138 lines
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138 lines
17 KiB
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<document ID-DOI="10.1098/rspb.2017.0544" ID-GBIF-Dataset="c6997856-1dd8-4f2a-8207-b0605f3e4392" ID-PMC="PMC5454271" ID-PubMed="28566488" ID-Zenodo-Dep="3748698" checkinTime="1586623297099" checkinUser="jeremy" docAuthor="Michael Buckley, Stacey Warwood, Bart van Dongen, Andrew C. Kitchener & Phillip L. Manning" docDate="2017" docId="D97B994EFFD7117EFF979E6486B3AAC0" docLanguage="en" docName="Buckleyetal2017CrossContamination.pdf" docOrigin="Proceedings of the Royal Society, Series B 284" docStyle="DocumentStyle{}" docTitle="Tyrannosaurus rex Osborn 1905" docType="treatment" docVersion="8" masterDocId="2542E136FFD6117FFFE69B0D8557AC22" masterDocTitle="A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination" masterLastPageNumber="544" masterPageNumber="544" pageNumber="544" updateTime="1668126661441" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Michael Buckley</mods:namePart>
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<mods:affiliation>Faculty of Science and Engineering, The University of Manchester, Manchester Institute of Biotechnology, Manchester M 1 7 DN, UK School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M 13 9 PL, UK</mods:affiliation>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Stacey Warwood</mods:namePart>
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<mods:affiliation>Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Manchester M 13 9 PL, UK</mods:affiliation>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Bart van Dongen</mods:namePart>
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<mods:affiliation>School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M 13 9 PL, UK</mods:affiliation>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Andrew C. Kitchener</mods:namePart>
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<mods:affiliation>Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH 1 1 JF, UK Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH 8 9 XP, UK</mods:affiliation>
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<mods:roleTerm>Author</mods:roleTerm>
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<mods:namePart>Phillip L. Manning</mods:namePart>
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<mods:affiliation>School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M 13 9 PL, UK Department of Geology and Environmental Geosciences, College of Charleston, 66 George Street, Charleston, SC 29424, USA</mods:affiliation>
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<mods:title>Proceedings of the Royal Society, Series B</mods:title>
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<mods:part>
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<mods:date>2017</mods:date>
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<mods:detail type="volume">
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<mods:number>284</mods:number>
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<mods:start>544</mods:start>
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<mods:identifier type="DOI">10.1098/rspb.2017.0544</mods:identifier>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.3808823" ID-GBIF-Taxon="163551220" ID-Zenodo-Dep="3808823" LSID="urn:lsid:plazi:treatment:D97B994EFFD7117EFF979E6486B3AAC0" httpUri="http://treatment.plazi.org/id/D97B994EFFD7117EFF979E6486B3AAC0" pageId="1">
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<subSubSection box="[113,606,1385,1418]" pageId="1" type="nomenclature">
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<paragraph blockId="1.[113,757,1385,2120]" box="[113,606,1385,1418]" pageId="1">
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<heading bold="true" box="[113,606,1385,1418]" fontSize="14" level="2" pageId="1" reason="0">
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<emphasis bold="true" box="[113,606,1385,1418]" pageId="1">
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(a)
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<taxonomicName authorityName="Osborn" authorityYear="1905" box="[164,370,1385,1418]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
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<emphasis bold="true" box="[164,370,1385,1418]" italics="true" pageId="1">Tyrannosaurus rex</emphasis>
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</taxonomicName>
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collagen sequences
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</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection pageId="1" type="discussion">
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<paragraph blockId="1.[113,757,1385,2120]" pageId="1">
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In the case of the
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<taxonomicName authorityName="Osborn" authorityYear="1905" box="[313,370,1427,1448]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
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<emphasis box="[313,370,1427,1448]" italics="true" pageId="1">T. rex</emphasis>
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</taxonomicName>
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specimen (
