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3 - Proteomics

from Part II - Biomolecular Archaeology

Published online by Cambridge University Press:  19 December 2019

By
Jessica Hendy ,
Nienke van Doorn  and
Matthew Collins
Edited by
Michael P. Richards  and
Kate Britton
Michael P. Richards
Affiliation:
Simon Fraser University, British Columbia
Kate Britton
Affiliation:
University of Aberdeen
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Summary

All the inheritable material possessed by an organism, the genome, is stored as DNA, the study of which has made an enormous impact upon archaeological science. The proteome is the suite of proteins produced by the genome at any one time. The field of proteomics is the study of this proteome, and uses mass spectrometry to identify proteins by their amino acid sequence.

Type
Chapter
Information
Archaeological Science
An Introduction
 , pp. 35 - 69
Publisher: Cambridge University Press
Print publication year: 2020

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References

Abelson, P. H., 1954. Amino acids in fossils. Science 119(3096):576.Google Scholar
Altmeyer, W. et al. 2002. Method for qualitative and/or quantitative determination of gender, species, race and/or geographical origin of biological materials. Patent. Available at: http://google.com/patents/CA2452851A1?cl=zh (accessed June 29, 2019).Google Scholar
Asara, J. M. et al. 2007. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316(5822):280–285.Google Scholar
Bada, J. L. 1991. Amino acid cosmogeochemistry. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 333(1268):349–358.Google Scholar
Bada, J. L. and Miller, S. L. 1968. Ammonium ion concentration in the primitive ocean. Science 159(3813):423–425.Google Scholar
Barker, A. 2011. Archaeological protein residues: New data for conservation science. Ethnobiology Letters 1:58–65.Google Scholar
Barker, A., Venables, B., Stevens, S. M. Jr., Seeley, K. W., Wang, P., and Wolverton, S. 2012. An optimized approach for protein residue extraction and identification from ceramics after cooking. Journal of Archaeological Method and Theory 19(3):407–439.CrossRefGoogle Scholar
Becker, M. A., Willman, P., and Tuross, N. C. 1995. The U.S. First Ladies’ gowns: A biochemical study of silk preservation. Journal of the American Institute for Conservation 34(2):141–152.CrossRefGoogle Scholar
Bern, M., Phinney, B. S., and Goldberg, D. 2009. Reanalysis of Tyrannosaurus rex mass spectra. Journal of Proteome Research 8(9):4328–4332.Google Scholar
Brandt, L. Ø., Schmidt, A. L., Mannering, U., Sarret, M., Kelstrup, C. D., Olsen, J. V., and Cappellini, E. 2014. Species identification of archaeological skin objects from Danish bogs: Comparison between mass spectrometry-based peptide sequencing and microscopy-based methods. PloS One 9(9):e106875.Google Scholar
Buckley, M. 2013. A molecular phylogeny of Plesiorycteropus reassigns the extinct mammalian order “Bibymalagasia.” PloS One 8(3):e59614.Google Scholar
Buckley, M. 2015. Ancient collagen reveals evolutionary history of the endemic South American “ungulates.” Proceedings of the Royal Society B-Biological Sciences 282(1806):20142671.Google Scholar
Buckley, M., Anderung, C., Penkman, K., Raney, B. J., Gotherstrom, A., Thomas-Oates, J., and Collins, M. J. 2008b. Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites. Journal of Archaeological Science 35:1756–1764.CrossRefGoogle Scholar
Buckley, M., Collins, M., Thomas-Oates, J., and Wilson, J. C. 2009. Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry 23:3843–3854.CrossRefGoogle ScholarPubMed
Buckley, M., Fraser, S., Herman, J., Melton, N. D., Mulville, J., and Palsdottir, A. H. 2014. Species identification of archaeological marine mammals using collagen fingerprinting. Journal of Archaeological Science 41:631–641.Google Scholar
Buckley, M. and Kansa, S. W. 2011. Collagen fingerprinting of archaeological bone and teeth remains from Domuztepe, South Eastern Turkey. Archaeological and Anthropological Sciences 3(3):271–280.Google Scholar
Kansa, S. W., Howard, S., Campbell, S., Thomas-Oates, J., and Collins, M. 2010. Distinguishing between archaeological sheep and goat bones using a single collagen peptide. Journal of Archaeological Science 37:13–20.Google Scholar
