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Cited by 161Archaeology and ancient environmental studiesPaleopathology and ancient diseasesCultural Heritage Materials Analysis

The DOI matches its Crossref record; 171 of the 171 references it cites were found in a registry or an index; 82 of the 151 sources its claims cite were checked for support.

Ancient protein analysis in archaeology

Open access
Hendy, Jessica·2021·Science Advances
DOI 10.1126/sciadv.abb9314PMC PMC7810370
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Abstract

The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

This review synthesizes the major advances and applications of ancient protein analysis (paleoproteomics) in archaeology, tracing the field from early amino acid detection through mass spectrometry–based approaches. It surveys applications across subsistence practices, human evolution, osteobiographies, and material culture, and argues that key future directions are protein survival/degradation research, minimally destructive techniques, and integration of multiple biomolecular methods.

Key findings

  • Mass spectrometry (MS) since the 2000s "revolutionized the scope and diversity of applications," enabling study of ancient proteomes and metaproteomes rather than just individual target proteins; proteins can survive in archaeological and paleontological materials for over 1 million years, with survival linked to mineralized substrates (bone, shell, dental calculus, enamel).
  • ZooMS (peptide mass fingerprinting via MALDI-TOF MS) is typically able to distinguish family- or even genus-level taxa but differentiating species "can be challenging due to insufficient sequence variability"; it has been applied to fragmented bone, parchment, ivory, eggshell, combs, and leather.
  • Immunoassay approaches to stone tools have been substantially criticized: tests on modern stone tools found protein residues absent within 1 year of manufacturing, and a commercial laboratory performing CIEP made correct identifications in only 37% of samples, with cross-reactions within and beyond the family level.
  • Quantitative metaproteomics of dental calculus from 20 medieval Danish individuals identified two groups—one with microbiome dysbiosis and one with a healthy microbiome—and classified human immune protein expression into healthy or diseased oral health states.

Methods

  • Narrative review synthesizing methodological approaches (amino acid analysis and racemization, immunoassays, peptide mass fingerprinting/ZooMS, LC-MS/MS bottom-up and top-down, quantification) and applications across four themes: subsistence practices and ecologies, osteobiographies and lifeways, material culture analysis, and human evolution.
  • Draws on cited case studies spanning archaeological, historical, and paleontological materials, including shell beads, lithic tools, parchment, combs, dental calculus, bone, enamel, mummified remains, and food residues.
  • No primary data collection or new analysis; the paper is a synthesis of previously published work.

Limitations

  • The paper states that there is currently no single identified marker of ancient protein degradation (unlike C-to-T transitions in DNA), and that much remains to be uncovered about influences on deamidation rates beyond time, including predepositional factors such as cooking.
  • The paper notes that quantitative approaches face open questions about differential degradation rates of different proteins and whether protein abundance in archaeological remains accurately reflects biological processes during life; dental calculus dietary analysis may not capture the full diversity of foods consumed and shows bias toward certain food groups (e.g., milk proteins).
  • Evident from the text: the review is a qualitative synthesis without systematic search criteria or meta-analysis, and several cited applications (e.g., dinosaur protein survival, cannibalism claims, immunoassay residue studies) are described as controversial or criticized, so findings rest on contested primary literature.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1126/sciadv.abb9314

Cites

171 of 171 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

82 of 151 cited sources checked · 54 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    AAR has seen particular success in highly mineralized substrates that act as closed systems, such as mollusk and avian shell and tooth enamel, where intracrystalline amino acids should remain endogenous and predictable.

    “However, AAR has seen particular success in highly mineralized substrates that act as closed systems (26). Such substrates for analyses include mollusk and avian shell (11, 26, 27) as well as tooth enamel (13, 28), which are substrates where intracrystalline amino acids should remain endogenous and predictable.”
    Quote in the paperNot a substantial claim3 of 5 sources checked
    • cites [26] Penkman K. E. H., Kaufman D. S., Maddy D., Collins M. J., Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells. Quat. Geochronol. 3, 2– 25 (2008). 19684879 PMC2727006 source
    • cites [11] Demarchi B., Williams M. G., Milner N., Russell N., Bailey G., Penkman K., Amino acid racemization dating of marine shells: A mound of possibilities. Quat. Int. 239, 114– 124 (2011). 21776187 PMC3117143 source

      The Introduction and ‘Testing the closed system in Chicoreus and Strombus’ support successful AAR dating using isolated intracrystalline amino acids in some mollusk shells. The paper cautions in ‘Bleaching and leaching tests: rationale’ that not all mollusks are suitable, and it does not establish closed-system behavior for avian shell, for which this citation is also supplied. Tooth enamel is cited to other sources in the citing sentence. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [27] Sykes G. A., Collins M. J., Walton D. I., The significance of a geochemically isolated intracrystalline organic fraction within biominerals. Org. Geochem. 23, 1059– 1065 (1995). source
    • cites [13] Dickinson M. R., Lister A. M., Penkman K. E. H., A new method for enamel amino acid racemization dating: A closed system approach. Quat. Geochronol. 50, 29– 46 (2019). source
    • cites [28] Griffin R. C., Chamberlain A. T., Hotz G., Age estimation of archaeological remains using amino acid racemization in dental enamel: A comparison of morphological, biochemical, and known ages-at-death. Am. J. Phys. Anthropol. 140, 244– 252 (2009). 19358293 source
  • Premisecitation

    The survival of ancient proteins in deep time has been linked to mineralized substrates.

    “what is known is that the survival of ancient proteins in deep time has been linked to mineralized substrates.”
    Quote in the paperNot a substantial claim4 of 7 sources checked
    • cites [63] Asara J. M., Schweitzer M. H., Freimark L. M., Phillips M., Cantley L. C., Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316, 280– 285 (2007). 17431180 source
    • cites [64] Schweitzer M. H., Zheng W., Organ C. L., Avci R., Suo Z., Freimark L. M., Lebleu V. S., Duncan M. B., Vander Heiden M. G., Neveu J. M., Lane W. S., Cottrell J. S., Horner J. R., Cantley L. C., Kalluri R., Asara J. M., Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324, 626– 631 (2009). 19407199 source
    • cites [65] Bern M., Phinney B. S., Goldberg D., Reanalysis of Tyrannosaurus rex mass spectra. J. Proteome Res. 8, 4328– 4332 (2009). 19603827 PMC2738754 source

      The Introduction describes reported collagen sequences in a 68-million-year-old fossilized bone, and Results and Discussion finds the spectra consistent with possibly ancient bone proteins. This supports an association with fossil bone, but the paper does not establish that mineralization explains their survival or extend the finding to mineralized substrates generally; it also notes unresolved contamination concerns. The indexed passages provide no page numbers. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [66] Schroeter E. R., DeHart C. J., Cleland T. P., Zheng W., Thomas P. M., Kelleher N. L., Bern M., Schweitzer M. H., Expansion for the Brachylophosaurus canadensis collagen I sequence and additional evidence of the preservation of cretaceous protein. J. Proteome Res. 16, 920– 932 (2017). 28111950 PMC5401637 source
    • cites [67] Pevzner P. A., Kim S., Ng J., Comment on “Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry”. Science 321, 1040 (2008). 18719266 source
    • cites [68] Buckley M., Walker A., Ho S. Y. W., Yang Y., Smith C., Ashton P., Oates J. T., Cappellini E., Koon H., Penkman K., Elsworth B., Ashford D., Solazzo C., Andrews P., Strahler J., Shapiro B., Ostrom P., Gandhi H., Miller W., Raney B., Zylber M. I., Gilbert M. T. P., Prigodich R. V., Ryan M., Rijsdijk K. F., Janoo A., Collins M. J., Comment on “Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry”. Science 319, 33 (2008). PMC2694913 18174420 source
    • cites [69] Buckley M., Warwood S., van Dongen B., Kitchener A. C., Manning P. L., A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination. Proc. Biol. Sci. 284, 20170544 (2017). 28566488 PMC5454271 source

      The Introduction (page unavailable) links mineralized hadrosaur tissue with possible persistence of organic material. It says the evidence was for protein breakdown products, not surviving protein sequences, so it does not establish the claimed link between mineralized substrates and the survival of ancient proteins. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
  • Premisecitation

    Through analysis of parchment, ZooMS is revealing temporal and geographic differences in use of animals in medieval economies.