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<materialsCitation ID-GBIF-Occurrence="2597534049" box="[495,611,1426,1448]" collectionCode="MOR" pageId="1" specimenCode="MOR 1125">MOR 1125</materialsCitation>
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)̗ these initial studies were supported by two main lines of supporting molecular evidence: immunological data and sequence information [
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<bibRefCitation author="Schweitzer MH & Wittmeyer JL & Horner JR & Toporski JK" box="[205,216,1521,1543]" journalOrPublisher="Science" pageId="1" pagination="1952 - 1955" part="307" refId="ref7107" refString="1. Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK. 2005 Soft-tissue vessels and cellular preservation in Tyrannosaurus rex. Science 307, 1952 - 1955. (doi: 10.1126 / science. 1108397)" title="Soft-tissue vessels and cellular preservation in Tyrannosaurus rex" type="journal article" year="2005">1</bibRefCitation>
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]. This first choice of support is no longer widely accepted as ideal for such claims̗ given that immunological techniques have been shown to yield false-positive results [
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<bibRefCitation author="Lendaro E & Ippoliti R & Bellelli A & Brunori M & Zito R & Citro G & Ascenzi A." box="[731,745,1585,1607]" journalOrPublisher="Am. J. Phys. Anthropol." pageId="1" pagination="429 - 432" part="86" refId="ref7394" refString="8. Lendaro E, Ippoliti R, Bellelli A, Brunori M, Zito R, Citro G, Ascenzi A. 1991 On the problem of immunological detection of antigens in skeletal remains. Am. J. Phys. Anthropol. 86, 429 - 432. (doi: 10.1002 / ajpa. 1330860308)" title="On the problem of immunological detection of antigens in skeletal remains" type="journal article" year="1991">8</bibRefCitation>
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]. The authenticity of any findings based on this approach rests solely on sequence interpretation. In its first release̗ this was fraught with multiple incorrect post-translational modification (PTM) assignments in the form of hydroxylated glycine residues [
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<bibRefCitation author="Asara JM & Schweitzer MH & Freimark LM & Phillips M & Cantley LC" box="[181,195,1745,1767]" journalOrPublisher="Science" pageId="1" pagination="280 - 285" part="316" refId="ref7259" refString="5. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC. 2007 Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316, 280 - 285. (doi: 10.1126 / science. 1137614)" title="Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry" type="journal article" year="2007">5</bibRefCitation>
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]; a clear indication of the potential problems is the reliance on probability-based matching algorithms of current proteomics-based techniques. In direct response to this first report̗ several criticisms arose related to potential forms of contamination [
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<bibRefCitation author="Buckley M" box="[277,289,1873,1895]" journalOrPublisher="Science" pageId="1" pagination="33" part="319" refId="ref7305" refString="6. Buckley M et al. 2008 Comment on ' Protein sequences from Mastodon and Tyrannosaurus rex revealed by mass spectrometry ̍. Science 319, 33. (doi: 10.1126 / science. 1147046)" title="Comment on ' Protein sequences from Mastodon and Tyrannosaurus rex revealed by mass spectrometry ̍" type="journal article" year="2008">6</bibRefCitation>
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̗
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<bibRefCitation author="Bern M & Phinney BS & Goldberg D." box="[295,307,1873,1895]" journalOrPublisher="J. Proteome Res." pageId="1" pagination="4328 - 4332" part="8" refId="ref7453" refString="9. Bern M, Phinney BS, Goldberg D. 2009 Reanalysis of Tyrannosaurus rex mass spectra. J. Proteome Res. 8, 4328 - 4332. (doi: 10.1021 / pr 900349 r)" title="Reanalysis of Tyrannosaurus rex mass spectra" type="journal article" year="2009">9</bibRefCitation>
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̗
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<bibRefCitation author="Kaye TG & Gaugler G & Sawlowicz Z." box="[314,339,1873,1895]" journalOrPublisher="PLoS ONE" pageId="1" pagination="e 2808" part="3" refId="ref7492" refString="10. Kaye TG, Gaugler G, Sawlowicz Z. 2008 Dinosaurian soft tissues interpreted as bacterial biofilms. PLoS ONE 3, e 2808. (doi: 10.1371 / journal. pone. 0002808)" title="Dinosaurian soft tissues interpreted as bacterial biofilms" type="journal article" year="2008">10</bibRefCitation>
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] or statistical artefact relating to such a proteomics approach [
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<bibRefCitation author="Pevzner PA & Kim S & Ng J." box="[344,371,1905,1927]" journalOrPublisher="Science" pageId="1" pagination="1040" part="321" refId="ref7530" refString="11. Pevzner PA, Kim S, Ng J. 2008 Comment on ' Protein sequences from Mastodon and Tyrannosaurus rex revealed by mass spectrometry ̍. Science 321, 1040. (doi: 10.1126 / science. 1155006)" title="Comment on ' Protein sequences from Mastodon and Tyrannosaurus rex revealed by mass spectrometry ̍" type="journal article" year="2008">11</bibRefCitation>
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].
