By extracting a tiny amount of collagen from an unidentified bone fragment and running it through the spectrometer, researchers can determine what family of animal the bone came from. For most bone fragments at a Paleolithic site—fragments from horses, deer, bovids, cave bears, hyenas—the collagen signature is clear and specific. For a fragment from an archaic human, the signature falls into a different category: detectable as primate and, with enough resolution, distinguishable from other mammals.
This was the method used to screen the Denisova Cave material in a systematic way. Tom Higham and Katerina Douka at the University of Oxford organized the project, and Samantha Brown, then an MSc student at Oxford, carried out the screening of more than two thousand fragments for her dissertation. Working with Michael Buckley’s laboratory at the University of Manchester, Brown identified one fragment—DC1227, which would become Denisova 11—as archaic human.
The ratio of hominin bones to animal bones at Denisova Cave, based on the ZooMS screening, was approximately one to one thousand. This meant that among any given thousand bone fragments, researchers could expect to find one that came from a hominin. Without ZooMS, that fragment would have remained in a box, unidentified, indefinitely.
With ZooMS, it became a candidate for further analysis.
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## From Protein to DNA
Identifying a bone fragment as hominin was the first step. The second step was extracting DNA from it and determining what that DNA could tell.
Ancient DNA is not like the DNA extracted from a living cell. Over thousands of years, the DNA in a bone or a tooth degrades—the long strands of the double helix break apart into shorter and shorter fragments, chemical damage accumulates, and the proportion of useful genetic information relative to contaminating material decreases steadily. A bone that is ninety thousand years old contains DNA that has spent ninety thousand years being damaged by hydrolysis, oxidation, and microbial activity. What remains is typically fragments of 50 to 150 base pairs—short snippets of a genome that, in its intact form, would contain more than three billion base pairs.