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Fabrizi I, Flament S, Delhon C, Gourichon L, Vuillien M, Oueslati T, Auguste P, Rolando C, Bray F. Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics. J Proteome Res 2024; 23:3404-3417. [PMID: 39042361 DOI: 10.1021/acs.jproteome.4c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.
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Affiliation(s)
- Isabelle Fabrizi
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
| | - Stéphanie Flament
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
| | - Claire Delhon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Lionel Gourichon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Manon Vuillien
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Tarek Oueslati
- Univ. Lille, CNRS UMR 8164─HALMA─Histoire, Archéologie et Littérature des Mondes Anciens, Lille F-59000, France
| | - Patrick Auguste
- Univ. Lille, CNRS UMR 8198─EEP─Evolution, Ecology and Paleontology, Lille F-59000, France
| | - Christian Rolando
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
- Shrieking Sixties, Villeneuve d'Ascq F-59650, France
| | - Fabrice Bray
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
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2
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Pittalà MG, Di Francesco A, Cucina A, Saletti R, Zilberstein G, Zilberstein S, Arhire T, Righetti PG, Cunsolo V. Count Dracula Resurrected: Proteomic Analysis of Vlad III the Impaler's Documents by EVA Technology and Mass Spectrometry. Anal Chem 2023; 95:12732-12744. [PMID: 37552208 PMCID: PMC10469356 DOI: 10.1021/acs.analchem.3c01461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023]
Abstract
The interest of scientists in analyzing items of World Cultural Heritage has been exponentially increasing since the beginning of the new millennium. These studies have grown considerably in tandem with the development and use of sophisticated and sensitive technologies such as high-resolution mass spectrometry (MS) and the non-invasive and non-damaging technique, known under the acronym EVA (ethylene-vinyl acetate). Here, we report the results of the MS characterization of the peptides and proteins harvested by the EVA technology applied to three letters written in 1457 and 1475 by the voivode of Wallachia, Vlad III, also known as Vlad the Impaler, or Vlad Dracula. The discrimination of the "original" endogenous peptides from contaminant ones was obtained by monitoring their different levels of deamidation and of other diagenetic chemical modifications. The characterization of the ancient proteins extracted from these documents allowed us to explore the environmental conditions, in the second half of the 15th century, of the Wallachia, a region considered as a meeting point for soldiers, migrants, and travelers that probably carried not only trade goods and cultural traditions but also diseases and epidemics. In addition, the identification of many human peptides and proteins harvested from the letters allowed us to uncover more about Vlad Dracula the Impaler. Particularly, the experimental data show that he probably suffered from inflammatory processes of the respiratory tract and/or of the skin. In addition, proteomics data, although not exhaustive, suggest that, according to some stories, he might also have suffered from a pathological condition called hemolacria, that is, he could shed tears admixed with blood. It is worth noting that more medieval people may have touched these documents, which cannot be denied, but it is also presumable that the most prominent ancient proteins should be related to Prince Vlad the Impaler, who wrote and signed these letters. The data have been deposited to the ProteomeXchange with the identifier ⟨PXD041350⟩.
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Affiliation(s)
- Maria
Gaetana Giovanna Pittalà
- Laboratory
of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, Catania 95125, Italy
| | - Antonella Di Francesco
- Laboratory
of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, Catania 95125, Italy
| | - Annamaria Cucina
- Laboratory
of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, Catania 95125, Italy
| | - Rosaria Saletti
- Laboratory
of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, Catania 95125, Italy
| | - Gleb Zilberstein
- SpringStyle
Tech Design Ltd, Oppenheimer
7, Rehovot 7670107, Israel
| | | | - Tudor Arhire
- Sibiu
County Department of Romania National Archives, Strada Arhivelor 3, Sibiu 557260, Romania
| | - Pier Giorgio Righetti
- Department
of Chemistry, Materials and Chemical Engineering ‘‘Giulio
Natta’’, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
| | - Vincenzo Cunsolo
- Laboratory
of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, Catania 95125, Italy
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3
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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4
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Ntasi G, Sbriglia S, Pitocchi R, Vinciguerra R, Melchiorre C, Dello Ioio L, Fatigati G, Crisci E, Bonaduce I, Carpentieri A, Marino G, Birolo L. Proteomic Characterization of Collagen-Based Animal Glues for Restoration. J Proteome Res 2022; 21:2173-2184. [PMID: 35969501 PMCID: PMC9442796 DOI: 10.1021/acs.jproteome.2c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Animal glues are widely used in restoration as adhesives,
binders,
and consolidants for organic and inorganic materials. Their variable
performances are intrinsically linked to the adhesive properties of
collagen, which determine the chemical, physical, and mechanical properties
of the glue. We have molecularly characterized the protein components
of a range of homemade and commercial glues using mass spectrometry
techniques. A shotgun proteomic analysis provided animal origin, even
when blended, and allowed us to distinguish between hide and bone
glue on the basis of the presence of collagen type III, which is abundant
in connective skin/leather tissues and poorly synthetized in bones.
