{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T01:12:10Z","timestamp":1775437930191,"version":"3.50.1"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T00:00:00Z","timestamp":1651708800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T00:00:00Z","timestamp":1651708800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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 \u201cSpecies by Proteome INvestigation\u201d (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.<\/jats:p>","DOI":"10.1038\/s41467-022-30097-x","type":"journal-article","created":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T10:08:32Z","timestamp":1651745312000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":74,"title":["SPIN enables high throughput species identification of archaeological bone by proteomics"],"prefix":"10.1038","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4461-9828","authenticated-orcid":false,"given":"Patrick Leopold","family":"R\u00fcther","sequence":"first","affiliation":[]},{"given":"Immanuel Mirnes","family":"Husic","sequence":"additional","affiliation":[]},{"given":"Pernille","family":"Bangsgaard","sequence":"additional","affiliation":[]},{"given":"Kristian Murphy","family":"Gregersen","sequence":"additional","affiliation":[]},{"given":"Pernille","family":"Pantmann","sequence":"additional","affiliation":[]},{"given":"Milena","family":"Carvalho","sequence":"additional","affiliation":[]},{"given":"Ricardo Miguel","family":"Godinho","sequence":"additional","affiliation":[]},{"given":"Lukas","family":"Friedl","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o","family":"Cascalheira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0378-1626","authenticated-orcid":false,"given":"Alberto John","family":"Taurozzi","sequence":"additional","affiliation":[]},{"given":"Marie Louise Schjellerup","family":"J\u00f8rkov","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2900-887X","authenticated-orcid":false,"given":"Michael M.","family":"Benedetti","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2047-4524","authenticated-orcid":false,"given":"Jonathan","family":"Haws","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9655-0549","authenticated-orcid":false,"given":"Nuno","family":"Bicho","sequence":"additional","affiliation":[]},{"given":"Frido","family":"Welker","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7885-7811","authenticated-orcid":false,"given":"Enrico","family":"Cappellini","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4747-4938","authenticated-orcid":false,"given":"Jesper Velgaard","family":"Olsen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,5,5]]},"reference":[{"key":"30097_CR1","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/nrg3935","volume":"16","author":"L Orlando","year":"2015","unstructured":"Orlando, L., Gilbert, M. T. P. & Willerslev, E. Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16, 395\u2013408 (2015).","journal-title":"Nat. Rev. Genet."},{"key":"30097_CR2","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/s41586-018-0455-x","volume":"561","author":"V Slon","year":"2018","unstructured":"Slon, V. et al. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature 561, 113\u2013116 (2018).","journal-title":"Nature"},{"key":"30097_CR3","doi-asserted-by":"publisher","first-page":"1320","DOI":"10.1126\/science.1249274","volume":"343","author":"E Cappellini","year":"2014","unstructured":"Cappellini, E., Collins, M. J. & Gilbert, M. T. P. Biochemistry. Unlocking ancient protein palimpsests. Science 343, 1320\u20131322 (2014).","journal-title":"Science"},{"key":"30097_CR4","doi-asserted-by":"publisher","first-page":"e17092","DOI":"10.7554\/eLife.17092","volume":"5","author":"B Demarchi","year":"2016","unstructured":"Demarchi, B. et al. Protein sequences bound to mineral surfaces persist into deep time. elife 5, e17092 (2016).","journal-title":"elife"},{"key":"30097_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.foodcont.2007.02.010","volume":"19","author":"L Asensio","year":"2008","unstructured":"Asensio, L., Gonz\u00e1lez, I., Garc\u00eda, T. & Mart\u00edn, R. Determination of food authenticity by enzyme-linked immunosorbent assay (ELISA). Food Control 19, 1\u20138 (2008).","journal-title":"Food Control"},{"key":"30097_CR6","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-64358-w","volume":"10","author":"NL Martisius","year":"2020","unstructured":"Martisius, N. L. et al. Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals. Sci. Rep. 10, 7746 (2020).","journal-title":"Sci. Rep."},{"key":"30097_CR7","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07148-3","volume":"9","author":"RR Jersie-Christensen","year":"2018","unstructured":"Jersie-Christensen, R. R. et al. Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. Nat. Commun. 9, 4744 (2018).","journal-title":"Nat. Commun."},{"key":"30097_CR8","doi-asserted-by":"publisher","first-page":"4590","DOI":"10.1021\/ac800515v","volume":"80","author":"C Solazzo","year":"2008","unstructured":"Solazzo, C., Fitzhugh, W. W., Rolando, C. & Tokarski, C. Identification of protein remains in archaeological potsherds by proteomics. Anal. Chem. 80, 4590\u20134597 (2008).","journal-title":"Anal. Chem."},{"key":"30097_CR9","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1038\/s41586-019-1728-8","volume":"576","author":"F Welker","year":"2019","unstructured":"Welker, F. et al. Enamel proteome shows that Gigantopithecus was an early diverging pongine. Nature 576, 262\u2013265 (2019).","journal-title":"Nature"},{"key":"30097_CR10","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nature01511","volume":"422","author":"R Aebersold","year":"2003","unstructured":"Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198\u2013207 (2003).","journal-title":"Nature"},{"key":"30097_CR11","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0960-9822(93)90195-T","volume":"3","author":"DJ Pappin","year":"1993","unstructured":"Pappin, D. J., Hojrup, P. & Bleasby, A. J. Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 3, 327\u2013332 (1993).","journal-title":"Curr. Biol."},{"key":"30097_CR12","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.cels.2016.02.015","volume":"2","author":"PE Geyer","year":"2016","unstructured":"Geyer, P. E. et al. Plasma proteome profiling to assess human health and disease. Cell Syst. 2, 185\u2013195 (2016).","journal-title":"Cell Syst."},{"key":"30097_CR13","doi-asserted-by":"publisher","unstructured":"Santos, A. et al. Clinical knowledge graph integrates proteomics data into clinical decision-making. bioRxiv https:\/\/doi.org\/10.1101\/2020.05.09.084897 (2020).","DOI":"10.1101\/2020.05.09.084897"},{"key":"30097_CR14","doi-asserted-by":"publisher","first-page":"9431","DOI":"10.1021\/ac201978j","volume":"83","author":"S Dallongeville","year":"2011","unstructured":"Dallongeville, S. et al. Identification of animal glue species in artworks using proteomics: application to a 18th century gilt sample. Anal. Chem. 83, 9431\u20139437 (2011).","journal-title":"Anal. Chem."},{"key":"30097_CR15","doi-asserted-by":"publisher","first-page":"7369","DOI":"10.1002\/anie.201713020","volume":"57","author":"M Mackie","year":"2018","unstructured":"Mackie, M. et al. Palaeoproteomic profiling of conservation layers on a 14th century Italian wall painting. Angew. Chem. Int. Ed. Engl. 57, 7369\u20137374 (2018).","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"30097_CR16","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1016\/S0016-7037(99)00381-6","volume":"64","author":"PH Ostrom","year":"2000","unstructured":"Ostrom, P. H. et al. New strategies for characterizing ancient proteins using matrix-assisted laser desorption ionization mass spectrometry. Geochim. Cosmochim. Acta 64, 1043\u20131050 (2000).","journal-title":"Geochim. Cosmochim. Acta"},{"key":"30097_CR17","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1002\/rcm.1570","volume":"18","author":"R Hynek","year":"2004","unstructured":"Hynek, R., Kuckova, S., Hradilova, J. & Kodicek, M. Matrix-assisted laser desorption\/ionization time-of-flight mass spectrometry as a tool for fast identification of protein binders in color layers of paintings. Rapid Commun. Mass Spectrom. 18, 1896\u20131900 (2004).","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"30097_CR18","doi-asserted-by":"publisher","first-page":"3843","DOI":"10.1002\/rcm.4316","volume":"23","author":"M Buckley","year":"2009","unstructured":"Buckley, M., Collins, M., Thomas-Oates, J. & Wilson, J. C. Species identification by analysis of bone collagen using matrix-assisted laser desorption\/ionisation time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 23, 3843\u20133854 (2009).","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"30097_CR19","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-48706-z","volume":"9","author":"V Sinet-Mathiot","year":"2019","unstructured":"Sinet-Mathiot, V. et al. Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy). Sci. Rep. 9, 12350 (2019).","journal-title":"Sci. Rep."},{"key":"30097_CR20","doi-asserted-by":"publisher","first-page":"757","DOI":"10.15252\/msb.20145625","volume":"10","author":"CS Hughes","year":"2014","unstructured":"Hughes, C. S. et al. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol. Syst. Biol. 10, 757 (2014).","journal-title":"Mol. Syst. Biol."},{"key":"30097_CR21","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1074\/mcp.TIR118.001270","volume":"18","author":"TS Batth","year":"2019","unstructured":"Batth, T. S. et al. Protein aggregation capture on microparticles enables multipurpose proteomics sample preparation. Mol. Cell. Proteomics 18, 1027\u20131035 (2019).","journal-title":"Mol. Cell. Proteomics"},{"key":"30097_CR22","doi-asserted-by":"publisher","first-page":"3976","DOI":"10.1021\/acs.jproteome.8b00637","volume":"17","author":"TP Cleland","year":"2018","unstructured":"Cleland, T. P. Human bone paleoproteomics utilizing the single-pot, solid-phase-enhanced sample preparation method to maximize detected proteins and reduce humics. J. Proteome Res. 17, 3976\u20133983 (2018).","journal-title":"J. Proteome Res."},{"key":"30097_CR23","doi-asserted-by":"publisher","unstructured":"Palmer, K. S. et al. Comparing the use of magnetic beads with ultrafiltration for ancient dental calculus proteomics. J. Proteome Res. https:\/\/doi.org\/10.1021\/acs.jproteome.0c00862 (2021).","DOI":"10.1021\/acs.jproteome.0c00862"},{"key":"30097_CR24","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1074\/mcp.TIR119.001906","volume":"19","author":"DB Bekker-Jensen","year":"2020","unstructured":"Bekker-Jensen, D. B. et al. A compact quadrupole-orbitrap mass spectrometer with FAIMS interface improves proteome coverage in short LC gradients. Mol. Cell. Proteomics 19, 716\u2013729 (2020).","journal-title":"Mol. Cell. Proteomics"},{"key":"30097_CR25","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/978-1-4939-3049-4_17","volume":"1355","author":"RR Jersie-Christensen","year":"2016","unstructured":"Jersie-Christensen, R. R., Sultan, A. & Olsen, J. V. Simple and reproducible sample preparation for single-shot phosphoproteomics with high sensitivity. Methods Mol. Biol. 1355, 251\u2013260 (2016).","journal-title":"Methods Mol. Biol."},{"key":"30097_CR26","doi-asserted-by":"publisher","first-page":"2284","DOI":"10.1074\/mcp.TIR118.000853","volume":"17","author":"N Bache","year":"2018","unstructured":"Bache, N. et al. A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics. Mol. Cell. Proteomics 17, 2284\u20132296 (2018).","journal-title":"Mol. Cell. Proteomics"},{"key":"30097_CR27","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1038\/nmeth.4398","volume":"14","author":"G Rosenberger","year":"2017","unstructured":"Rosenberger, G. et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nat. Methods 14, 921\u2013927 (2017).","journal-title":"Nat. Methods"},{"key":"30097_CR28","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","volume":"17","author":"V Demichev","year":"2020","unstructured":"Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41\u201344 (2020).","journal-title":"Nat. Methods"},{"key":"30097_CR29","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1021\/acs.jproteome.7b00602","volume":"17","author":"CD Kelstrup","year":"2018","unstructured":"Kelstrup, C. D. et al. Performance evaluation of the Q exactive HF-X for shotgun proteomics. J. Proteome Res. 17, 727\u2013738 (2018).","journal-title":"J. Proteome Res."},{"key":"30097_CR30","doi-asserted-by":"publisher","first-page":"6187","DOI":"10.1021\/pr500985w","volume":"13","author":"CD Kelstrup","year":"2014","unstructured":"Kelstrup, C. D. et al. Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer. J. Proteome Res. 13, 6187\u20136195 (2014).","journal-title":"J. Proteome Res."},{"key":"30097_CR31","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1038\/s41467-019-13973-x","volume":"11","author":"Y Bian","year":"2020","unstructured":"Bian, Y. et al. Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC\u2013MS\/MS. Nat. Commun. 