Buckley, M., Larkin, N., and Collins, M. 2011. Mammoth and mastodon collagen sequences: Survival and utility. Geochimica et Cosmochimica Acta 75(7):2007–2016.Google Scholar
Buckley, M., Melton, N. D., and Montgomery, J. 2013. Proteomics analysis of ancient food vessel stitching reveals >4000-year-old milk protein. Rapid Communications in Mass Spectrometry 27(4):531–538.Google Scholar
Buckley, M. and Wadsworth, C. 2014. Proteome degradation in ancient bone: Diagenesis and phylogenetic potential. Palaeogeography, Palaeoclimatology, Palaeoecology 416:69–79.CrossRefGoogle Scholar
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., and Collins, M. J. 2008a. Comment on “protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.” Science 319:33.Google Scholar
Buckley, M., Warwood, S., Van Dongen, B., Kitchener, A. C., and Manning, P. L. 2017. A fossil protein chimera: Difficulties in discriminating dinosaur peptide sequences from modern cross-contamination. Proceedings of the Royal Society B-Biological Sciences 284:20170544.Google Scholar
Cappellini, E., Gilbert, M. T. P., Geuna, F., Fiorentino, G., Hall, A., Thomas-Oates, J., Ashton, P. D., Ashford, D. A., Arthur, P., Campos, P. F., Kool, J., Willerslev, E., and Collins, M. J. 2010. A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97:205–217.Google Scholar
Cappellini, E., Jensen, L. J., Szklarczyk, D., Ginolhac, A., Da Fonseca, R. a. R., Stafford, T. W., Holen, S. R., Collins, M. J., Orlando, L., Willerslev, E., Gilbert, M. T. P., and Olsen, J. V. 2012. Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins. Journal of Proteome Research 11:917–926.CrossRefGoogle ScholarPubMed
Cattaneo, C., Gelsthorpe, K., Phillips, P., and Sokol, R. J. 1992. Detection of human proteins in buried blood using Elisa and monoclonal-antibodies – Towards the reliable species indentification of blood stains on buried material. Forensic Science International 57:139–146.Google Scholar
Chamberlain, P., Drewello, R., Korn, L., Bauer, W., Gough, T., Al-Fouzan, A., Collins, M., Van Doorn, N., Craig, O., and Heron, C. 2011. Construction of the Khoja Zaynuddin mosque: Use of animal glue modified with urine. Archaeometry 53:830–841.Google Scholar
Chambery, A., Di Maro, A., Sanges, C., Severino, V., Tarantino, M., Lamberti, A., Parente, A., and Arcari, P. 2009. Improved procedure for protein binder analysis in mural painting by LC-ESI/Q-q-TOF mass spectrometry: Detection of different milk species by casein proteotypic peptides. Analytical and Bioanalytical Chemistry 395:2281–2291.Google Scholar
Cleland, T. P., Schroeter, E. R., and Schweitzer, M. H. 2015. Biologically and diagenetically derived peptide modifications in moa collagens. Proceedings of the Royal Society B-Biological Sciences 282:20150015.CrossRefGoogle ScholarPubMed
Collins, M. J., Nielsen-Marsh, C. M., Hiller, J., Smith, C. I., Roberts, J. P., Prigodich, R. V., Weiss, T. J., Csapo, J., Millard, A. R., and Turner-Walker, G. 2002. The survival of organic matter in bone: A review. Archaeometry 44:383–394.Google Scholar
Collins, M. J., Riley, M. S., Child, A. M., and Turnerwalker, G. 1995. A basic mathematical simulation of the chemical degradation of ancient collagen. Journal of Archaeological Science 22:175–183.Google Scholar
Corthals, A., Koller, A., Martin, D. W., Rieger, R., Chen, E. I., Bernaski, M., Recagno, G., and Davalos, L. M. 2012. Detecting the immune system response of a 500 year-old Inca mummy. PLoS One 7(7):e41244.Google Scholar
Craig, O. E. and Collins, M. J. 2000. An improved method for the immunological detection of mineral bound protein using hydrofluoric acid and direct capture. Journal of Immunological Methods 236(1–2):89–97.Google Scholar
Craig, O., Mulville, J., Pearson, M. P., Sokol, R., Gelsthorpe, K., Stacey, R., and Collins, M. 2000. Detecting milk proteins in ancient pots. Nature 408:312.CrossRefGoogle ScholarPubMed
Dallongeville, S., Garnier, N., Casasola, D. B., Bonifay, M., Rolando, C., and Tokarski, C. 2011. Dealing with the identification of protein species in ancient amphorae. Analytical and Bioanalytical Chemistry 399:3053–3063.Google Scholar