Furthermore, chemical modifications, a consequence of the preparation
protocols from the original animal tissue, were thoroughly evaluated.
Deamidation, methionine oxidation, and backbone cleavage have been
analyzed as major collagen modifications, demonstrating their variability
among different glues and showing that, on average, bone glues are
less deamidated than hide glues, but more fragmented, and mixed-collagen
glues are overall less deamidated than pure glues. We believe that
these data may be of general analytical interest in the characterization
of collagen-based materials and may help restorers in the selection
of the most appropriate materials to be used in conservation treatments.
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Affiliation(s)
- Georgia Ntasi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Sara Sbriglia
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Rossana Pitocchi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy
| | | | - Giancarlo Fatigati
- Department of Humanities, University Suor Orsola Benincasa, via Santa Caterina da Siena 37, 80132, Naples, Italy
| | - Emanuele Crisci
- Department of Chemistry and Industrial Chemistry, University of Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Ilaria Bonaduce
- Department of Chemistry and Industrial Chemistry, University of Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Andrea Carpentieri
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy.,Department of Humanities, University Suor Orsola Benincasa, via Santa Caterina da Siena 37, 80132, Naples, Italy.,Task Force "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, 80138 Naples, Italy
| | - Gennaro Marino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy.,Department of Humanities, University Suor Orsola Benincasa, via Santa Caterina da Siena 37, 80132, Naples, Italy
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy.,Task Force "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, 80138 Naples, Italy
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5
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Abstract
Collagen peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. Minimally destructive and cost effective, ZooMS enables rapid taxonomic identification of large bone assemblages, cultural heritage objects, and other organic materials of animal origin. As its importance grows as both a research and a conservation tool, it is critical to ensure that its expanding body of users understands its fundamental principles, strengths, and limitations. Here, we outline the basic functionality of ZooMS and provide guidance on interpreting collagen spectra from archaeological bones. We further examine the growing potential of applying ZooMS to nonmammalian assemblages, discuss available options for minimally and nondestructive analyses, and explore the potential for peptide mass fingerprinting to be expanded to noncollagenous proteins. We describe the current limitations of the method regarding accessibility, and we propose solutions for the future. Finally, we review the explosive growth of ZooMS over the past decade and highlight the remarkably diverse applications for which the technique is suited.
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6
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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7
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Meta-proteomic analysis of two mammoth's trunks by EVA technology and high-resolution mass spectrometry for an indirect picture of their habitat and the characterization of the collagen type I, alpha-1 and alpha-2 sequence. Amino Acids 2022; 54:935-954. [PMID: 35434776 PMCID: PMC9213349 DOI: 10.1007/s00726-022-03160-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/27/2022] [Indexed: 12/30/2022]
Abstract
The recent paleoproteomic studies, including paleo-metaproteomic analyses, improved our understanding of the dietary of ancient populations, the characterization of past human diseases, the reconstruction of the habitat of ancient species, but also provided new insights into the phylogenetic relationships between extant and extinct species. In this respect, the present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 30,000 years old. In particular, proteins were extracted by applying EVA (Ethylene-Vinyl Acetate studded with hydrophilic and hydrophobic resins) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: (i) an indirect description of the habitat of these two mammoths, and (ii) an improved characterization of the collagen type I, alpha-1 and alpha-2 chains (col1a1 and col1a2). Sequence characterization of the col1a1 and col1a2 highlighted some differences between M. primigenius and other Proboscidea together with the identification of three (two for col1a1, and one for col1a2) potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius with respect to the other two genera of elephantids (i.e., Elephas and Loxodonta), and the extinct American mastodon (i.e., Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the "original" endogenous peptides from contaminant ones. The data have been deposited to the ProteomeXchange with identifier < PXD029558 > .