11, 157 (2020).","journal-title":"Nat. Commun"},{"key":"30097_CR32","doi-asserted-by":"publisher","first-page":"e0249296","DOI":"10.1371\/journal.pone.0249296","volume":"16","author":"J Bradfield","year":"2021","unstructured":"Bradfield, J., Kitchener, A. C. & Buckley, M. Selection preferences for animal species used in bone-tool-manufacturing strategies in KwaZulu-Natal, South Africa. PLoS ONE 16, e0249296 (2021).","journal-title":"PLoS ONE"},{"key":"30097_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2221-3","volume":"19","author":"M Gu","year":"2018","unstructured":"Gu, M. & Buckley, M. Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting. BMC Bioinformatics 19, 241 (2018).","journal-title":"BMC Bioinformatics"},{"key":"30097_CR34","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/nmeth.3901","volume":"13","author":"S Tyanova","year":"2016","unstructured":"Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731\u2013740 (2016).","journal-title":"Nat. Methods"},{"key":"30097_CR35","doi-asserted-by":"publisher","first-page":"e31443","DOI":"10.1371\/journal.pone.0031443","volume":"7","author":"TP Cleland","year":"2012","unstructured":"Cleland, T. P., Voegele, K. & Schweitzer, M. H. Empirical evaluation of bone extraction protocols. PLoS ONE 7, e31443 (2012).","journal-title":"PLoS ONE"},{"key":"30097_CR36","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/nmeth.1322","volume":"6","author":"JR Wi\u015bniewski","year":"2009","unstructured":"Wi\u015bniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359\u2013362 (2009).","journal-title":"Nat. Methods"},{"key":"30097_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06335-6","volume":"9","author":"J Hendy","year":"2018","unstructured":"Hendy, J. et al. Ancient proteins from ceramic vessels at \u00c7atalh\u00f6y\u00fck West reveal the hidden cuisine of early farmers. Nat. Commun. 9, 4064 (2018).","journal-title":"Nat. Commun."},{"key":"30097_CR38","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.1002\/pmic.201300553","volume":"14","author":"A Zougman","year":"2014","unstructured":"Zougman, A., Selby, P. J. & Banks, R. E. Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 14, 1006\u20131000 (2014).","journal-title":"Proteomics"},{"key":"30097_CR39","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1021\/pr200721u","volume":"11","author":"E Cappellini","year":"2012","unstructured":"Cappellini, E. et al. Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins. J. Proteome Res. 11, 917\u2013926 (2012).","journal-title":"J. Proteome Res."},{"key":"30097_CR40","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/s41586-020-2153-8","volume":"580","author":"F Welker","year":"2020","unstructured":"Welker, F. et al. The dental proteome of Homo antecessor. Nature 580, 235\u2013238 (2020).","journal-title":"Nature"},{"key":"30097_CR41","doi-asserted-by":"publisher","first-page":"6176","DOI":"10.1021\/pr500893m","volume":"13","author":"TS Batth","year":"2014","unstructured":"Batth, T. S., Francavilla, C. & Olsen, J. V. Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics. J. Proteome Res. 13, 6176\u20136186 (2014).","journal-title":"J. Proteome Res."},{"key":"30097_CR42","first-page":"231","volume":"68","author":"O Bennike","year":"2020","unstructured":"Bennike, O., Pantmann, P. & Aarsleff, E. Lateglacial and Holocene floras and faunas from the Salpetermosen area, north-east Sj\u00e6lland, Denmark. Bull. Geol. Soc. Den. 68, 231\u2013244 (2020).","journal-title":"Bull. Geol. Soc. Den."},{"key":"30097_CR43","doi-asserted-by":"crossref","unstructured":"Aaris-S\u00f8rensen, K. Diversity and dynamics of the mammalian fauna in Denmark throughout the last glacial-interglacial cycle, 115-0 kyr BP. (John Wiley & Sons, 2010).","DOI":"10.18261\/9781444334838-2009"},{"key":"30097_CR44","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1002\/gea.21735","volume":"34","author":"MM Benedetti","year":"2019","unstructured":"Benedetti, M. M., Haws, J. A., Bicho, N. F., Friedl, L. & Ellwood, B. B. Late Pleistocene site formation and paleoclimate at Lapa do Picareiro, Portugal. Geoarchaeology 34, 698\u2013726 (2019).","journal-title":"Geoarchaeology"},{"key":"30097_CR45","doi-asserted-by":"publisher","first-page":"25414","DOI":"10.1073\/pnas.2016062117","volume":"117","author":"JA Haws","year":"2020","unstructured":"Haws, J. A. et al. The early Aurignacian dispersal of modern humans into westernmost Eurasia. Proc. Natl Acad. Sci. USA 117, 25414\u201325422 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"30097_CR46","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.quaint.2013.06.029","volume":"318","author":"N Bicho","year":"2013","unstructured":"Bicho, N. et al. The ecodynamics of the first modern humans in Southwestern Iberia: the case of Vale Boi, Portugal. Quat. Int. 318, 102\u2013116 (2013).","journal-title":"Quat. Int."