    “Through the analysis of another substrate, ZooMS is also revealing temporal and geographic differences in the use of animals in medieval economies (52–54).”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [52] Kirby D. P., Buckley M., Promise E., Trauger S. A., Holdcraft T. R., Identification of collagen-based materials in cultural heritage. Analyst 138, 4849– 4858 (2013). 23807214 source
    • cites [53] Fiddyment S., Holsinger B., Ruzzier C., Devine A., Binois A., Albarella U., Fischer R., Nichols E., Curtis A., Cheese E., Teasdale M. D., Checkley-Scott C., Milner S. J., Rudy K. M., Johnson E. J., Vnouček J., Garrison M., McGrory S., Bradley D. G., Collins M. J., Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proc. Natl. Acad. Sci. U.S.A. 112, 15066– 15071 (2015). 26598667 PMC4679014 source
    • cites [54] Teasdale M. D., Fiddyment S., Vnouček J., Mattiangeli V., Speller C., Binois A., Carver M., Dand C., Newfield T. P., Webb C. C., Bradley D. G., Collins M. J., The York Gospels: A 1000-year biological palimpsest. R. Soc. Open Sci. 4, 170988 (2017). 29134095 PMC5666278 source

      The Results (Species identification; page unavailable) show a temporal difference: the original York Gospels are predominantly calfskin, while fourteenth-century additions are sheepskin. The Discussion (Population genetic analysis; page unavailable) describes geolocating parchment as a future possibility based on genetic analysis, not a geographic difference already revealed by ZooMS. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Premisecitation

    Ancient protein analysis has been particularly informative in exploring past patterns of dairy consumption.

    “Where this technique has been particularly informative is in exploring past patterns of dairy consumption (108–112).”
    Quote in the paperSubstantial claim5 of 5 sources checked
    • cites [108] Warinner C., Hendy J., Speller C., Cappellini E., Fischer R., Trachsel C., Arneborg J., Lynnerup N., Craig O. E., Swallow D. M., Fotakis A., Christensen R. J., Olsen J. V., Liebert A., Montalva N., Fiddyment S., Charlton S., Mackie M., Canci A., Bouwman A., Rühli F., Gilbert M. T. P., Collins M., Direct evidence of milk consumption from ancient human dental calculus. Sci. Rep. 4, 7104 (2014). 25429530 PMC4245811 source
    • cites [109] Jeong C., Wilkin S., Amgalantugs T., Bouwman A. S., Taylor W. T. T., Hagan R. W., Bromage S., Tsolmon S., Trachsel C., Grossmann J., Littleton J., Makarewicz C. A., Krigbaum J., Burri M., Scott A., Davaasambuu G., Wright J., Irmer F., Myagmar E., Boivin N., Robbeets M., Rühli F. J., Krause J., Frohlich B., Hendy J., Warinner C., Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe. Proc. Natl. Acad. Sci. U.S.A. 115, E11248– E11255 (2018). 30397125 PMC6275519 source
    • cites [110] Mays S., Roberts D., Marshall P., Pike A. W. G., van Heekeren V., Bronk Ramsey C., Dunbar E., Reimer P., Linscott B., Radini A., Lowe A., Dowle A., Speller C., Vallender J., Bedford J., Lives before and after Stonehenge: An osteobiographical study of four prehistoric burials recently excavated from the Stonehenge World Heritage Site. J. Archaeol. Sci. Rep. 20, 692– 710 (2018). source
    • cites [111] Charlton S., Ramsøe A., Collins M., Craig O. E., Fischer R., Alexander M., Speller C. F., New insights into Neolithic milk consumption through proteomic analysis of dental calculus. Archaeol. Anthropol. Sci. 11, 6183– 6196 (2019). source
    • cites [112] Wilkin S., Miller A. V., Taylor W. T. T., Miller B. K., Hagan R. W., Bleasdale M., Scott A., Gankhuyg S., Ramsøe A., Uliziibayar S., Trachsel C., Nanni P., Grossmann J., Orlando L., Horton M., Stockhammer P. W., Myagmar E., Boivin N., Warinner C., Hendy J., Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years. Nat. Ecol. Evol. 4, 346– 355 (2020). 32127685 PMC7212056 source
  • Premisecitation

    The survival of proteins or peptides in eggshell has been linked to the binding of uterine proteins to the calcium mineral of egg shell, facilitating its long-term survival in the paleontological record.

    “Similarly, the survival of proteins or peptides in eggshell has been linked to the binding of uterine proteins to the calcium mineral of egg shell, facilitating its long-term survival in the paleontological record (21).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [21] Demarchi B., Hall S., Roncal-Herrero T., Freeman C. L., Woolley J., Crisp M. K., Wilson J., Fotakis A., Fischer R., Kessler B. M., Jersie-Christensen R. R., Olsen J. V., Haile J., Thomas J., Marean C. W., Parkington J., Presslee S., Lee-Thorp J., Ditchfield P., Hamilton J. F., Ward M. W., Wang C. M., Shaw M. D., Harrison T., Domínguez-Rodrigo M., MacPhee R. D. E., Kwekason A., Ecker M., Horwitz L. K., Chazan M., Kröger R., Thomas-Oates J., Harding J. H., Cappellini E., Penkman K., Collins M. J., Protein sequences bound to mineral surfaces persist into deep time. eLife 5, e17092 (2016). 2766851 source

      The Results section ('Eggshell contains proteins...'; page unavailable) identifies struthiocalcin-1 and -2 in ostrich eggshell and links their binding to the calcite surface with long-term peptide survival. The cited paper does not identify these proteins as uterine proteins, so that part of the claim is unsupported by our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Probably not a substantial claim. 23
  • It may state two separate claims as one. 40

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    The survival of amino acids continues to be explored, particularly in investigations of amino acid racemization (AAR) dating and bulk amino acid analysis to investigate the biological origin of artifacts and objects.

