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SPIN enables high throughput species identification of archaeological bone by proteomics

2022Journal article Open access
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dc.contributor.authorRüther, Patrick Leopold
dc.contributor.authorHusic, Immanuel Mirnes
dc.contributor.authorBangsgaard, Pernille
dc.contributor.authorGregersen, Kristian Murphy
dc.contributor.authorPantmann, Pernille
dc.contributor.authorCarvalho, Milena
dc.contributor.authorGodinho, Ricardo Miguel
dc.contributor.authorFriedl, Lukas
dc.contributor.authorCascalheira, João
dc.contributor.authorTaurozzi, Alberto John
dc.contributor.authorJørkov, Marie Louise Schjellerup
dc.contributor.authorBenedetti, Michael
dc.contributor.authorHaws, Jonathan
dc.contributor.authorBicho, Nuno
dc.contributor.authorWelker, Frido
dc.contributor.authorCappellini, Enrico
dc.contributor.authorOlsen, Jesper Velgaard
dc.date.accessioned2022-10-10T13:10:27Z
dc.date.available2022-10-10T13:10:27Z
dc.date.issued2022
dc.description.abstractSpecies 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.pt_PT
dc.description.sponsorshipALG-01-0145-FEDER-29680; 722606; 101021361; 948365
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1038/s41467-022-30097-xpt_PT
dc.identifier.issn2041-1723
dc.identifier.urihttp://hdl.handle.net/10400.1/18355
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherNature Portfoliopt_PT
dc.relationThe origins and evolution of Human Cognition and the impact of Southwestern European coastal ecology
dc.relationNot Available
dc.relationAssessing the relationship between masticatory and paramasticatory function and cranial form in Neandertals.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleSPIN enables high throughput species identification of archaeological bone by proteomicspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleThe origins and evolution of Human Cognition and the impact of Southwestern European coastal ecology
oaire.awardTitleNot Available
oaire.awardTitleAssessing the relationship between masticatory and paramasticatory function and cranial form in Neandertals.
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/9471 - RIDTI/PTDC%2FHAR-ARQ%2F27833%2F2017/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/DL 57%2F2016/DL 57%2F2016%2FCP1361%2FCT0026/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND 3ed/2020.00499.CEECIND%2FCP1613%2FCT0002/PT
oaire.citation.issue1pt_PT
oaire.citation.titleNature Communicationspt_PT
oaire.citation.volume13pt_PT
oaire.fundingStream9471 - RIDTI
oaire.fundingStreamDL 57/2016
oaire.fundingStreamCEEC IND 3ed
person.familyNameCarvalho
person.familyNameGodinho
person.familyNameFriedl
person.familyNameCascalheira
person.familyNameBenedetti
person.familyNameHaws
person.familyNameBicho
person.givenNameMilena
person.givenNameRicardo Miguel
person.givenNameLukas
person.givenNameJoão
person.givenNameMichael
person.givenNameJonathan
person.givenNameNuno
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person.identifier.orcid0000-0003-0107-9577
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person.identifier.orcid0000-0003-0321-8892
person.identifier.orcid0000-0002-2900-887X
person.identifier.orcid0000-0002-2047-4524
person.identifier.orcid0000-0001-9655-0549
person.identifier.ridP-2263-2015
person.identifier.ridB-8343-2014
person.identifier.scopus-author-id35329721400
person.identifier.scopus-author-id55069924600
person.identifier.scopus-author-id8505322400
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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