unequivocal human we have so far whose parents belonged to two separate and now-extinct archaic human groups. How cool is that?

We had we previously named Denisova 11 “Denny” from the name of her last residence, and we never thought that she’d be as special, or as geneticist Pontus Skoglund put it “the most fascinating person who’s ever had their genome sequenced”.

The story made the cover of Nature’s September issue with the ingenious design of A. Günzel.

Nature cover Issue 7721 (September 2018) by Annette Günzel

There are several implications stemming from this work, not least the frequency of interbreeding between these human groups at the periphery (?) of their geographic ranges. The DNA analyses give us fascinating leads about population movement and the timing of it, since the Neanderthal mother of Denny shares more in common with a later Neanderthal from Vindija cave in Croatia than a Neanderthal found at Denisova Cave, all three fossils now sequenced to high coverage.

We have some ideas how to follow these leads with further work and if you’re interested in PhD research do get in touch.