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8
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Abstract
The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27605, United States.,Department of Geology, Lund University, Lund SE-221 00, Sweden
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9
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Cucina A, Cunsolo V, Di Francesco A, Saletti R, Zilberstein G, Zilberstein S, Tikhonov A, Bublichenko AG, Righetti PG, Foti S. Meta-proteomic analysis of the Shandrin mammoth by EVA technology and high-resolution mass spectrometry: what is its gut microbiota telling us? Amino Acids 2021; 53:1507-1521. [PMID: 34453585 PMCID: PMC8519927 DOI: 10.1007/s00726-021-03061-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022]
Abstract
During the last decade, paleoproteomics allowed us to open a direct window into the biological past, improving our understanding of the phylogenetic relationships of extant and extinct species, past human diseases, and reconstruction of the human diet. In particular, meta-proteomic studies, mainly carried out on ancient human dental calculus, provided insights into past oral microbial communities and ancient diets. On the contrary, very few investigations regard the analysis of ancient gut microbiota, which may enable a greater understanding of how microorganisms and their hosts have co-evolved and spread under the influence of changing diet practices and habitat. In this respect, this paper reports the results of the first-ever meta-proteomic analysis carried out on a gut tissue sample some 40,000 years old. Proteins were extracted by applying EVA (ethylene–vinyl acetate) films to the surface of the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), and then investigated via a shotgun MS-based approach. Proteomic and peptidomic analysis allowed in-depth exploration of its meta-proteome composition. The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. Overall, the results of the meta-proteomic analysis here reported agreeing with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth and provided insight into its diet. The data have been deposited to the ProteomeXchange with identifier < PXD025518 > .
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Affiliation(s)
- Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | | | | | - Alexei Tikhonov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Andrey G Bublichenko
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering ''Giulio Natta'', Politecnico di Milano, Via Mancinelli 7, 20131, Milan, Italy
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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10
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Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. Sci Rep 2021; 11:7795. [PMID: 33833277 PMCID: PMC8032661 DOI: 10.1038/s41598-021-87125-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published palaeoproteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in BLG recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.
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11
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Cleland TP, Sarancha JJ, France CAM. Proteomic profile of bone "collagen" extracted for stable isotopes: Implications for bulk and single amino acid analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9025. [PMID: 33332665 DOI: 10.1002/rcm.9025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
RATIONALE Protein studies in archaeology and paleontology have been dominated by stable isotope studies to understand diet and trophic levels, but recent applications of proteomic techniques have resulted in a more complete understanding of protein diagenesis than stable isotopes alone. In stable isotope analyses, samples are retained or discarded based on their properties. Proteomics can directly determine what proteins are present within the sample and may be able to allow previously discarded samples to be analyzed. METHODS Protein samples that had been previously analyzed for stable isotopes, including those with marginal and poor sample quality, were characterized by liquid chromatography/mass spectrometry using an LTQ Orbitrap Velos mass spectrometer after separation on a Dionex Ultimate 3000 LC system. Data were analyzed using MetaMorpheus and custom R scripts. RESULTS We found a variety of proteins in addition to collagen, although collagen I was found in the majority of the samples (most samples >80%). We also found a positive correlation between total deamidation and wt% N, suggesting that deamidation may impact the overall nitrogen signal in bulk analyses. The amino acid profiles of samples, including those of marginal or poor stable isotope quality, reflect the expected collagen I percentages, allowing their use in single amino acid stable isotope analyses. CONCLUSIONS All the samples regardless of quality were found to have high concentrations of collagen I, making interpretations of dietary routing based on collagen I reasonably valid. The amino acid profiles on the marginal and poor samples reflect an expected collagen I profile and allow these samples to be recovered for single amino acid analyses.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD, USA