Daniel, R. M., Dines, M., and Petach, H. H. 1996. The denaturation and degradation of stable enzymes at high temperatures. Biochemical Journal 317(Pt 1):1–11.Google Scholar
Demarchi, B. and Collins, M., 2014. Amino acid racemisation dating. In: `Rink, W. J and `Thompson, J. (eds.) Encyclopedia of Scientific Dating Methods, pp. 1–22. Springer Netherlands.Google Scholar
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-Christensens, 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., Dominguez-Rodrigo, M., Macpheel, R. D. E., Kwekason, A., Ecker, M., Horwitz, L. K., Chazan, M., Kroger, R., Thomas-Oates, J., Harding, J. H., Cappellini, E., Penkman, K., and Collins, M. J. 2016. Protein sequences bound to mineral surfaces persist into deep time. Elife 5:e17092.CrossRefGoogle ScholarPubMed
Demarchi, B., O’Connor, S., Ponzoni, A. D., Ponzoni, R. D. R., Sheridan, A., Penkman, K., Hancock, Y., and Wilson, J. 2014. An integrated approach to the taxonomic identification of prehistoric shell ornaments. PLoS One 9(6):e99839.CrossRefGoogle Scholar
Derbyshire, E., Harris, N., Boulter, D., and Jope, E. M. 1977. The extraction, composition and intra-cellular distribution of protein in early maize grains from an archaeological site in NE Arizona. New Phytologist 78:499–504.Google Scholar
Doberenz, A. R. and Wyckoff, R. W. 1967. Fine structure in fossil collagen. Proceedings of the National Academy of Sciences of the United States of America 57(3):539–541.Google Scholar
Domon, B. and Aebersold, R. 2006. Mass spectrometry and protein analysis. Science 312(5771):212–217.Google Scholar
Downs, E. F. and Lowenstein, J. M. 1995. Identification of archaeological blood proteins: A cautionary note. Journal of Archaeological Science 22(1):11–16.Google Scholar
El-Aneed, A., Cohen, A., and Banoub, J. 2009. Mass spectrometry, review of the basics: Electrospray, MALDI, and commonly used mass analyzers. Applied Spectroscopy Reviews 44(3):210–230.CrossRefGoogle Scholar
Eöry, L., Gilbert, M. T. P., Li, C., Li, B., Archibald, A., Aken, B. L., Zhang, G. J., Jarvis, E., Flicek, P., and Burt, D. W. 2015. Avianbase: A community resource for bird genomics. Genome Biology 16:21.Google Scholar
Evershed, R. P. and Tuross, N. 1996. Proteinaceous material from potsherds and associated soils. Journal of Archaeological Science 23(3):429–436.CrossRefGoogle Scholar
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., Vnoucek, J., Garrison, M., Mcgrory, S., Bradley, D. G., and Collins, M. J. 2015. Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proceedings of the National Academy of Sciences of the United States of America 112:15066–15071.Google Scholar
Heaton, K., Solazzo, C., Collins, M. J., Thomas-Oates, J., and Bergstrom, E. T. 2009. Towards the application of desorption electrospray ionisation mass spectrometry (DESI-MS) to the analysis of ancient proteins from artefacts. Journal of Archaeological Science 36(10):2145–2154.CrossRefGoogle Scholar
Henzel, W. J., Watanabe, C., and Stults, J. T. 2003. Protein identification: The origins of peptide mass fingerprinting. Journal of the American Society for Mass Spectrometry 14(9):931–942.Google Scholar
Hill, R. C., Wither, M. J., Nemkov, T., Barrett, A., D’alessandro, A., Dzieciatkowska, M., and Hansen, K. C. 2015. Preserved proteins from extinct bison latifrons identified by tandem mass spectrometry: Hydroxylysine glycosides are a common feature of ancient collagen. Molecular and Cellular Proteomics 14 :1946–1958.CrossRefGoogle ScholarPubMed
Hillenkamp, F., Karas, M., Beavis, R. C., and Chait, B. T. 1991. Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Analytical chemistry 63(24):1193A–1203A.Google Scholar
Hollemeyer, K., Altmeyer, W., and Heinzle, E. 2002. Identification and quantification of feathers, down, and hair of avian and mammalian origin using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Analytical Chemistry 74(23):5960–5968.Google Scholar
Hollemeyer, K., Altmeyer, W., Heinzle, E., and Pitra, C. 2008. Species identification of Oetzi’s clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests. Rapid Communications in Mass Spectrometry 22(18):2751–2767.Google Scholar