    “The survival of amino acids continues to be explored to the present day, in particular, in investigations of amino acid racemization (AAR) dating, as well as bulk amino acid analysis to investigate the biological origin of particular artifacts and objects”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [11] Demarchi B., Williams M. G., Milner N., Russell N., Bailey G., Penkman K., Amino acid racemization dating of marine shells: A mound of possibilities. Quat. Int. 239, 114– 124 (2011). 21776187 PMC3117143 source

      The Introduction describes AAR dating of archaeological marine shells, and the Chiral amino acid analysis section describes measuring their amino acids. The paper uses those measurements to assess degradation and age; it does not support the separate claim that bulk amino acid analysis is used to determine the biological origin of artifacts or objects. Page numbers were not available in our copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [12] Demarchi B., O’Connor S., de Lima Ponzoni A., de Almeida Rocha Ponzoni R., Sheridan A., Penkman K., Hancock Y., Wilson J., An integrated approach to the taxonomic identification of prehistoric shell ornaments. PLOS ONE 9, e99839 (2014). 24936797 PMC4061022 source
    • cites [13] Dickinson M. R., Lister A. M., Penkman K. E. H., A new method for enamel amino acid racemization dating: A closed system approach. Quat. Geochronol. 50, 29– 46 (2019). source

      The introduction describes AAR as a dating technique, and the Conclusions report a method for analysing amino acids in fossil enamel. The paper does not describe using bulk amino acid analysis to determine the biological origin of artifacts or objects; that part of the claim is unsupported. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Interpretationcitation

    While analysis of fats, oils, and waxes is typically applied to ceramic material culture, analysis of proteins has potential to yield further insights into taxa used and food mixing.

    “While the analysis of fats, oils, and waxes is typically applied to this ceramic material culture [e.g., (113–116)], the analysis of proteins has the potential to yield further insights into the taxa used, as well as insights into food mixing (116).”
    Quote in the paperSubstantial claim3 of 4 sources checked
    • cites [113] Dunne J., Evershed R. P., Salque M., Cramp L., Bruni S., Ryan K., Biagetti S., di Lernia S., First dairying in green Saharan Africa in the fifth millennium BC. Nature 486, 390– 394 (2012). 22722200 source
    • cites [114] Roffet-Salque M., Regert M., Evershed R. P., Outram A. K., Cramp L. J. E., Decavallas O., Dunne J., Gerbault P., Mileto S., Mirabaud S., Pääkkönen M., Smyth J., Šoberl L., Whelton H. L., Alday-Ruiz A., Asplund H., Bartkowiak M., Bayer-Niemeier E., Belhouchet L., Bernardini F., Budja M., Cooney G., Cubas M., Danaher E. M., Diniz M., Domboróczki L., Fabbri C., González-Urquijo J. E., Guilaine J., Hachi S., Hartwell B. N., Hofmann D., Hohle I., Ibáñez J. J., Karul N., Kherbouche F., Kiely J., Kotsakis K., Lueth F., Mallory J. P., Manen C., Marciniak A., Maurice-Chabard B., Gonigle M. A. M., Mulaz source

      The ‘Lipid residue analyses’ section describes analysing lipids extracted from pottery sherds, supporting the citation’s use for the first clause. The paper also identifies animal fats and beeswax in some vessels, but the passages do not discuss protein analysis or its potential to reveal taxa and food mixing; searches for those terms found no such passage. Page numbers are not available in our copy. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [115] Lucquin A., Gibbs K., Uchiyama J., Saul H., Ajimoto M., Eley Y., Radini A., Heron C. P., Shoda S., Nishida Y., Lundy J., Jordan P., Isaksson S., Craig O. E., Ancient lipids document continuity in the use of early hunter-gatherer pottery through 9,000 years of Japanese prehistory. Proc. Natl. Acad. Sci. U.S.A. 113, 3991– 3996 (2016). 27001829 PMC4839459 source

      The 'Lipid analysis of ceramic samples' section (page unavailable) describes extracting and analysing lipids from pottery and charred deposits, supporting the lipid-analysis portion of the citation. The paper does not address protein analysis or its potential to identify taxa and food mixing. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [116] Spiteri C. D., Gillis R. E., Roffer-Salque M., Navarro L. C., Guilaine J., Manen C., Muntoni I. M., Segui M. S., Urem-Kotsou D., Whelton H. L., Craig O. E., Vigne J. D., Evershed R. P., Regional asynchronicity in dairy production and processing in early farming communities of the northern Mediterranean. Proc. Natl. Acad. Sci. U.S.A. 113, 13594– 13599 (2016). 27849595 PMC5137723 source

      Materials and Methods (p. 10) describes lipid analysis of ceramic potsherds, supporting the citation’s use for that part of the sentence. The paper’s Overview of biomarker and isotopic analyses (p. 5) discusses fatty-acid evidence, but the passages found do not address whether protein analysis can reveal taxa or food mixing. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Premisecitation

    ZooMS has been applied to understanding past ecologies and environments through expansion of zooarcheological identifications in archeological assemblages, particularly useful for highly fragmented bone assemblages.

    “ZooMS has also been applied to understanding past ecologies and environments through the expansion of zooarcheological identifications in archeological assemblages, an approach that can be particularly useful when examining highly fragmented bone assemblages (95–97).”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [95] Buckley M., Harvey V. L., Chamberlain A. T., Species identification and decay assessment of Late Pleistocene fragmentary vertebrate remains from Pin Hole Cave (Creswell Crags, UK) using collagen fingerprinting. Boreas 46, 402– 411 (2017). source
    • cites [96] Sinet-Mathiot V., Smith G. M., Romandini M., Wilcke A., Peresani M., Hublin J.-J., Welker F., Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy). Sci. Rep. 9, 12350 (2019). 31451791 PMC6710433 source
    • cites [97] Pothier Bouchard G., Riel-Salvatore J., Negrino F., Buckley M., Archaeozoological, taphonomic and ZooMS insights into The Protoaurignacian faunal record from Riparo Bombrini. Quat. Int. 551, 243– 263 (2020). source

      The available indexed passages contain the paper’s title and citation metadata, but no substantive text on ZooMS applications. Searches for fragmented bones, expanded faunal identifications, and environmental interpretation returned only that metadata, so the claim cannot be checked against our copy. (LLM, conf=0.70)

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Premisecitation

    While some success from extracting proteins from ceramics has been reported, challenges have arisen in removal of protein from the silica matrix and protein preservation in this context is not fully understood.

    “While some success from extracting proteins from ceramics has been reported (117–120), challenges have arisen in the removal of protein from the silica matrix and protein preservation in this context is not fully understood (7, 121, 122).”
    Quote in the paperNot a substantial claim1 of 7 sources checked
    • cites [117] Craig O., Mulville J., Pearson M. P., Sokol R., Gelsthorpe K., Stacey R., Collins M., Detecting milk proteins in ancient pots. Nature 408, 312 (2000). 11099030 source
    • cites [118] Barker A., Venables B., Stevens S. M., Seeley K. W., Wang P., Wolverton S., An optimized approach for protein residue extraction and identification from ceramics after cooking. J. Archaeol. Method Theory 19, 407– 439 (2012). source
    • cites [119] Solazzo C., Fitzhugh W. W., Rolando C., Tokarski C., Identification of protein remains in archaeological potsherds by proteomics. Anal. Chem. 80, 4590– 4597 (2008). 18494502 source
    • cites [120] Hendy J., Colonese A. C., Franz I., Fernandes R., Fischer R., Orton D., Lucquin A., Spindler L., Anvari J., Stroud E., Biehl P. F., Speller C., Boivin N., Mackie M., Jersie-Christensen R. R., Olsen J. V., Collins M. J., Craig O. E., Rosenstock E., Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers. Nat. Commun. 9, 4064 (2018). 30283003 PMC6170438 source

      The Introduction (page unavailable) says it was unclear whether dietary proteins would survive long-term burial or whether extraction strategies could more effectively recover proteins from vessel walls. That supports the preservation uncertainty and a general extraction challenge, but the paper does not specifically identify difficulty removing proteins from a silica matrix. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [7] Craig O. E., Collins M. J., An improved method for the immunological detection of mineral bound protein using hydrofluoric acid and direct capture. J. Immunol. Methods 236, 89– 97 (2000). 10699582 source
    • cites [121] Evershed R. P., Tuross N., Proteinaceous material from potsherds and associated soils. J. Archaeol. Sci. 23, 429– 436 (1996). source
    • cites [122] Barker A., Dombrosky J., Venables B., Wolverton S., Taphonomy and negative results: An integrated approach to ceramic-bound protein residue analysis. J. Archaeol. Sci. 94, 32– 43 (2018). source

  • It may state two separate claims as one.

