SPIN enables high throughput species identification of archaeological bone by proteomics

Patrick Leopold Rüther (), Immanuel Mirnes Husic, Pernille Bangsgaard, Kristian Murphy Gregersen, Pernille Pantmann, Milena Carvalho, Ricardo Miguel Godinho, Lukas Friedl, João Cascalheira, Alberto John Taurozzi, Marie Louise Schjellerup Jørkov, Michael M. Benedetti, Jonathan Haws, Nuno Bicho, Frido Welker, Enrico Cappellini and Jesper Velgaard Olsen ()
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Patrick Leopold Rüther: University of Copenhagen
Immanuel Mirnes Husic: University of Copenhagen
Pernille Bangsgaard: University of Copenhagen
Kristian Murphy Gregersen: Royal Danish Academy
Pernille Pantmann: Museum Nordsjælland
Milena Carvalho: University of Algarve
Ricardo Miguel Godinho: University of Algarve
Lukas Friedl: University of Algarve
João Cascalheira: University of Algarve
Alberto John Taurozzi: University of Copenhagen
Marie Louise Schjellerup Jørkov: University of Copenhagen
Michael M. Benedetti: University of Algarve
Jonathan Haws: University of Algarve
Nuno Bicho: University of Algarve
Frido Welker: University of Copenhagen
Enrico Cappellini: University of Copenhagen
Jesper Velgaard Olsen: University of Copenhagen

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.

Date: 2022
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DOI: 10.1038/s41467-022-30097-x

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