},{"key":"30097_CR47","doi-asserted-by":"crossref","unstructured":"Pereira, T. et al. Territory and abiotic resources between 33 and 15.6 ka at Vale Boi (SW Portugal). Quat. Int. 412, 124\u2013134 (2016).","DOI":"10.1016\/j.quaint.2015.08.071"},{"key":"30097_CR48","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.jas.2013.12.003","volume":"43","author":"T Manne","year":"2014","unstructured":"Manne, T. Early Upper Paleolithic bone processing and insights into small-scale storage of fats at Vale Boi, southern Iberia. J. Archaeol. Sci. 43, 111\u2013123 (2014).","journal-title":"J. Archaeol. Sci."},{"key":"30097_CR49","first-page":"102678","volume":"35","author":"J Dekker","year":"2021","unstructured":"Dekker, J. et al. Human and cervid osseous materials used for barbed point manufacture in Mesolithic Doggerland. J. Archaeol. Sci. Rep. 35, 102678 (2021).","journal-title":"J. Archaeol. Sci. Rep."},{"key":"30097_CR50","doi-asserted-by":"publisher","first-page":"e2109019118","DOI":"10.1073\/pnas.2109019118","volume":"118","author":"S Hotaling","year":"2021","unstructured":"Hotaling, S., Kelley, J. L. & Frandsen, P. B. Toward a genome sequence for every animal: where are we now? Proc. Natl Acad. Sci. USA 118, e2109019118 (2021).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"30097_CR51","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1126\/science.1128994","volume":"313","author":"H R\u00f6mpler","year":"2006","unstructured":"R\u00f6mpler, H. et al. Nuclear gene indicates coat-color polymorphism in mammoths. Science 313, 62 (2006).","journal-title":"Science"},{"key":"30097_CR52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7146\/dja.v10i0.130000","volume":"10","author":"P Bangsgaard","year":"2022","unstructured":"Bangsgaard, P. & Pantmann, P. The phenomenon of primary and secondary animals within Iron Age deposits in Denmark. Danish J. Archaeol. 10, 1\u201320 (2022).","journal-title":"Danish J. Archaeol."},{"key":"30097_CR53","unstructured":"Bicho, N., Cascalheira, J., T\u00e1t\u00e1, F. & Horta, P. in Mudan\u00e7as em Sistemas Ambientais e sua Express\u00e3o Temporal: Livro de Resumos da IX Reuni\u00e3o do Quatern\u00e1rio Ib\u00e9rico 113\u2013114 (Asociaci\u00f3n Espa\u00f1ola para el Estudio del Cuaternario, 2017)."},{"key":"30097_CR54","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1021\/ac026117i","volume":"75","author":"J Rappsilber","year":"2003","unstructured":"Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption\/ionization, nanoelectrospray, and LC\/MS sample pretreatment in proteomics. Anal. Chem. 75, 663\u2013670 (2003).","journal-title":"Anal. Chem."},{"key":"30097_CR55","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1002\/rcm.6821","volume":"28","author":"C Wadsworth","year":"2014","unstructured":"Wadsworth, C. & Buckley, M. Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone. Rapid Commun. Mass Spectrom. 28, 605\u2013615 (2014).","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"30097_CR56","doi-asserted-by":"publisher","first-page":"D506","DOI":"10.1093\/nar\/gky1049","volume":"47","author":"UniProt Consortium.","year":"2019","unstructured":"UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47, D506\u2013D515 (2019).","journal-title":"Nucleic Acids Res."},{"key":"30097_CR57","doi-asserted-by":"publisher","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","volume":"44","author":"NA O\u2019Leary","year":"2016","unstructured":"O\u2019Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733\u2013D745 (2016).","journal-title":"Nucleic Acids Res."},{"key":"30097_CR58","doi-asserted-by":"publisher","DOI":"10.1038\/srep04958","volume":"4","author":"J Huang","year":"2014","unstructured":"Huang, J. et al. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype. Sci. Rep. 4, 4958 (2014).","journal-title":"Sci. Rep."