    Premisecitation

    While rates of deamidation vary with temperature, pH, secondary and tertiary structures, and laboratory procedures, deamidation can be a useful indicator of protein degradation, although more work is needed to untangle contributing factors to these rates.

    “While rates of deamidation vary with temperature, pH, secondary and tertiary structures, and laboratory procedures (78, 79), deamidation can be a useful indicator of protein degradation, although still more work is needed to untangle contributing factors to these rates.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [78] Simpson J. P., Penkman K. E. H., Demarchi B., Koon H., Collins M. J., Thomas-Oates J., Shapiro B., Stark M., Wilson J., The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone. J. Archaeol. Sci. 69, 29– 38 (2016). source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [79] Procopio N., Buckley M., Minimizing laboratory-induced decay in bone proteomics. J. Proteome Res. 16, 447– 458 (2017). 28152590 source

      Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured

  • It may state two separate claims as one.

    Premisecitation

    The dental calculus proteomic approach may not capture the diversity of foods consumed by an individual, and there is a bias toward certain food groups.

    “While informative on the consumption of particular foodstuffs, it is clear that this approach may not capture the diversity of foods consumed by that individual, and there is a bias toward certain food groups (107).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [107] Hendy J., Warinner C., Bouwman A., Collins M. J., Fiddyment S., Fischer R., Hagan R., Hofman C. A., Holst M., Chaves E., Klaus L., Larson G., Mackie M., McGrath K., Mundorff A. Z., Radini A., Rao H., Trachsel C., Velsko I. M., Speller C. F., Proteomic evidence of dietary sources in ancient dental calculus. Proc. Biol. Sci. 285, 20180977 (2018). 30051838 PMC6083251 source

  • It may state two separate claims as one.

    Premisecitation

    ZooMS is typically applied to fragmented or morphologically nondiagnostic bone fragments and has also been applied to parchments, ivory, eggshell, combs, and leather objects.

    “For archeological questions, this analysis not only is typically applied to fragmented or morphologically nondiagnostic bone fragments but also has been applied to a range of other archeological material culture, including parchments (52–54), ivory (55), eggshell (19, 22), combs (56), and leather objects (57).”
    Quote in the paperNot a substantial claim4 of 6 sources checked
    • cites [52] Kirby D. P., Buckley M., Promise E., Trauger S. A., Holdcraft T. R., Identification of collagen-based materials in cultural heritage. Analyst 138, 4849– 4858 (2013). 23807214 source
    • cites [53] Fiddyment S., Holsinger B., Ruzzier C., Devine A., Binois A., Albarella U., Fischer R., Nichols E., Curtis A., Cheese E., Teasdale M. D., Checkley-Scott C., Milner S. J., Rudy K. M., Johnson E. J., Vnouček J., Garrison M., McGrory S., Bradley D. G., Collins M. J., Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proc. Natl. Acad. Sci. U.S.A. 112, 15066– 15071 (2015). 26598667 PMC4679014 source
    • cites [54] Teasdale M. D., Fiddyment S., Vnouček J., Mattiangeli V., Speller C., Binois A., Carver M., Dand C., Newfield T. P., Webb C. C., Bradley D. G., Collins M. J., The York Gospels: A 1000-year biological palimpsest. R. Soc. Open Sci. 4, 170988 (2017). 29134095 PMC5666278 source
    • cites [55] Coutu A. N., Whitelaw G., le Roux P., Sealy J., Earliest evidence for the ivory trade in Southern Africa: Isotopic and ZooMS analysis of seventh–tenth century ad ivory from KwaZulu-Natal. Afr. Archaeol. Rev. 33, 411– 435 (2016). source
    • cites [19] Stewart J. R. M., Allen R. B., Jones A. K. G., Penkman K. E. H., Collins M. J., ZooMS: Making eggshell visible in the archaeological record. J. Archaeol. Sci. 40, 1797– 1804 (2013). source
    • cites [22] Presslee S., Wilson J., Woolley J., Best J., Russell D., Radini A., Fischer R., Kessler B., Boano R., Collins M., Demarchi B., The identification of archaeological eggshell using peptide markers. STAR Sci. Technol. Archaeol. Res. 3, 89– 99 (2017). source

  • It may state two separate claims as one.

    Premisecitation

    Where environmental contexts have enabled good organic preservation, proteins have been extracted and identified from whole foodstuffs to identify their constituents, for example, from food remains at cemetery sites in the Tarim Basin, China, including whole cheese curds and bread, and in Egyptian tombs.

    “Where environmental contexts have enabled good organic preservation, proteins have been extracted and identified from whole foodstuffs to identify their constituents, for example, from food remains found at cemetery sites in the Tarim Basin, China, including whole cheese curds (100–102) and bread (103), and in Egyptian tombs (104), where dry conditions may have slowed biomolecular deterioration.”
    Quote in the paperNot a substantial claim2 of 5 sources checked
    • cites [100] Hong C., Jiang H., Lü E., Wu Y., Guo L., Xie Y., Wang C., Yang Y., Identification of milk component in ancient food residue by proteomics. PLOS ONE 7, e37053 (2012). 22615887 PMC3353977 source

      Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [101] Yang Y., Shevchenko A., Knaust A., Abuduresule I., Li W., Hu X., Wang C., Shevchenko A., Proteomics evidence for kefir dairy in Early Bronze Age China. J. Archaeol. Sci. 45, 178– 186 (2014). source
    • cites [102] Xie M., Shevchenko A., Wang B., Shevchenko A., Wang C., Yang Y., Identification of a dairy product in the grass woven basket from Gumugou Cemetery (3800 BP, northwestern China). Quat. Int. 426, 158– 165 (2016). source
    • cites [103] Shevchenko A., Yang Y., Knaust A., Thomas H., Jiang H., Lu E., Wang C., Shevchenko A., Proteomics identifies the composition and manufacturing recipe of the 2500-year old sourdough bread from Subeixi cemetery in China. J. Proteomics 105, 363– 371 (2014). 24291353 source
    • cites [104] Greco E., El-Aguizy O., Ali M. F., Foti S., Cunsolo V., Saletti R., Ciliberto E., Proteomic analyses on an ancient Egyptian cheese and biomolecular evidence of brucellosis. Anal. Chem. 90, 9673– 9676 (2018). 30044608 source

  • It may state two separate claims as one.

    Premisecitation

    Enamel has been explored as a well-preserved source of ancient proteins that can be analyzed to enable phylogenetic analysis of extinct animals and humans, as well as identification of sex based on sequence differences in amelogenin.