Hollemeyer, K., Altmeyer, W., Heinzle, E., and Pitra, C. 2012. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with multidimensional scaling, binary hierarchical cluster tree and selected diagnostic masses improves species identification of Neolithic keratin sequences from furs of the Tyrolean Iceman Oetzi. Rapid Communications in Mass Spectrometry 26(16):1735–1745.Google Scholar
Hong, C., Jiang, H. G., Lu, E. G., Wu, Y. F., Guo, L. H., Xie, Y. M., Wang, C. S., and Yang, Y. M. 2012. Identification of milk component in ancient food residue by proteomics. PLoS One 7(5):e37053.CrossRefGoogle ScholarPubMed
Huq, N. L., Tseng, A., and Chapman, G. E. 1990. Partial amino acid sequence of osteocalcin from an extinct species of ratite bird. Biochemistry International 21(3):491–496.Google Scholar
Hyland, D. C., Tersak, J. M., Adovasio, J. M., and Siegel, M. I. 1990. Identification of the species of origin of residual blood on lithic material. American Antiquity 55(1):104–112.Google Scholar
Kirby, D. P., Buckley, M., Promise, E., Trauger, S. A., and Holdcraft, T. R. 2013. Identification of collagen-based materials in cultural heritage. The Analyst 138(17):4849–4858.CrossRefGoogle ScholarPubMed
Kooyman, B., Newman, M. E., and Ceri, H. 1992. Verifying the reliability of blood residue analysis on archaeological tools. Journal of Archaeological Science 19(3):265–269.CrossRefGoogle Scholar
Krizkova, M. C., Kuckova, S. H., Santrucek, J., and Hynek, R. 2014. Peptide mass mapping as an effective tool for historical mortar analysis. Construction and Building Materials 50:219–225.Google Scholar
Kuckova, S., Crhova, M., Vankova, L., Hnizda, A., Hynek, R., and Kodicek, M. 2009b. Towards proteomic analysis of milk proteins in historical building materials. International Journal of Mass Spectrometry 284:42–46.Google Scholar
Kuckova, S., Hynek, R., and Kodicek, M. 2007. Identification of proteinaceous binders used in artworks by MALDI-TOF mass spectrometry. Analytical and Bioanalytical Chemistry 388(1):201–206.Google Scholar
Kuckova, S., Hynek, R., and Kodicek, M., 2009a. Application of peptide mass mapping on proteins in historical mortars. Journal of Cultural Heritage 10(2):244–247.Google Scholar
Kuckova, S., Nemec, I., Hynek, R., Hradilova, J., and Grygar, T. 2005. Analysis of organic colouring and binding components in colour layer of art works. Analytical and Bioanalytical Chemistry 382(2):275–282.Google Scholar
Leach, J. D. and Mauldin, R. P. 1995. Additional comments on blood residue analysis in archaeology. Antiquity 69(266):1020–1022.Google Scholar
Lees, S. 1989. Some characteristics of mineralised collagen. In: Calcified Tissue, pp. 153–173. Topics in Molecular and Structural Biology. London: Macmillan.CrossRefGoogle Scholar
Leo, G., Bonaduce, I., Andreotti, A., Marino, G., Pucci, P., Colombini, M. P., and Birolo, L. 2011. Deamidation at asparagine and glutamine as a major modification upon deterioration/aging of proteinaceous binders in mural paintings. Analytical Chemistry 83(6):2056–2064.CrossRefGoogle Scholar
Lowenstein, J. M. 1981. Immunological reactions from fossil material. Philosophical Transactions of the Royal Society of London. Series B, Biological sciences 292(1057):143–149.Google Scholar
Loy, T. H. 1983. Prehistoric blood residues: Detection on tool surfaces and identification of species of origin. Science 220(4603):1269–1271.Google Scholar
Loy, T. H. 1994. Response. Science 266(5183):299–300.Google Scholar
Loy, T. H. and Hardy, B. L. 1992. Blood residue analysis of 90,000-year-old stone tools from Tabun Cave, Israel. Antiquity 66(250):24–35.CrossRefGoogle Scholar
Maixner, F., Overath, T., Linke, D., Janko, M., Guerriero, G., Van Den Berg, B. H. J., Stade, B., Leidinger, P., Backes, C., Jaremek, M., Kneissl, B., Meder, B., Franke, A., Egarter-Vigl, E., Meese, E., Schwarz, A., Tholey, A., Zink, A., and Keller, A. 2013. Paleoproteomic study of the Iceman’s brain tissue. Cellular and Molecular Life Sciences 70(19):3709–3722.CrossRefGoogle ScholarPubMed
Malainey, M. E. 2011. Blood and protein residue analysis. In: `Malainey, M. E. (ed.) A Consumer’s Guide to Archaeological Science. Manuals in Archaeological Method, Theory and Technique, pp. 219–236. Springer New York.Google Scholar
