Global InformationAncient protein information
Ancient proteins are complex mixtures and the term palaeoproteomics is used to characterise the study of proteomes in the past.[1] Ancients proteins have been recovered from a wide range of archaeological materials, including bones,[2] teeth,[3] eggshells,[4] leathers,[5] parchments,[6] ceramics,[7] painting binders[8] and well-preserved soft tissues like gut intestines.[9] These preserved proteins have provided valuable information about taxonomic identification, evolution history (phylogeny), diet, health, disease, technology and social dynamics in the past.
Like modern proteomics, the study of ancient proteins has also been enabled by technological advances. Various analytical techniques, for example, amino acid profiling, racemisation dating, immunodetection, Edman sequencing, peptide mass fingerprinting, and tandem mass spectrometry have been used to analyse ancient proteins.[10] The introduction of high-performance mass spectrometry (for example, Orbitrap) in 2000 has revolutionised the field, since the entire preserved sequences of complex proteomes can be characterised.[11]
Over the past decade, the study of ancient proteins has evolved into a well-established field in archaeological science. However, like the research of aDNA (ancient DNA preserved in archaeological remains), it has been limited by several challenges such as the coverage of reference databases, identification, contamination and authentication.[12] Researchers have been working on standardising sampling, extraction, data analysis and reporting for ancient proteins.[13] Novel computational tools such as de novo sequencing[14] and open research[15] may also improve the identification of ancient proteomes.
- ^ Warinner C, Korzow Richter K, Collins MJ (August 2022). "Paleoproteomics". Chemical Reviews. 122 (16): 13401–13446. doi:10.1021/acs.chemrev.1c00703. PMC 9412968. PMID 35839101.
- ^ Buckley M, Collins M, Thomas-Oates J, Wilson JC (December 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 (23): 3843–3854. Bibcode:2009RCMS...23.3843B. doi:10.1002/rcm.4316. PMID 19899187.
- ^ Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, et al. (October 2019). "Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny". Nature. 574 (7776): 103–107. Bibcode:2019Natur.574..103C. doi:10.1038/s41586-019-1555-y. PMC 6894936. PMID 31511700.
- ^ Demarchi B, Stiller J, Grealy A, Mackie M, Deng Y, Gilbert T, et al. (October 2022). "Ancient proteins resolve controversy over the identity of Genyornis eggshell". Proceedings of the National Academy of Sciences of the United States of America. 119 (43): e2109326119. Bibcode:2022PNAS..11909326D. doi:10.1073/pnas.2109326119. PMC 9995833. PMID 35609205. S2CID 249045755.
- ^ Elnaggar A, Osama A, Anwar AM, Ezzeldin S, Abou Elhassan S, Ebeid H, et al. (2022-11-09). "Paleoproteomic profiling for identification of animal skin species in ancient Egyptian archaeological leather using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)". Heritage Science. 10 (1): 182. doi:10.1186/s40494-022-00816-0. ISSN 2050-7445. S2CID 253399828.
- ^ Fiddyment S, Teasdale MD, Vnouček J, Lévêque É, Binois A, Collins MJ (2019-06-07). "So you want to do biocodicology? A field guide to the biological analysis of parchment". Heritage Science. 7 (1): 35. doi:10.1186/s40494-019-0278-6. ISSN 2050-7445. S2CID 195245888.
- ^ Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, et al. (October 2018). "Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers". Nature Communications. 9 (1): 4064. Bibcode:2018NatCo...9.4064H. doi:10.1038/s41467-018-06335-6. PMC 6170438. PMID 30283003.
- ^ Dallongeville S, Garnier N, Rolando C, Tokarski C (January 2016). "Proteins in Art, Archaeology, and Paleontology: From Detection to Identification". Chemical Reviews. 116 (1): 2–79. doi:10.1021/acs.chemrev.5b00037. PMID 26709533.
- ^ Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, et al. (July 2018). "The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals". Current Biology. 28 (14): 2348–2355.e9. Bibcode:2018CBio...28E2348M. doi:10.1016/j.cub.2018.05.067. PMC 6065529. PMID 30017480.
- ^ Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, et al. (June 2018). "Ancient Biomolecules and Evolutionary Inference". Annual Review of Biochemistry. 87 (1): 1029–1060. doi:10.1146/annurev-biochem-062917-012002. hdl:21.11116/0000-0001-DF45-7. PMID 29709200. S2CID 14004952.
- ^ Hendy J (January 2021). "Ancient protein analysis in archaeology". Science Advances. 7 (3). Bibcode:2021SciA....7.9314H. doi:10.1126/sciadv.abb9314. PMC 7810370. PMID 33523896.
- ^ Hendy J, van Doorn N, Collins M (2020). "Proteomics". In Britton K, Richards MP (eds.). Archaeological Science: An Introduction. Cambridge: Cambridge University Press. pp. 35–69. doi:10.1017/9781139013826.003. ISBN 978-0-521-19522-5. S2CID 241941528.
- ^ Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ (May 2018). "A guide to ancient protein studies" (PDF). Nature Ecology & Evolution. 2 (5): 791–799. Bibcode:2018NatEE...2..791H. doi:10.1038/s41559-018-0510-x. PMID 29581591. S2CID 256704765.
- ^ Yilmaz M, Fondrie WE, Bittremieux W, Nelson R, Ananth V, Oh S, Noble WS (2023-01-04). "Sequence-to-sequence translation from mass spectra to peptides with a transformer model". bioRxiv: 2023.01.03.522621. doi:10.1101/2023.01.03.522621. S2CID 255441838.
- ^ Chi H, Liu C, Yang H, Zeng WF, Wu L, Zhou WJ, et al. (October 2018). "Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine". Nature Biotechnology. 36 (11): 1059–1061. doi:10.1038/nbt.4236. PMID 30295672. S2CID 52930101.