    “Recently, enamel has been explored as a well-preserved source of ancient proteins that can be analyzed to enable the phylogenetic analysis of extinct animals and humans (71, 72), as well as the identification of sex based on sequence differences in the enamel protein amelogenin (73–75).”
    Quote in the paperNot a substantial claim3 of 5 sources checked
    • cites [71] Welker F., Ramos-Madrigal J., Kuhlwilm M., Liao W., Gutenbrunner P., de Manuel M., Samodova D., Mackie M., Allentoft M. E., Bacon A.-M., Collins M. J., Cox J., Lalueza-Fox C., Olsen J. V., Demeter F., Wang W., Marques-Bonet T., Cappellini E., Enamel proteome shows that Gigantopithecus was an early diverging pongine. Nature 576, 262– 265 (2019). 31723270 PMC6908745 source
    • cites [72] Cappellini E., Welker F., Pandolfi L., Ramos-Madrigal J., Samodova D., Rüther P. L., Fotakis A. K., Lyon D., Moreno-Mayar J. V., Bukhsianidze M., Jersie-Christensen R. R., Mackie M., Ginolhac A., Ferring R., Tappen M., Palkopoulou E., Dickinson M. R., Stafford T. W., Chan Y. L., Götherström A., Senthilvel K. S., Heintzman P. D., Kapp J. D., Kirillova I., Moodley Y., Agusti J., Kahlke R.-D., Kiladze G., Martínez-Navarro B., Liu S., Velasco M. S., Sinding M.-H. S., Kelstrup C. D., Allentoft M. E., Orlando L., Penkman K., Shapiro B., Rook L., Dalén L., Gilbert M. T. P., Olsen J. V., Lordkipanidze source

      The paper’s Abstract reports that ancient enamel proteins preserve phylogenetic information and describes phylogenetic analysis of Dmanisi animal remains. It mentions hominin fossils at the site but does not report a phylogenetic analysis of humans. The sex-identification clause is attached to separate citations (73–75), although this paper also reports identifying male specimens using Y-specific amelogenin peptides. (LLM, conf=0.85)

      Experimental — accuracy not yet measured
    • cites [73] Porto I. M., Laure H. J., Tykot R. H., de Sousa F. B., Rosa J. C., Gerlach R. F., Recovery and identification of mature enamel proteins in ancient teeth. Eur. J. Oral Sci. 119, Suppl 1, 83– 87 (2011). 22243232 source
    • cites [74] Stewart N. A., Gerlach R. F., Gowland R. L., Gron K. J., Montgomery J., Sex determination of human remains from peptides in tooth enamel. Proc. Natl. Acad. Sci. U.S.A. 114, 13649– 13654 (2017). 29229823 PMC5748210 source
    • cites [75] Parker G. J., Yip J. M., Eerkens J. W., Salemi M., Durbin-Johnson B., Kiesow C., Haas R., Buikstra J. E., Klaus H., Regan L. A., Rocke D. M., Phinney B. S., Sex estimation using sexually dimorphic amelogenin protein fragments in human enamel. J. Archaeol. Sci. 101, 169– 180 (2019). source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    The use of antibody-based testing for the detection of ancient infectious disease has been questioned.

    “although their use in antibody-based testing for the detection of ancient infectious disease has been questioned”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [154] Kendall R., Hendy J., Collins M. J., Millard A. R., Gowland R. L., Poor preservation of antibodies in archaeological human bone and dentine. Sci. Technol. Archaeol. Res. 2, 15– 24 (2016). source

  • It may state two separate claims as one.

    Premisecitation

    Warinner et al. used both aDNA and ancient protein approaches in the analysis of ancient dental calculus, where aDNA yielded insights into the taxonomic diversity of the ancient oral microbiome and protein analysis demonstrated the survival of biofilm functional profiles.

    “Warinner et al. (155) used both aDNA and ancient protein approaches in the analysis of ancient dental calculus, where aDNA yielded insights into the taxonomic diversity of the ancient oral microbiome and protein analysis demonstrated the survival of biofilm functional profiles.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [155] Warinner C., Rodrigues J. F. M., Vyas R., Trachsel C., Shved N., Grossmann J., Radini A., Hancock Y., Tito R. Y., Fiddyment S., Speller C., Hendy J., Charlton S., Luder H. U., Salazar-García D. C., Eppler E., Seiler R., Hansen L. H., Castruita J. A. S., Barkow-Oesterreicher S., Teoh K. Y., Kelstrup C. D., Olsen J. V., Nanni P., Kawai T., Willerslev E., von Mering C., Lewis C. M. Jr., Collins M. J., Gilbert M. T. P., Rühli F., Cappellini E., Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336– 344 (2014). 24562188 PMC3969750 source

  • It may state two separate claims as one.

    Premisecitation

    Distinct SAPs in the bone protein COL1a2 enabled the identification of Denisovan remains found in the Tibetan plateau, the first Denisovan-like individual found outside of Denisova cave.

    “distinct SAPs in the bone protein COL1a2 enabled the identification of Denisovan remains found in the Tibetan plateau, the first Denisovan-like individual found outside of Denisova cave”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [144] Chen F., Welker F., Shen C.-C., Bailey S. E., Bergmann I., Davis S., Xia H., Wang H., Fischer R., Freidline S. E., Yu T.-L., Skinner M. M., Stelzer S., Dong G., Fu Q., Dong G., Wang J., Zhang D., Hublin J.-J., A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. Nature 569, 409– 412 (2019). 31043746 source

      The Main Text reports that SAPs in the Xiahe dentine proteome supported a close relationship to Denisovans, and calls the Xiahe mandible the first Denisovan found outside Denisova Cave. The Ancient protein analysis section lists COL1α2 among the proteins used for phylogenetic analysis, but our copy does not specify that the decisive SAPs were in COL1α2. The Main Text also says the ancient proteome survived in dentine, not in the bone sample. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Complementary aDNA and ancient protein analysis has proven useful for studies of evolution and phylogeny, where one can be used to verify the findings of the other.

    “complementary aDNA and ancient protein analysis has proven useful for studies of evolution and phylogeny, where one can be used to verify the findings of the other”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [3] Cappellini E., Prohaska A., Racimo F., Welker F., Pedersen M. W., Allentoft M. E., de Barros Damgaard P., Gutenbrunner P., Dunne J., Hammann S., Roffet-Salque M., Ilardo M., Moreno-Mayar J. V., Wang Y., Sikora M., Vinner L., Cox J., Evershed R. P., Willerslev E., Ancient biomolecules and evolutionary inference. Annu. Rev. Biochem. 20, 1029– 1060 (2018). 29709200 source

  • It may state two separate claims as one.

    Premisecitation

    Deamidation of glutamine and asparagine has been extensively explored, and tools have been developed to identify patterns of deamidation associated with time.

    “Deamidation of glutamine and asparagine has been extensively explored (described above), and tools have been developed to identify patterns of deamidation associated with time”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [83] Ramsøe A., van Heekeren V., Ponce P., Fischer R., Barnes I., Speller C., Collins M. J., DeamiDATE 1.0: Site-specific deamidation as a tool to assess authenticity of members of ancient proteomes. J. Archaeol. Sci. 115, 105080 (2020). source
    • Rests on an assumption: Ancient biomolecules undergo degradation over time, including fragmentation into smaller constituents and chemical alteration.
    • Rests on an assumption: There is currently no single identified marker of ancient protein degradation.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Hendy et al. reported that in samples of ancient dental calculus there appears to be a bias toward detection of milk proteins over other foods.

    “For example, Hendy et al. (107) reported that in samples of ancient dental calculus there appears to be a bias toward the detection of milk proteins over other foods.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [107] Hendy J., Warinner C., Bouwman A., Collins M. J., Fiddyment S., Fischer R., Hagan R., Hofman C. A., Holst M., Chaves E., Klaus L., Larson G., Mackie M., McGrath K., Mundorff A. Z., Radini A., Rao H., Trachsel C., Velsko I. M., Speller C. F., Proteomic evidence of dietary sources in ancient dental calculus. Proc. Biol. Sci. 285, 20180977 (2018). 30051838 PMC6083251 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisecitation

    Fiddyment et al. developed and applied minimally invasive techniques to study parchments by gently rubbing parchments with an eraser and extracting collagen proteins from the eraser shavings.