| | - Julianne J Sarancha
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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12
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Tanasi D, Cucina A, Cunsolo V, Saletti R, Di Francesco A, Greco E, Foti S. Paleoproteomic profiling of organic residues on prehistoric pottery from Malta. Amino Acids 2021; 53:295-312. [PMID: 33582869 PMCID: PMC7910365 DOI: 10.1007/s00726-021-02946-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/22/2021] [Indexed: 11/02/2022]
Abstract
Mass spectrometry-based approaches have been successfully applied for identifying ancient proteins in bones and other tissues. On the contrary, there are relatively few examples of the successful recovery and identification of archeological protein residues from ceramic artifacts; this is because ceramics contain much lower levels of proteins which are extensively degraded by diagenetic effects. In this paper, we report the results of the characterization of proteins extracted from pottery of the Maltese site of Baħrija, the guide-site for the Baħrija period (half of 9th-second half of eighth century BCE), recently identified as the final part of the Borġ in-Nadur culture. Proteomic data here reported confirm that one of the major issue of these kind of studies is represented by contamination of animal and human agents that may complicate endogenous protein identification and authentication. The samples tested included a small group of ceramic forms, namely three tableware and six coarse ware thought to have been used in food preparation and/or storage. In this context, the limited availability of paleobotanical and archeozoological analyses may be compensated by the outcomes of the first proteomics profiling which, even if obtained on a limited selection of vessels, revealed the centrality of wheat in the diet of the ancient community of Baħrija. The data have been deposited to the ProteomeXchange with identifier < PXD022848 > .
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Affiliation(s)
- Davide Tanasi
- Department of History, University of South Florida, SOC107 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Enrico Greco
- Aix-Marseille Université, Institut de Chimie Radicalaire, Service 512, Avenue Escadrille Normandie Niemen, 13013, Marseille, France
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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13
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
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.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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14
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Cleland TP, Schroeter ER, Colleary C. Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics. J Proteomics 2020; 230:103992. [PMID: 32992016 DOI: 10.1016/j.jprot.2020.103992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022]
Abstract
The term proteoform describes all combinations of change in a protein, as elucidated through intact mass proteomics. Paleoproteomic studies have begun using digestion-free and top-down techniques to access information from ancient and historical remains. However, to discuss protein changes that uniquely occur to archaeological and paleontological proteomes as the result of diagenesis (i.e., physical and chemical change imparted by burial), a novel term is needed that both addresses issues of combinatorics and distinguishes diagenetic-specific alteration. SIGNIFICANCE: The term diagenetiform provides the opportunity to communicate clearly the sets of diagenetic changes found on preserved proteins. The diagenetiform nomenclature will allow for top-down paleoproteomic studies to accurately describe the total changes detected on ancient proteins.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD 20746, United States of America.
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Caitlin Colleary
- Department of Vertebrate Paleontology, Cleveland Museum of Natural History, Cleveland, OH 44106, United States of America
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15
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Schroeter ER, Blackburn K, Goshe MB, Schweitzer MH. Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181433. [PMID: 31598217 PMCID: PMC6731700 DOI: 10.1098/rsos.181433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800-1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27513, USA
| | - Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27513, USA
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27513, USA
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27513, USA
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16
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Horn IR, Kenens Y, Palmblad NM, van der Plas-Duivesteijn SJ, Langeveld BW, Meijer HJM, Dalebout H, Marissen RJ, Fischer A, Vincent Florens FB, Niemann J, Rijsdijk KF, Schulp AS, Laros JFJ, Gravendeel B. Palaeoproteomics of bird bones for taxonomic classification. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ivo R Horn
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
| | - Yvo Kenens
