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Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification

2023Journal article Open Access
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dc.contributor.authorMylopotamitaki, Dorothea
dc.contributor.authorHarking, Florian S.
dc.contributor.authorTaurozzi, Alberto J.
dc.contributor.authorFagernäs, Zandra
dc.contributor.authorGodinho, Ricardo Miguel
dc.contributor.authorSmith, Geoff M.
dc.contributor.authorWeiss, Marcel
dc.contributor.authorSchüler, Tim
dc.contributor.authorMcPherron, Shannon P.
dc.contributor.authorMeller, Harald
dc.contributor.authorCascalheira, João
dc.contributor.authorBicho, Nuno
dc.contributor.authorOlsen, Jesper V.
dc.contributor.authorHublin, Jean-Jacques
dc.contributor.authorWelker, Frido
dc.date.accessioned2024-01-12T11:16:20Z
dc.date.available2024-01-12T11:16:20Z
dc.date.issued2023
dc.description.abstractHigh-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.pt_PT
dc.description.sponsorshipALG-01-0145-FEDER-27833; DL57/2016/CP1361/CT0026pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.1038/s41598-023-44885-ypt_PT
dc.identifier.issn2045-2322
dc.identifier.urihttp://hdl.handle.net/10400.1/20285
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherNature Portfoliopt_PT
dc.relationHominin phyloproteomics for the Pleistocene: PalaeoPROteomics of Skeletal Parts for Evolutionary Research
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.subjectEvolutionary historypt_PT
dc.subjectMass-spectrometerpt_PT
dc.subjectProteomicspt_PT
dc.subjectSequencept_PT
dc.subjectZoomspt_PT
dc.subjectProteinspt_PT
dc.subjectRevealspt_PT
dc.titleComparing extraction method efficiency for high-throughput palaeoproteomic bone species identificationpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleHominin phyloproteomics for the Pleistocene: PalaeoPROteomics of Skeletal Parts for Evolutionary Research
oaire.awardTitleAssessing the relationship between masticatory and paramasticatory function and cranial form in Neandertals.
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/948365/EU
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND 3ed/2020.00499.CEECIND%2FCP1613%2FCT0002/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/2022.07737.PTDC/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/Concurso para Financiamento de Projetos de Investigação Científica e Desenvolvimento Tecnológico em Todos os Domínios Científicos - 2017/PTDC%2FHAR-ARQ%2F27833%2F2017/PT
oaire.citation.issue1pt_PT
oaire.citation.titleScientific Reportspt_PT
oaire.citation.volume13pt_PT
oaire.fundingStreamH2020
oaire.fundingStreamCEEC IND 3ed
oaire.fundingStream3599-PPCDT
oaire.fundingStreamConcurso para Financiamento de Projetos de Investigação Científica e Desenvolvimento Tecnológico em Todos os Domínios Científicos - 2017
person.familyNameGodinho
person.familyNameCascalheira
person.familyNameBicho
person.givenNameRicardo Miguel
person.givenNameJoão
person.givenNameNuno
person.identifierJ-2841-2012
person.identifier.ciencia-idE01A-0CC3-D631
person.identifier.ciencia-idFD10-4F70-0FF0
person.identifier.ciencia-id7619-7089-221C
person.identifier.orcid0000-0003-0107-9577
person.identifier.orcid0000-0003-0321-8892
person.identifier.orcid0000-0001-9655-0549
person.identifier.ridP-2263-2015
person.identifier.ridB-8343-2014
person.identifier.scopus-author-id55069924600
project.funder.identifierhttp://doi.org/10.13039/501100008530
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.nameEuropean Commission
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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