Zooarchaeology by Mass Spectrometry (ZooMS) uses a protein, called collagen, as a molecular barcode to read the identity of bones.  Dr Kristine Richter's research project MAFRI (Molecular Ancient Fish Remains Identification) funded by the European Union and the British Academy is developing this technique for archaeological fish bones.  Read below to see how it works.

What are bones made from?

What is collagen?

How does ZooMS work?

What is a spectra?

Read more. . .

Bone is a living, growing tissue that changes and remodels over the course of your life.  While about 50% of our body is water, bones only contain 25% water.  Along with the water, the bone consists of collagen, a protein, that provides a soft framework for the bone and allows for flexibility, and calcium phosphate, a mineral, that adds strength and hardens the framework.  This combination makes bones strong and flexible enough to withstand stress.  Bones also contain other organic molecules including other proteins, DNA, and lipids and other minerals including potassium,  sodium, magnesium, and carbonate.
When something dies and is buried the bones also die and changes happen to the bone composition.  This includes changing some of the minerals and the degradation of some of the organic components.  Ultimately through time the collagen and other organic components are replaced entirely with mineral making a fossil.  This process can take millions of year so until the bone is fossilized, the collagen can be extracted and analysed.

Collagen is the most abundant protein in most animals.  There are over 28 types of collagen that play different roles in the body.  In addition to being the main structural protein in bones, it also can be found in connective tissues like tendons and cartilage.  In addition it is found in the cornea, blood vessels, intervertebral discs, dentin in teeth, and muscle tissue.  Bone collagen is mostly Collagen Type 1 and consists of amino acids wound together to form triple-helices which then bind together to for elongated fibrils and then larger fibers.

Because it forms this very specific structure, the sequence of Collagen Type 1 is highly conserved between different species, but differences do occur that are unique to a particular species.  For example sheep and goat differ by 4 amino acids.  These changes can be measured using a Matrix Assisted Laser Desorption/Ionization - Time of Flight Mass Spectrometer (MALDI-TOF)

We extract collagen from archaeological bones by heating or with acid.  Then the collagen is cut using an enzyme which works like a pair of molecular scissors that cut in the same locations in collagen.  After that the peptides (small bits of collagen) are purified and then run on the MALDI-TOF.  This produces a spectra that is related to the weight of the peptides that were in the sample.  If there are differences in amino acids between two species, these can been seen in differences in the weights of the peptides in the samples.  We can then compare the spectra from our sample to the spectra from known fish species to identify the unknown sample.

Two fish that are difficult to distinguish are the freshwater fish: perch (Perca fluviatis) and pike-perch or zander (Sander lucioperca).  While their bones may look almost identical, their collagen has clear differences.  In the spectra below you can see the differences between perch (going up) and pike-perch (going down).

These differences can be seen more clearly when we zoom in on the area in the red box.

Using a combination of methods we can learn more about what the bones of old fish can tell us about our past.