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
| | - N Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Bram W Langeveld
- Natural History Museum Rotterdam, Museumpark, Rotterdam, The Netherlands
| | - Hanneke J M Meijer
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
- University Museum, Department of Natural History, University of Bergen, Bergen, Norway
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob J Marissen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anja Fischer
- University of Amsterdam, Faculty of Humanities, Amsterdam, The Netherlands
| | - F B Vincent Florens
- Tropical Island Biodiversity, Ecology and Conservation Pole of Research, University of Mauritius, Réduit, Mauritius
| | - Jonas Niemann
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - Kenneth F Rijsdijk
- BIOMAC group, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Faculty of Natural Sciences, Science Park, Amsterdam, The Netherlands
| | - Anne S Schulp
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
| | | | - Barbara Gravendeel
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg, BE Leiden, The Netherlands
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17
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Buckley M, Lawless C, Rybczynski N. Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America. J Proteomics 2019; 194:218-225. [DOI: 10.1016/j.jprot.2018.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 11/27/2022]
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18
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Schweitzer MH, Zheng W, Moyer AE, Sjövall P, Lindgren J. Preservation potential of keratin in deep time. PLoS One 2018; 13:e0206569. [PMID: 30485294 PMCID: PMC6261410 DOI: 10.1371/journal.pone.0206569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 10/16/2018] [Indexed: 11/18/2022] Open
Abstract
Multiple fossil discoveries and taphonomic experiments have established the durability of keratin. The utility and specificity of antibodies to identify keratin peptides has also been established, both in extant feathers under varying treatment conditions, and in feathers from extinct organisms. Here, we show localization of feather-keratin antibodies to control and heat-treated feathers, testifying to the repeatability of initial data supporting the preservation potential of keratin. We then show new data at higher resolution that demonstrates the specific response of these antibodies to the feather matrix, we support the presence of protein in heat-treated feathers using ToF-SIMS, and we apply these methods to a fossil feather preserved in the unusual environment of sinter hot springs. We stress the importance of employing realistic conditions such as sediment burial when designing experiments intended as proxies for taphonomic processes occurring in the fossil record. Our data support the hypothesis that keratin, particularly the β-keratin that comprises feathers, has potential to preserve in fossil remains.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
- Department of Geology, Lund University, Lund, Sweden
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alison E. Moyer
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Peter Sjövall
- RISE Research Institutes of Sweden, Chemistry and Materials, Borås, Sweden
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19
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Cleland TP. Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics. J Proteome Res 2018; 17:3976-3983. [DOI: 10.1021/acs.jproteome.8b00637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
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20
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Prieto-Bonete G, Pérez-Cárceles MD, Maurandi-López A, Pérez-Martínez C, Luna A. Association between protein profile and postmortem interval in human bone remains. J Proteomics 2018; 192:54-63. [PMID: 30145274 DOI: 10.1016/j.jprot.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/08/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
Abstract
Proteomic techniques in bones forensic samples are increasingly, being applied. The main aim of forensic sciences is the estimation of postmortem interval. Most current techniques are useful for the first post-mortem stages. However, in the case of osseous remains, these techniques may be difficult to use due to the high level of decomposition of the sample. Our objective was to attempt to know whether there is a protein profile in human bone remains that would enable a late postmortem. interval ranging from 5 to 20 years postmortem to be estimated. A total of 40 femur bones from 40 different cadavers (data range 5-20 years) were use. Of the 275 total proteins, we excluded the circulating ones (n = 227), leaving a total of 48 proteins (29 structural and 19 functional) were found. A multiple correspondence analysis was applied on the 48 proteins. Finally selecting 32 proteins that allowed us to discriminate between the. two groups of postmortem interval. Analysis of the protein profile present in bone permits an approximation of the date of death within the studied interval, and could be used to complement other tests for estimating the postmortem interval.