},{"key":"30097_CR59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix016","volume":"6","author":"K Wang","year":"2017","unstructured":"Wang, K. et al. The genome sequence of the wisent (Bison bonasus). Gigascience 6, 1\u20135 (2017).","journal-title":"Gigascience"},{"key":"30097_CR60","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0790-2","volume":"16","author":"SDE Park","year":"2015","unstructured":"Park, S. D. E. et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol. 16, 234 (2015).","journal-title":"Genome Biol."},{"key":"30097_CR61","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"30097_CR62","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","volume":"28","author":"K Okonechnikov","year":"2012","unstructured":"Okonechnikov, K., Golosova, O. & Fursov, M., UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28, 1166\u20131167 (2012).","journal-title":"Bioinformatics"},{"key":"30097_CR63","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792\u20131797 (2004).","journal-title":"Nucleic Acids Res."},{"key":"30097_CR64","doi-asserted-by":"publisher","first-page":"3276","DOI":"10.1093\/bioinformatics\/btu531","volume":"30","author":"A Larsson","year":"2014","unstructured":"Larsson, A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30, 3276\u20133278 (2014).","journal-title":"Bioinformatics"},{"key":"30097_CR65","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).","journal-title":"PLoS ONE"},{"key":"30097_CR66","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/nbt.1511","volume":"26","author":"J Cox","year":"2008","unstructured":"Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367 (2008).","journal-title":"Nat. Biotechnol."},{"key":"30097_CR67","doi-asserted-by":"publisher","first-page":"2296","DOI":"10.1074\/mcp.RA117.000314","volume":"16","author":"R Bruderer","year":"2017","unstructured":"Bruderer, R. et al. Optimization of experimental parameters in data-Independent mass spectrometry significantly increases depth and reproducibility of results. Mol. Cell. Proteomics 16, 2296\u20132309 (2017).","journal-title":"Mol. Cell. Proteomics"},{"key":"30097_CR68","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14609-1","volume":"11","author":"DB Bekker-Jensen","year":"2020","unstructured":"Bekker-Jensen, D. B. et al. Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nat. Commun. 11, 787 (2020).","journal-title":"Nat. Commun."},{"key":"30097_CR69","doi-asserted-by":"publisher","unstructured":"R\u00fcther, P. L. et al. SPIN\u2014Species by Proteome INvestigation: Code, databases, and example data. https:\/\/doi.org\/10.5281\/zenodo.6406044. (2022).","DOI":"10.5281\/zenodo.6406044"},{"key":"30097_CR70","doi-asserted-by":"publisher","first-page":"104041","DOI":"10.1016\/j.jprot.2020.104041","volume":"235","author":"S Brown","year":"2021","unstructured":"Brown, S., Douka, K., Collins, M. J. & Richter, K. K. On the standardization of ZooMS nomenclature. J. Proteomics 235, 104041 (2021).","journal-title":"J. Proteomics"},{"key":"30097_CR71","doi-asserted-by":"publisher","first-page":"11162","DOI":"10.1073\/pnas.1605834113","volume":"113","author":"F Welker","year":"2016","unstructured":"Welker, F. et al. Palaeoproteomic evidence identifies archaic hominins associated with the Ch\u00e2telperronian at the Grotte du Renne. Proc. Natl Acad. Sci. USA 113, 11162\u201311167 (2016).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"30097_CR72","doi-asserted-by":"publisher","first-page":"D442","DOI":"10.1093\/nar\/gky1106","volume":"47","author":"Y Perez-Riverol","year":"2019","unstructured":"Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442\u2013D450 (2019).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-022-30097-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-022-30097-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-022-30097-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T02:36:04Z","timestamp":1700534164000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-022-30097-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,5]]},"references-count":72,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["30097"],"URL":"https:\/\/doi.org\/10.1038\/s41467-022-30097-x","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,5]]},"assertion":[{"value":"23 March 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 April 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 May 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"2458"}}