Mann, K. and Mann, M. 2013. The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell. Proteome Science 11(1):40.Google Scholar
Frei, K. M., Mannering, U., Kristiansen, K., Allentoft, M. E., Wilson, A. S., Skals, I., Tridico, S., Nosch, M. L., Willerslev, E., Clarke, L., and Frei, R. 2015. Tracing the dynamic life story of a Bronze Age female. Scientific Reports 5:10431.Google Scholar
Mazel, V., Richardin, P., Debois, D., Touboul, D., Cotte, M., Brunelle, A., Walter, P., and Laprevote, O. 2007. Identification of ritual blood in African artifacts using TOF-SIMS and synchrotron radiation microspectroscopies. Analytical Chemistry 79(24):9253–9260.Google Scholar
Moini, M., Klauenberg, K., and Ballard, M. 2011. Dating silk by capillary electrophoresis mass spectrometry. Analytical Chemistry 83(19):7577–7581.CrossRefGoogle ScholarPubMed
Nielsen-Marsh, C. M., Ostrom, P. H., Gandhi, H., Shapiro, B., Cooper, A., Hauschka, P. V., and Collins, M. J. 2002. Sequence preservation of osteocalcin protein and mitochondrial DNA in bison bones older than 55 ka. Geology 30(12):1099–1102.Google Scholar
Nielsen-Marsh, C. M., Richards, M. P., Hauschka, P. V., Thomas-Oates, J. E., Trinkaus, E., Pettitt, P. B., Karavanic, I., Poinar, H., and Collins, M. J. 2005. Osteocalcin protein sequences of Neanderthals and modern primates. Proceedings of the National Academy of Sciences of the United States of America 102(12):4409–4413.Google Scholar
O’Connor, S., Solazzo, C., and Collins, M. 2015. Advances in identifying archaeological traces of horn and other keratinous hard tissues. Studies in Conservation 60(6):393–417.CrossRefGoogle Scholar
Orlando, L., Ginolhac, A., Zhang, G. J., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P. L. F., Fumagalli, M., Vilstrup, J. T., Raghavan, M., Korneliussen, T., Malaspinas, A. S., Vogt, J., Szklarczyk, D., Kelstrup, C. D., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X. L., Min, J. M., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Roed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. a. S., Ryder, O., Andersson, L., Mundy, J., Krogh, A., Gilbert, M. T. P., Kjaer, K., Sicheritz-Ponten, T., Jensen, L. J., Olsen, J. V., Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J., and Willerslev, E. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499(7456):74–78.Google Scholar
Ostrom, P. H., Schall, M., Gandhi, H., Shen, T. L., Hauschka, P. V., Strahler, J. R., and Gage, D. A. 2000. New strategies for characterizing ancient proteins using matrix-assisted laser desorption ionization mass spectrometry. Geochimica et Cosmochimica Acta 64(6):1043–1050.Google Scholar
Palmqvist, P., Grokke, D. R., Arribas, A., and Farina, R. A. 2003. Paleoecological reconstruction of a lower Pleistocene large mammal community using biogeochemical (δ13C, δ15N, δ18O, Sr: Zn) and ecomorphological approaches. Paleobiology 29(2):205–229.Google Scholar
Penkman, K. E. H., Kaufman, D. S., Maddy, D., and Collins, M. J. 2008. Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells. Quaternary Geochronology 3(1–2)2–25.Google Scholar
Penkman, K. E. H., Preece, R. C., Bridgland, D. R., Keen, D. H., Meijer, T., Parfitt, S. A., White, T. S., and Collins, M. J. 2013. An aminostratigraphy for the British Quaternary based on Bithynia opercula. Quaternary Science Reviews 61(C):111–134.Google Scholar
Peris-Vicente, J., Simo-Alfonso, E., Adelantado, J. V. G., and Carbo, M. T. D. 2005. Direct infusion mass spectrometry as a fingerprint of protein-binding media used in works of art. Rapid Communications in Mass Spectrometry 19(23):3463–3467.Google Scholar
Pevzner, P. A., Kim, S., and Ng, J. 2008. Comment on “Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.” Science 321(5892):1040.Google Scholar
Potter, B. A., Reuther, J. D., Lowenstein, J. M., and Scheuenstuhl, G. 2010. Assessing the reliability of pRIA for identifying ancient proteins from archaeological contexts. Journal of Archaeological Science 37(5):910–918.Google Scholar
Rao, H. Y., Li, B., Yang, Y. M., Ma, Q. L., and Wang, C. S. 2015. Proteomic identification of organic additives in the mortars of ancient Chinese wooden buildings. Analytical Methods 7(1):143–149.Google Scholar
