TY - JOUR

T1 - SPIN enables high throughput species identification of archaeological bone by proteomics

AU - Rüther, Patrick Leopold

AU - Husic, Immanuel Mirnes

AU - Bangsgaard, Pernille

AU - Gregersen, Kristian Murphy

AU - Pantmann, Pernille

AU - Carvalho, Milena

AU - Godinho, Ricardo Miguel

AU - Friedl, Lukas

AU - Cascalheira, João

AU - Taurozzi, Alberto John

AU - Jørkov, Marie Louise Schjellerup

AU - Benedetti, Michael M

AU - Haws, Jonathan

AU - Bicho, Nuno

AU - Welker, Frido

AU - Cappellini, Enrico

AU - Olsen, Jesper Velgaard

N1 - © 2022. The Author(s).

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Animals

KW - Archaeology/methods

KW - Chromatography, Liquid

KW - Mammals

KW - Peptides

KW - Proteome

KW - Proteomics/methods

KW - Tandem Mass Spectrometry

U2 - 10.1038/s41467-022-30097-x

DO - 10.1038/s41467-022-30097-x

M3 - Journal article

C2 - 35513387

VL - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 2458

ER -