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</paragraph>
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<paragraph blockId="1.[113,757,1385,2120]" lastBlockId="1.[831,1475,748,1762]" pageId="1">
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On the grounds that mineralized and non-mineralized coatings have been found extensively in the porous trabecular bone of a variety of vertebrate fossils across time̗ including dinosaurs̗ Kaye
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<emphasis box="[291,340,2034,2056]" italics="true" pageId="1">et al.</emphasis>
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[
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<bibRefCitation author="Kaye TG & Gaugler G & Sawlowicz Z." box="[355,381,2033,2055]" journalOrPublisher="PLoS ONE" pageId="1" pagination="e 2808" part="3" refId="ref7492" refString="10. Kaye TG, Gaugler G, Sawlowicz Z. 2008 Dinosaurian soft tissues interpreted as bacterial biofilms. PLoS ONE 3, e 2808. (doi: 10.1371 / journal. pone. 0002808)" title="Dinosaurian soft tissues interpreted as bacterial biofilms" type="journal article" year="2008">10</bibRefCitation>
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] proposed that the
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<taxonomicName authorityName="Osborn" authorityYear="1905" box="[593,649,2035,2056]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
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<emphasis box="[593,649,2035,2056]" italics="true" pageId="1">T. rex</emphasis>
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</taxonomicName>
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specimen was likely similarly contaminated with bacterial biofilm̗ thus explaining the morphological similarity to the blood vessels and osteocytes that they attack. In addition̗ the blood-celllike iron–oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Interestingly̗ similar thin linings on Haversian canals within apatite were identified by infrared and electron microprobe analysis of ossified tendon by Manning
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<emphasis box="[1172,1222,909,931]" italics="true" pageId="1">et al.</emphasis>
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[
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<bibRefCitation author="Manning PL" box="[1237,1251,908,930]" journalOrPublisher="Proc. R. Soc. B" pageId="1" pagination="2777 - 2783" part="273" refId="ref7343" refString="7. Manning PL et al. 2009 Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA). Proc. R. Soc. B 273, 2777 - 2783. (doi: 10.1098 / rspb. 2009.0812)" title="Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA)" type="journal article" year="2009">7</bibRefCitation>
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] and clearly showed preserved mineral zonation̗ with silica and trapped carbon dioxide. FTIR analysis of the tendon showed clear structural control of organic compounds within the Haversian canals̗ suggesting that organic material may have persisted. However̗ this study concluded that the organic signal may have been associated with breakdown products of the original biomaterial deposited within the tendon̗ consistent with the presence of the endogenous breakdown products of organic material identified from other regions of the specimen but not able to yield any such sequence information [
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<bibRefCitation author="Manning PL" box="[1230,1245,1228,1250]" journalOrPublisher="Proc. R. Soc. B" pageId="1" pagination="2777 - 2783" part="273" refId="ref7343" refString="7. Manning PL et al. 2009 Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA). Proc. R. Soc. B 273, 2777 - 2783. (doi: 10.1098 / rspb. 2009.0812)" title="Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA)" type="journal article" year="2009">7</bibRefCitation>
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].
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</paragraph>
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<paragraph blockId="1.[831,1475,748,1762]" pageId="1">
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Bern
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<emphasis box="[923,968,1261,1282]" italics="true" pageId="1">et al.</emphasis>
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[
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<bibRefCitation author="Bern M & Phinney BS & Goldberg D." box="[979,993,1260,1282]" journalOrPublisher="J. Proteome Res." pageId="1" pagination="4328 - 4332" part="8" refId="ref7453" refString="9. Bern M, Phinney BS, Goldberg D. 2009 Reanalysis of Tyrannosaurus rex mass spectra. J. Proteome Res. 8, 4328 - 4332. (doi: 10.1021 / pr 900349 r)" title="Reanalysis of Tyrannosaurus rex mass spectra" type="journal article" year="2009">9</bibRefCitation>
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] reanalysed the original
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<taxonomicName authorityName="Osborn" authorityYear="1905" box="[1245,1298,1261,1282]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
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<emphasis box="[1245,1298,1261,1282]" italics="true" pageId="1">T. rex</emphasis>
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</taxonomicName>
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sequence data to infer that the sample was predominantly laboratory contaminants̗ soil bacteria and bird-like haemoglobin and collagen. They suggested that of the six peptides that Asara
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<emphasis box="[1388,1438,1357,1378]" italics="true" pageId="1">et al.</emphasis>
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[
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<bibRefCitation author="Asara JM & Schweitzer MH & Freimark LM & Phillips M & Cantley LC" box="[1453,1466,1356,1378]" journalOrPublisher="Science" pageId="1" pagination="280 - 285" part="316" refId="ref7259" refString="5. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC. 2007 Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316, 280 - 285. (doi: 10.1126 / science. 1137614)" title="Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry" type="journal article" year="2007">5</bibRefCitation>
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] deposited in GenBank (GATGAPGIAGAPGFPGARGA- PGPQGPSGAPGPK̗ GSAGPPGATGFPGAAGR̗ GVQG- PPGPQGPR̗ and GVVGLPGQR from collagen alpha-I type I̗ GLVGAPGLRGLPGK from collagen alpha-1 type II and GLPGESGAVGPAGPIGSR from collagen alpha-2 type I)̗ only the first three of these could be considered statistically significant̗ calling for the latter to be dropped from GenBank. However̗ despite the unexpected presence of haemoglobin̗ a protein only typically seen in relatively recent samples [12̗
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<bibRefCitation author="Wadsworth C & Buckley M." box="[870,894,1676,1698]" journalOrPublisher="Rapid Commun. Mass Spectrom." pageId="1" pagination="605 - 615" part="28" refId="ref7616" refString="13. Wadsworth C, Buckley M. 2014 Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone. Rapid Commun. Mass Spectrom. 28, 605 - 615. (doi: 10.1002 / rcm. 6821)" title="Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone" type="journal article" year="2014">13</bibRefCitation>
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]̗ the presence of the remaining collagen peptides was not accepted as being contamination for reasons that remain unclear.
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</paragraph>
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</subSubSection>
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</treatment>
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</document> |