Rasmussen, M., Li, Y. R., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, M. T. P., Wang, Y., Raghavan, M., Campos, P. F., Kamp, H. M., Wilson, A. S., Gledhill, A., Tridico, S., Bunce, M., Lorenzen, E. D., Binladen, J., Guo, X. S., Zhao, J., Zhang, X. Q., Zhang, H., Li, Z., Chen, M. F., Orlando, L., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T. L., Gronnow, B., Meldgaard, M., Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F. G., Ramsey, C. B., Hansen, T. V. O., Nielsen, F. C., Crawford, M. H., Brunak, S., Sicheritz-Ponten, T., Villems, R., Nielsen, R., Krogh, A., Wang, J., and Willerslev, E. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282):757–762.Google Scholar
Rasmussen, K. L., Tenorio, A. L., Bonaduce, I., Colombini, M. P., Birolo, L., Galano, E., Amoresano, A., Doudna, G., Bond, A. D., Palleschi, V., Lorenzetti, G., Legnaioli, S., Van Der Plicht, J., and Gunneweg, J. 2012. The constituents of the ink from a Qumran inkwell: New prospects for provenancing the ink on the Dead Sea Scrolls. Journal of Archaeological Science 39(9):2956–2968.CrossRefGoogle Scholar
Remington, S. J. 1994. Identifying species of origin from prehistoric blood residues. Science 266(5183):298–300.Google Scholar
Richter, K. K., Wilson, J., Jones, A. K. G., Buckley, M., van Doorn, N., and Collins, M. J. 2011. Fish’n chips: ZooMS peptide mass fingerprinting in a 96 well plate format to identify fish bone fragments. Journal of Archaeological Science, 38(7):1502–1510.Google Scholar
Rybczynski, N., Gosse, J. C., Harington, C. R., Wogelius, R. A., Hidy, A. J., and Buckley, M. 2013. Mid-Pliocene warm-period deposits in the high Arctic yield insight into camel evolution. Nature Communications 4:1550.Google Scholar
Sawafuji, R., Cappellini, E., Nagaoka, T., Fotakis, A. K., Jersie-Christensen, R. R., Olsen, J. V., Hirata, K., and Ueda, S. 2017. Proteomic profiling of archaeological human bone. Royal Society Open Science 4(6):161004.Google Scholar
Schmidt-Schultz, T. H. and Schultz, M. 2007. Well preserved non-collagenous extracellular matrix proteins in ancient human bone and teeth. International Journal of Osteoarchaeology 17(1):91–99.Google Scholar
Schroeter, E. R. and Cleland, T. P. 2016. Glutamine deamidation: An indicator of antiquity, or preservational quality? Rapid Communications in Mass Spectrometry 30(2):251–255.Google Scholar
Schweitzer, M. H., Zheng, W. X., Organ, C. L., Avci, R., Suo, Z. Y., Freimark, L. M., Lebleu, V. S., Duncan, M. B., Heiden, M. G. V., Neveu, J. M., Lane, W. S., Cottrell, J. S., Horner, J. R., Cantley, L. C., Kalluri, R., and Asara, J. M. 2009. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324(5927):626–631.CrossRefGoogle ScholarPubMed
Shevchenko, A., Yang, Y. M., Knaust, A., Thomas, H., Jiang, H. E., Lu, E. G., Wang, C. S., and Shevchenko, A. 2014. Proteomics identifies the composition and manufacturing recipe of the 2500-year-old sourdough bread from Subeixi cemetery in China. Journal of Proteomics 105:363–371.CrossRefGoogle Scholar
Shewry, P. R., Kirkman, M. A., Burgess, S. R., Festenstein, G. N., and Miflin, B. J. 1982. A comparison of the protein and amino acid composition of old and recent barley grain. The New Phytologist 90(3):455–466.Google Scholar
Smith, P. R. and Wilson, M. T. 1992. Blood residues on ancient tool surfaces: A cautionary note. Journal of Archaeological Science 19(3):237–241.Google Scholar
Solazzo, C., Clerens, S., Plowman, J. E., Wilson, J., Peacock, E. E., and Dyer, J. M. 2015. Application of redox proteomics to the study of oxidative degradation products in archaeological wool. Journal of Cultural Heritage 16:896–903.Google Scholar
Solazzo, C., Dyer, J. M., Clerens, S., Plowman, J., Peacock, E. E., and Collins, M. J. 2013a. Proteomic evaluation of the biodegradation of wool fabrics in experimental burials. International Biodeterioration and Biodegradation 80:48–59.Google Scholar
Solazzo, C., Dyer, J. M., Deb-Choudhury, S., Clerens, S., and Wyeth, P. 2012. Proteomic profiling of the photo-oxidation of silk fibroin: Implications for historic tin-weighted silk. Photochemistry and Photobiology 88(5):1217–1226.Google Scholar