    “Fiddyment et al. (53) developed and applied minimally invasive techniques to study parchments (manuscripts) made of animal skin by gently rubbing parchments with an eraser, which pulls off loose collagen fibers, and extracting collagen proteins from the eraser shavings.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [53] Fiddyment S., Holsinger B., Ruzzier C., Devine A., Binois A., Albarella U., Fischer R., Nichols E., Curtis A., Cheese E., Teasdale M. D., Checkley-Scott C., Milner S. J., Rudy K. M., Johnson E. J., Vnouček J., Garrison M., McGrory S., Bradley D. G., Collins M. J., Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proc. Natl. Acad. Sci. U.S.A. 112, 15066– 15071 (2015). 26598667 PMC4679014 source
    • Rests on an assumption: Protein analysis is often destructive.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    MALDI-TOF-based analyses have been used as a screening tool for LC-MS/MS analysis.

    “For some studies, MALDI-TOF–based analyses have been used as a screening tool for LC-MS/MS analysis”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [174] Welker F., Smith G. M., Hutson J. M., Kindler L., Garcia-Moreno A., Villaluenga A., Turner E., Gaudzinski-Windheuser S., Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 5, e3033, (2017). PMC5354071 28316883 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.

    Interpretationnone given

    The invention and adoption of MS markedly altered protein identification approaches in archaeology and paleontology.

    “the invention and adoption of MS markedly altered protein identification approaches in archaeology and paleontology.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim.

    Interpretationreasoning

    Recent applications of ancient protein analysis to archeological and paleontological samples beyond the limit of DNA preservation and to cultural heritage and ancient lifeways are increasingly revealing the utility of ancient protein analysis.

    “recent applications to archeological and paleontological samples beyond the limit of DNA preservation as well as more nuanced insights into cultural heritage and ancient lifeways are increasingly revealing the utility of ancient protein analysis.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    Complexities to AAR arise from varying influence of environmental factors such as temperature, pH, and humidity, and AAR has been subject to criticism and skepticism.

    “Complexities to AAR arise in the varying influence of environmental factors affecting rates of racemization, such as temperature, pH, and humidity, and at times, AAR has been subject to criticism and skepticism (25).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [25] Johnson B. J., Miller G. H., Archaeological applications of amino acid racemization. Archaeometry 39, 265– 287 (1997). source

  • It may state two separate claims as one.

    Premisereasoning

    By looking at overall proportions of amino acids in different biological tissues, it can be possible to identify their taxonomic origin, because the overall composition of amino acids can differ between taxa.

    “By looking at overall proportions of amino acids in different biological tissues, it can be possible to identify their taxonomic origin, because the overall composition of amino acids can differ between taxa.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim.

    Interpretationreasoning

    MS-based techniques generating protein sequence information, paleoproteomics, and metaproteomics are being applied to a diversity of paleontological and archeological materials in history and prehistory.

    “techniques based on MS, generating protein sequence information, as well as insights into ancient proteomes (paleoproteomics) and metaproteomes are being applied to a diversity of paleontological and archeological materials in history and prehistory.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    AAR has been extensively applied to understanding quaternary chronologies, including identifying early human activity in Europe, formation of terrestrial deposits in the British Isles, speed of local shell midden accumulations, and improved dating coverage in shell midden sites.

    “AAR has been extensively applied to understanding quaternary chronologies, for example, in identifying the presence of early human activity in Europe (29), the formation of terrestrial deposits in the British Isles (30), as well as the speed of local shell midden accumulations (31) and improved dating coverage in shell midden sites (11).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [29] Parfitt S. A., Barendregt R. W., Breda M., Candy I., Collins M. J., Coope G. R., Durbidge P., Field M. H., Lee J. R., Lister A. M., Mutch R., Penkman K. E. H., Preece R. C., Rose J., Stringer C. B., Symmons R., Whittaker J. E., Wymer J. J., Stuart A. J., The earliest record of human activity in northern Europe. Nature 438, 1008– 1012 (2005). 16355223 source
    • cites [30] Penkman K. E. H., Preece R. C., Keen D. H., Maddy D., Schreve D. C., Collins M. J., Testing the aminostratigraphy of fluvial archives: The evidence from intra-crystalline proteins within freshwater shells. Quat. Sci. Rev. 26, 2958– 2969 (2007). 19684880 PMC2727059 source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [31] Koppel B., Szabó K., Moore M. W., Morwood M. J., Untangling time-averaging in shell middens: Defining temporal units using amino acid racemisation. J. Archaeol. Sci. Rep. 7, 741– 750 (2016). source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.

    Interpretationnone given

    Methodological advances in mass spectrometry since the 2000s have revolutionized the scope and diversity of applications of ancient protein analysis.

    “methodological advances in the field of mass spectrometry (MS) since the 2000s have revolutionized the scope and diversity of applications.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationcitation

    Top-down proteomics has so far seen limited application to ancient protein archeological contexts but offers great potential for understanding protein survival and degradation.

    “However, this emerging approach has so far seen limited application to ancient protein archeological contexts but offers great potential for understanding protein survival and degradation (4).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [4] Dallongeville S., Garnier N., Rolando C., Tokarski C., Proteins in art, archaeology, and paleontology: From detection to identification. Chem. Rev. 116, 2– 79 (2016). 26709533 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.

    Premisenone given

    Proteins undergo damage via bond cleavage through hydrolysis or enzymatic attack, resulting in protein fragmentation.

    “Proteins undergo damage via bond cleavage through hydrolysis or enzymatic attack (particularly from the burial environment), resulting in protein fragmentation.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisenone given

    Bottom-up LC-MS/MS analyses in ancient proteomics have typically not been quantitative, making it challenging to compare protein abundance between samples.

    “Bottom-up approaches used by LC-MS/MS analyses in ancient proteomics have typically not been quantitative, meaning it is challenging to make reasonable comparisons of protein abundance between samples.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisereasoning

    Biological substrates composed of a mineral component, such as bone, shell, and dental calculus, have been targeted as sources of ancient proteins, as have rare, well-preserved organic remains from cold or frozen, arid, or oxygen-deprived environments.

    “Biological substrates composed of a mineral component, such as bone, shell, and dental calculus, have been targeted as sources of ancient proteins, although rare, well-preserved organic remains sometimes found in cold or frozen, arid, or oxygen-deprived environments have also been targeted.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationnone given

    In contrast to other biomolecular approaches to study past dairying, ancient protein analysis is able to identify the taxa consumed, acting as a "zooarchaeology by proxy," enabling identification of animal taxa that may have been important in local economies, environments, and cuisines.

    “In contrast to other biomolecular approaches to study past dairying, ancient protein analysis is able to identify the taxa consumed, acting as a “zooarchaeology by proxy,” enabling the identification of animal taxa that may have been important in local economies, environments, and cuisines.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    Early studies revealed that proteins undergo diagenesis into shorter, fragmented peptides, generating challenges for downstream analysis.

    “Early studies provided important insight into the survival and degradation of ancient biomolecules, revealing that proteins undergo diagenesis into shorter, fragmented peptides—generating challenges for downstream analysis.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.

    Premisenone given

    In aDNA, detecting markers of DNA degradation is integral for discriminating modern contamination from authentically old endogenous aDNA.