Solazzo, C., Fitzhugh, W. W., Rolando, C., and Tokarski, C. 2008. Identification of protein remains in archaeological potsherds by proteomics. Analytical Chemistry 80(12):4590–4597.Google Scholar
Solazzo, C., Heald, S., Ballard, M. W., Ashford, D. A., Depriest, P. T., Koestler, R. J., and Collins, M. J. 2011. Proteomics and Coast Salish blankets: A tale of shaggy dogs? Antiquity 85(330):1418–1432.Google Scholar
Solazzo, C., Wadsley, M., Dyer, J. M., Clerens, S., Collins, M. J., and Plowman, J. 2013b. Characterisation of novel α-keratin peptide markers for species identification in keratinous tissues using mass spectrometry. Rapid Communications in Mass Spectrometry 27(23):2685–2698.Google Scholar
Solazzo, C., Wadsley, M., Dyer, J. M., Clerens, S., Collins, M. J., and Plowman, J. 2014. Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles. Analytical Chemistry 86(1):567–575.Google Scholar
Steele, T. E. 2015. The contributions of animal bones from archaeological sites: The past and future of zooarchaeology. Journal of Archaeological Science 56:168–176.Google Scholar
Stewart, J. R. M., Allen, R. B., Jones, A. K. G., Kendall, T., Penkman, K. E. H., Demarchi, B., O’connor, T., and Collins, M. J. 2013. ZooMS: Making eggshell visible in the archaeological record. Journal of Archaeological Science 40(4):1797–1804.Google Scholar
Stewart, J. R. M., Allen, R. B., Jones, A. K. G., Kendall, T., Penkman, K. E. H., Demarchi, B., O’Connor, T., and Collins, M. J. 2014. Walking on eggshells: A study of egg use in Anglo-Scandinavian York based on eggshell identification using ZooMS. International Journal of Osteoarchaeology 24(3):247–255.Google Scholar
Sykes, N., 2014. Beastly Questions: Animal Answers to Archaeological Issues. London: Bloomsbury Academic.Google Scholar
Terwilliger, T. C. and Clarke, S. 1981. Methylation of membrane proteins in human erythrocytes. Identification and characterization of polypeptides methylated in lysed cells. The Journal of Biological Chemistry 256(6):3067–3076.Google Scholar
Tokarski, C., Martin, E., Rolando, C., and Cren-Olive, C. 2006. Identification of proteins in renaissance paintings by proteomics. Analytical Chemistry 78(5):1494–1502.Google Scholar
Towe, K. M. 1972. Collagen-like structures in Ordovician graptolite periderm. Nature 237:443–445.Google Scholar
Tran, T. N. N., Aboudharam, G., Gardeisen, A., Davoust, B., Bocquet-Appel, J. P., Flaudrops, C., Belghazi, M., Raoult, D., and Drancourt, M. 2011. Classification of ancient mammal individuals using dental pulp MALDI-TOF MS peptide profiling. PLoS One 6(2):e17319.Google Scholar
Tuross, N., Barnes, I., and Potts, R. 1996. Protein identification of blood residues on experimental stone tools. Journal of Archaeological Science 23(2):289–296.Google Scholar
Toniolo, L., D’amato, A., Saccenti, R., Gulotta, D., and Righetti, P. G. 2012. The Silk Road, Marco Polo, a Bible and its proteome: A detective story. Journal of Proteomics 75(11):3365–3373.Google Scholar
Vaiglova, P., Bogaard, A., Collins, M., Cavanagh, W., Mee, C., Renard, J., Lamb, A., Gardeisen, A., and Fraser, R. 2014. An integrated stable isotope study of plants and animals from Kouphovouno, southern Greece: A new look at Neolithic farming. Journal of Archaeological Science 42:201–215.Google Scholar
Vanden Berghe, I. 2012. Towards an early warning system for oxidative degradation of protein fibres in historical tapestries by means of calibrated amino acid analysis. Journal of Archaeological Science 39(5):1349–1359.Google Scholar
Van Der Sluis, L. G., Hollund, H. I., Buckley, M., De Louw, P. G. B., Rijsdijk, K. F., and Kars, H. 2014. Combining histology, stable isotope analysis and ZooMS collagen fingerprinting to investigate the taphonomic history and dietary behaviour of extinct giant tortoises from the Mare aux Songes deposit on Mauritius. Palaeogeography, Palaeoclimatology, Palaeoecology 416:80–91.Google Scholar
van Der Werf, I. D., Calvano, C. D., Palmisano, F., and Sabbatini, L. 2012. A simple protocol for Matrix Assisted Laser Desorption Ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis of lipids and proteins in single microsamples of paintings. Analytica Chimica Acta 718:1–10.Google Scholar