    “In the field of aDNA, detecting markers of DNA degradation is integral for discriminating modern contamination from authentically old endogenous aDNA.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisereasoning

    Top-down proteomics involves protein identification while the protein is still in its unbroken native state, and its data can inform on protein fragmentation and posttranslational modifications.

    “In contrast, top-down–based proteomics involves protein identification while the protein is still in its unbroken (native) state. Some advantages of such a strategy are that the data produced can inform on protein fragmentation and posttranslational modifications (PTMs)”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisereasoning

    MS involves ionization of molecules whose mass and charge are precisely detected, and in contrast to immunoassays, it is possible to study ancient proteomes rather than just individual target proteins.

    “MS involves the ionization of molecules, whose mass and charge are precisely detected. In contrast to techniques based on immunoassays, this means that it is possible to study ancient proteomes (paleoproteomics) rather than just individual target proteins of interest.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.

    Premisereasoning

    Enamel is the densest mineral in the human body, a trait that enables it to preserve well in archeological and even paleontological contexts.

    “While not as protein-rich as other skeletal tissues, enamel is the densest mineral in the human body, a trait that enables it to preserve well in archeological and even paleontological contexts.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisenone given

    LC-MS/MS approaches have been applied to a diversity of substrates and archeological inquiries, including human and animal skeletal tissues, artifacts and artifact residues, and well-preserved organic remains.

    “Like peptide mass fingerprinting, LC-MS/MS approaches have been applied to a diversity of substrates and archeological inquiries, including human and animal skeletal tissues, artifacts and artifact residues, and well-preserved organic remains”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisereasoning

    The degree of taxonomic specificity of ZooMS is variable and depends on evolutionary distance between taxa; it is typically possible to distinguish family or genera-level taxa, but differentiating between species can be challenging due to insufficient sequence variability.

    “The degree of taxonomic specificity is variable and depends on the evolutionary distance between taxa. It is typically possible to distinguish between family or even genera-level taxa, but differentiating between species can be challenging due to insufficient sequence variability between protein sequences of different taxa.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationreasoning

    Research has tended to move away from studies of protein preservation on stone tools, and many of these studies were performed before the invention and application of MS technologies.

    “As such, research has tended to move away from studies of protein preservation on stone tools; moreover, many of these studies were performed before the invention and application of MS technologies.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisecitation

    Modifications to amino acid side chains have been linked to age-induced degradation, which may be a useful indicator of protein degradation or authentically ancient proteins, although other factors such as heat may also induce modifications.

    “While PTMs can be the result of biological processes integral to protein function, modifications to amino acid side chains have also been linked to age-induced degradation, which may be a useful indicator of protein degradation or even authentically ancient proteins, although other factors, such as heat, may also induce modifications (76).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [76] Schroeter E. R., Cleland T. P., Glutamine deamidation: An indicator of antiquity, or preservational quality? Rapid Commun. Mass Spectrom. 30, 251– 255 (2016). 26689157 source

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisenone given

    Typically, LC-MS/MS approaches in paleoproteomics are bottom-up protein identifications, where proteins are fragmented into peptides during extraction and identified using LC-MS/MS.

    “Typically, LC-MS/MS approaches in paleoproteomics are “bottom-up” protein identifications. In this approach, proteins are fragmented into peptides during the extraction process, and these peptides are identified using LC-MS/MS”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Interpretationnone given

    A diversity of methodologies has been developed and applied to archeological materials, including a focus on developing strategies of ancient protein authentication.

    “A diversity of methodologies, described above, has been developed and applied to archeological materials, including a focus on developing strategies of ancient protein authentication.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Interpretationown data

    Quantitative proteomic approaches can gain rich and more refined insights into identifying disease processes, although there is still much to explore with understanding differential degradation rates and whether protein abundance in archeological remains accurately reflects biological processes during life.

    “This study demonstrates that rich and more refined insights can be gained into identifying disease processes using quantitative proteomic approaches, although there is still much to explore with understanding differential degradation rates of different proteins and whether protein abundance in archeological remains is an accurate reflection of biological processes occurring during life.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisereasoning

    Ancient proteins have been studied for their patterns of degradation and how these patterns can be used as markers for endogenous, ancient proteins as opposed to potential modern contaminants.

    “Similarly, ancient proteins have been studied for their patterns of degradation and how these patterns can be used as markers for endogenous, ancient proteins as opposed to potential modern contaminants.”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisecitation

    Deamidation of glutamine and asparagine is the most well studied modification, with glutamine deamidation more commonly applied as asparagine is subject to more influence from a protein's tertiary structure.

    “The most well studied of these modifications is deamidation (the removal of an amide group) of glutamine and asparagine (a process that transforms these amino acids into glutamic acid and aspartic acid, respectively), with glutamine deamidation more commonly applied as asparagine is subject to more influence from a protein’s tertiary structure (77).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [77] Kossiakoff A. A., Tertiary structure is a principal determinant to protein deamidation. Science 240, 191– 194 (1988). 3353715 source

  • It may state two separate claims as one.

    Premisecitation

    Some immunoassay approaches have been substantially criticized for lack of reliability in archeological contexts, with main criticisms including false positives and negatives due to protein degradation, problems with kits or assays, lack of blind testing and replication, and cross-reactions within and beyond the family level.

    “However, some of these approaches have been substantially criticized for their lack of reliability in archeological contexts. The main criticisms include the potential of false positives and negatives due to protein degradation, problems with the performance of kits or assays developed for the medical or food sciences, lack of blind testing and replication, and cross-reactions both within and bey”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisecitation

    ZooMS has been extensively applied to identifying and expanding faunal assemblages pertaining to ancient animal husbandry practices, particularly in identification of taxa that are morphologically challenging to discriminate, such as sheep and goat remains, and through analysis of fragmented, unidentifiable remains.

    “ZooMS has been extensively applied to identifying and expanding faunal assemblages pertaining to ancient animal husbandry practices, in particular in the identification of taxa that can be morphologically challenging to discriminate, such as sheep and goat remains (87, 88), as well as the expansion of zooarcheological datasets through the analysis of fragmented, unidentifiable remains.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [87] Zeder M. A., Pilaar S. E., Assessing the reliability of criteria used to identify mandibles and mandibular teeth in sheep, Ovis, and goats, Capra. J. Archaeol. Sci. 37, 225– 242 (2010).

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites [88] Zeder M. A., Lapham H. A., Assessing the reliability of criteria used to identify postcranial bones in sheep, Ovis, and goats, Capra. J. Archaeol. Sci. 37, 2887– 2905 (2010).

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisereasoning

    LC-MS/MS-based approaches result in identification of peptide or protein sequences through two or more fragmentation steps.

    “liquid chromatography–tandem mass spectrometry (LC-MS/MS)–based approaches result in the identification of peptide or protein sequences. This identification is achieved through two or more fragmentation steps”
    Quote in the paperNot a substantial claim

  • It may state two separate claims as one.

    Premisecitation

    Deamidation rates are influenced by the presence of adjacent amino acids, through steric hindrance and presence of charged amino acids, with some amino acids adjacent to glutamine causing slower deamidation rates.

    “Deamidation rates are also influenced by the presence of adjacent amino acids, through steric hindrance and the presence of charged amino acids, with some amino acids adjacent to glutamine causing slower deamidation rates.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim. The authors may not put it forward as true. The paper’s conclusions may not depend on it.

    Premisecitation

    The more specific taxonomic resolve of aDNA analysis can be used in tandem with the functional information gained from ancient proteins.

    “the more specific taxonomic resolve of aDNA analysis can be used in tandem with the functional information gained from ancient proteins”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    FTIR has been proposed as an in-field screening ahead of downstream ZooMS analysis through the detection of amide bonds that may be the result of the presence of amino acids.

    “Recently, FTIR has been proposed as an in-field screening ahead of downstream ZooMS analysis through the detection of amide bonds that may be the result of the presence of amino acids”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [173] Pothier Bouchard G., Mentzer S. M., Riel-Salvatore J., Hodgkins J., Miller C. E., Negrino F., Wogelius R., Buckley M., Portable FTIR for on-site screening of archaeological bone intended for ZooMS collagen fingerprint analysis. J. Archaeol. Sci. Rep. 26, 101862 (2019). source
    • Rests on an assumption: Ancient biomolecules undergo degradation over time, including fragmentation into smaller constituents and chemical alteration.

  • It may state two separate claims as one.

    Premisecitation

    Nielsen-Marsh et al. first applied the amelogenin sex identification concept and also applied the technique to identifying the sex of Neanderthal remains.

    “this concept was first applied by Nielsen-Marsh et al. (151), who also applied the technique to identifying the sex of Neanderthal remains”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [151] Nielsen-Marsh C. M., Stegemann C., Hoffmann R., Smith T., Feeney R., Toussaint M., Harvati K., Panagopoulou E., Hublin J.-J., Richards M. P., Extraction and sequencing of human and Neanderthal mature enamel proteins using MALDI-TOF/TOF MS. J. Archaeol. Sci. 36, 1758– 1763 (2009). source
    • Rests on an assumption: Estimating age and sex are key facets of osteological identification.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it.

    Premisecitation

    Applied polymer discs have been explored as a potential route to identifying proteinaceous components with minimal damage to artworks, manuscripts, and other cultural heritage objects.

    “To artworks, manuscripts, and other cultural heritage objects, applied polymer discs have also been explored as a potential route to identifying proteinaceous components with minimal damage”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [168] Righetti P. G., Zilberstein G., D’Amato A., What Sherlock sorely missed: The EVA technology for cultural heritage exploration. Expert Rev. Proteomics 16, 533– 542 (2019). 31144542 source
    • Rests on an assumption: Protein analysis is often destructive.

  • Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.

    Premisenone given

    Several strategies have been developed to mitigate artifact damage, including minimally invasive sampling strategies and the use of buffers that enable sample reuse.

    “several strategies have been developed to mitigate artifact damage, including minimally invasive sampling strategies and the use of buffers that enable sample reuse”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Protein analysis is often destructive.

  • It may state two separate claims as one.

    Premisereasoning

    Protein sequences of amelogenin differ in the X and Y variants, meaning that it is possible to use this protein as a marker of biological sex.

    “Protein sequences of amelogenin differ in the X and Y variants, meaning that it is possible to use this protein as a marker of biological sex.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Estimating age and sex are key facets of osteological identification.

  • It may state two separate claims as one.

    Interpretationreasoning

    Insights from paleoproteomics on personal objects help to understand manufacturing practices, resource use and object movement, and cultural exchange.

    “Such insights help to understand manufacturing practices, resource use and object movement, and cultural exchange.”
    Quote in the paperSubstantial claim

  • It may state two separate claims as one.

    Premisenone given

    Early approaches focused on the detection of protein content to assess ancient protein survival; now, the use of MS is enabling the detection of sequence information in samples of greater complexity.

    “Early approaches focused on the detection of protein content to assess ancient protein survival; now, the use of MS is enabling the detection of sequence information in samples of greater complexity.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Ancient biomolecules undergo degradation over time, including fragmentation into smaller constituents and chemical alteration.

  • It may state two separate claims as one.

    Premisecitation

    In the last several years, ancient protein analysis has gained particular attention, especially with regard to the technique's reach into deeper time and the generation of new conclusions unattainable using other biomolecular approaches.

    “In the last several years, ancient protein analysis has gained particular attention (175–177), especially with regard to the technique’s reach into deeper time and the generation of new conclusions unattainable using other biomolecular approaches.”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [175] Warren M., Move over, DNA: Ancient proteins are starting to reveal humanity’s history. Nature 570, 433– 436 (2019). 31243383 source
    • cites [176] C. H. Arnaud, Ancient proteins tell tales of our ancestors, Chemical & Engineering News (2019); https://cen.acs.org/analytical-chemistry/art-&-artifacts/Ancient-proteins-tell-tales-ancestors/97/i20.
    • cites [177] The science stories likely to make headlines in 2020, Science | AAAS (2020); https://www.sciencemag.org/news/2020/01/science-stories-likely-make-headlines-2020.
56 of 56

  • The paper relies on this without support.

    Protein analysis is often destructive.

    “The analysis of proteins, as is typical of most biomolecular analysis, is often destructive.”

  • The paper relies on this without support.

    Ancient biomolecules undergo degradation over time, including fragmentation into smaller constituents and chemical alteration.

    “Ancient biomolecules undergo degradation over time, including fragmentation into smaller constituents and chemical alteration.”

  • The paper relies on this without support.

    Estimating age and sex are key facets of osteological identification.

    “Estimating age and sex are key facets of osteological identification.”

  • The paper relies on this without support.

    There is currently no single identified marker of ancient protein degradation.

    “Unlike, for example, C to T transitions occurring at the ends of DNA reads, there is currently no single identified marker of ancient protein degradation.”
4 of 4

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 5

  1. P. H. Abelson, Amino acids in fossils. Science 119, 576 (1954).
  2. P. E. Hare T. C. Hoering K. King Biogeochemistry of Amino Acids (Wiley 1980).
  3. M. Mackie A. Radini C. Speller in Shallow Pasts Endless Horizons: Sustainability & Archaeology Proceedings of the 48th Annual Chacmool Conference J. Favreau R. Patalano Eds. (The Chacmool Archaeological Association of the University of Calgary 2017) pp. 74–81.
  4. C. H. Arnaud Ancient proteins tell tales of our ancestors Chemical & Engineering News (2019); https://cen.acs.org/analytical-chemistry/art-&-artifacts/Ancient-proteins-tell-tales-ancestors/97/i20.
  5. The science stories likely to make headlines in 2020 Science | AAAS (2020); https://www.sciencemag.org/news/2020/01/science-stories-likely-make-headlines-2020.

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Related

Metadata

Authors
Hendy, J.
Affiliations
Max Planck Institute of Geoanthropology (DE)
Corresponding author
Hendy, Jessica
ORCID
Hendy, Jessica
Venue
Science Advances
Publisher
American Association for the Advancement of Science (AAAS)
Published
2021-01-15
Volume
7
Issue
3
ISSN
2375-2548 (ISSN-L)
DOI
10.1126/sciadv.abb9314
PMC
PMC7810370
OpenAlex
W3119601144
Cited by
161
References
170
Citations by year
2026: 38 · 2025: 37 · 2024: 30 · 2023: 28 · 2022: 18 · 2021: 9
FWCI
2.18
Type
journal article
Language
en
Open access
Licence
Locations
  • Science Advances (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Funders
Leverhulme Trust (Philip Leverhulme Prize)
Topics
  • Social Sciences › Archeology › Archaeology and ancient environmental studies
  • Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Paleopathology and ancient diseases
  • Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Cultural Heritage Materials Analysis
Keywords
ancient proteins, archaeology, paleontology, subsistence strategies, health and disease, past environments, minimally invasive technique, non-destructive analysis, biomolecular archaeology

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