van Doorn, N. L. 2014. Zooarchaeology by Mass Spectrometry (ZooMS). In: Encyclopedia of Global Archaeology, pp. 7998–8000. New York: Springer.Google Scholar
van Doorn, N. L., Wilson, J., Hollund, H., Soressi, M., and Collins, M. J. 2012. Site-specific deamidation of glutamine: A new marker of bone collagen deterioration. Rapid Communications in Mass Spectrometry 26:2319–2327.Google Scholar
von Holstein, I. C. C., Ashby, S. P., van Doorn, N. L., Sachs, S. M., Buckley, M., Meiri, M., Barnes, I., Brundle, A., and Collins, M. J. 2014. Searching for Scandinavians in pre-Viking Scotland: Molecular fingerprinting of Early Medieval combs. Journal of Archaeological Science 41:1–6.Google Scholar
Wadsworth, C. and Buckley, M. 2014. Proteome degradation in fossils: Investigating the longevity of protein survival in ancient bone. Rapid Communications in Mass Spectrometry 28(6):605–615.Google Scholar
Wang, S.-Y., Cappellini, E., and Zhang, H.-Y. 2012. Why collagens best survived in fossils? Clues from amino acid thermal stability. Biochemical and Biophysical Research Communications 422(1):5–7.Google Scholar
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., Ruhli, F., Gilbert, M. T. P., and Collins, M. J. 2014a. Direct evidence of milk consumption from ancient human dental calculus. Scientific Reports 4:7104.Google Scholar
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-Garcia, 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., Collins, M. J., Gilbert, M. T. P., Ruhli, F., and Cappellini, E. 2014b. Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46(4):336–344.Google Scholar
Welker, F., Collins, M. J., Thomas, J. A., Wadsley, M., Brace, S., Cappellini, E., Turvey, S. T., Reguero, M., Gelfo, J. N., Kramarz, A., Burger, J., Thomas-Oates, J., Ashford, D. A., Ashton, P. D., Rowsell, K., Porter, D. M., Kessler, B., Fischer, R., Baessmann, C., Kaspar, S., Olsen, J. V., Kiley, P., Elliott, J. A., Kelstrup, C. D., Mullin, V., Hofreiter, M., Willerslev, E., Hublin, J. J., Orlando, L., Barnes, I., and Macphee, R. D. E. 2015a. Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates. Nature 522(7554):81–84.Google Scholar
Welker, F., Soressi, M., Rendu, W., Hublin, J. J., and Collins, M. 2015b. Using ZooMS to identify fragmentary bone from the Late Middle/Early Upper Palaeolithic sequence of Les Cottés, France. Journal of Archaeological Science 54:279–286.Google Scholar
Whiteaker, J. R., Zhao, L., Zhang, H. Y., Feng, L. C., Piening, B. D., Anderson, L., and Paulovich, A. G. 2007. Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Analytical Biochemistry 362(1):44–54.Google Scholar
Wilson, A. S., Brown, E. L., Villa, C., Lynnerup, N., Healey, A., Ceruti, M. C., Reinhard, J., Previgliano, C. H., Araoz, F. A., Diez, J. G., and Taylor, T. 2013. Archaeological, radiological, and biological evidence offer insight into Inca child sacrifice. Proceedings of the National Academy of Sciences of the United States of America 110(33):13322–13327.Google Scholar
Wilson, J., van Doorn, N. L., and Collins, M. J. 2012. Assessing the extent of bone degradation using glutamine deamidation in collagen. Analytical Chemistry 84(21):9041–9048.Google Scholar
Yamashita, M. and Fenn, J. B. 1984. Electrospray ion source. Another variation on the free-jet theme. The Journal of Physical Chemistry 88(20):4451–4459.Google Scholar
Yan, H. T., An, J. J., Zhou, T., Xia, Y., and Rong, B. 2014. Identification of proteinaceous binding media for the polychrome terracotta army of Emperor Qin Shihuang by MALDI-TOF-MS. Chinese Science Bulletin = Kexue tongbao 59(21):2574–2581.Google Scholar
Yang, Y. M., Shevchenko, A., Knaust, A., Abuduresule, I., Li, W. Y., Hu, X. J., Wang, C. S., and Shevchenko, A. 2014. Proteomics evidence for kefir dairy in Early Bronze Age China. Journal of Archaeological Science 45:178–186.Google Scholar
Zhu, Z. Y., Chen, H. F., Li, L., Gong, D. C., Gao, X., Yang, J. C., Zhao, X. C., and Ji, K. Z. 2014. Biomass spectrometry identification of the fibre material in the pall imprint excavated from Grave M1, Peng-state Cemetery, Shanxi, China. Archaeometry 56(4):681–688.Google Scholar

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