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Affiliation(s)
| | | | - Antonio Maurandi-López
- Department of Didactics of Mathematical and Social Sciences, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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21
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Mackie M, Rüther P, Samodova D, Di Gianvincenzo F, Granzotto C, Lyon D, Peggie DA, Howard H, Harrison L, Jensen LJ, Olsen JV, Cappellini E. Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Meaghan Mackie
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Patrick Rüther
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Diana Samodova
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Fabiana Di Gianvincenzo
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Clara Granzotto
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - David Lyon
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research; Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - David A. Peggie
- Scientific Department; National Gallery London; Trafalgar Square London WC2N 5DN UK
| | - Helen Howard
- Scientific Department; National Gallery London; Trafalgar Square London WC2N 5DN UK
| | - Lynne Harrison
- Conservation Department; National Gallery London; Trafalgar Square London WC2N 5DN UK
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research; Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Jesper V. Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Enrico Cappellini
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
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22
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Mackie M, Rüther P, Samodova D, Di Gianvincenzo F, Granzotto C, Lyon D, Peggie DA, Howard H, Harrison L, Jensen LJ, Olsen JV, Cappellini E. Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting. Angew Chem Int Ed Engl 2018; 57:7369-7374. [PMID: 29603563 PMCID: PMC6032867 DOI: 10.1002/anie.201713020] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/08/2018] [Indexed: 01/24/2023]
Abstract
Ahead of display, a non-original layer was observed on the surface of a fragment of a wall painting by Ambrogio Lorenzetti (active 1319, died 1348/9). FTIR analysis suggested proteinaceous content. Mass spectrometry was used to better characterise this layer and revealed two protein components: sheep and cow glue and chicken and duck egg white. Analysis of post-translational modifications detected several photo-oxidation products, which suggest that the egg experienced prolonged exposure to UV light and was likely applied long before the glue layer. Additionally, glycation products detected may indicate naturally occurring glycoprotein degradation or reaction with a carbohydrate material such as starch, identified by ATR-FTIR in a cross-section of a sample taken from the painting. Palaeoproteomics is shown to provide detailed characterisation of organic layers associated with mural paintings and therefore aids reconstruction of the conservation history of these objects.
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Affiliation(s)
- Meaghan Mackie
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Patrick Rüther
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Diana Samodova
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Fabiana Di Gianvincenzo
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
| | - Clara Granzotto
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
| | - David Lyon
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein ResearchFaculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - David A. Peggie
- Scientific DepartmentNational Gallery LondonTrafalgar SquareLondonWC2N 5DNUK
| | - Helen Howard
- Scientific DepartmentNational Gallery LondonTrafalgar SquareLondonWC2N 5DNUK
| | - Lynne Harrison
- Conservation DepartmentNational Gallery LondonTrafalgar SquareLondonWC2N 5DNUK
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein ResearchFaculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Jesper V. Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Enrico Cappellini
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
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23
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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24
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Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ. A guide to ancient protein studies. Nat Ecol Evol 2018; 2:791-799. [PMID: 29581591 DOI: 10.1038/s41559-018-0510-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Beatrice Demarchi
- Department of Life Science and Systems Biology, University of Turin, Turin, Italy.,BioArCh, Department of Archaeology, University of York, York, UK
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,BioArCh, Department of Archaeology, University of York, York, UK
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25
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Welker F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment. BMC Evol Biol 2018; 18:23. [PMID: 29463217 PMCID: PMC5819086 DOI: 10.1186/s12862-018-1141-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/15/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. RESULTS Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. CONCLUSIONS The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.
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Affiliation(s)
- F Welker
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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26
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Cleland TP, Schroeter ER. A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics. J Proteome Res 2018; 17:936-945. [PMID: 29384680 DOI: 10.1021/acs.jproteome.7b00703] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution , Suitland, Maryland 20746, United States
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina 27695, United States
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Buckley M, Warwood S, van Dongen B, Kitchener AC, Manning PL. A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination. Proc Biol Sci 2017; 284:rspb.2017.0544. [PMID: 28566488 PMCID: PMC5454271 DOI: 10.1098/rspb.2017.0544] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 02/05/2023] Open
Abstract
A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus The resulting LC-MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.
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Affiliation(s)
- Michael Buckley
- Faculty of Science and Engineering, The University of Manchester, Manchester Institute of Biotechnology, Manchester M1 7DN, UK .,School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M13 9PL, UK
| | - Stacey Warwood
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Manchester M13 9PL, UK
| | - Bart van Dongen
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M13 9PL, UK
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Phillip L Manning
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M13 9PL, UK.,Department of Geology and Environmental Geosciences, College of Charleston, 66 George Street, Charleston, SC 29424, USA
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Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics. Proc Biol Sci 2017; 283:rspb.2016.0593. [PMID: 27306052 DOI: 10.1098/rspb.2016.0593] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and in vivo and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place C. ohioensis within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Cleland TP. Solid Digestion of Demineralized Bone as a Method To Access Potentially Insoluble Proteins and Post-Translational Modifications. J Proteome Res 2017; 17:536-542. [DOI: 10.1021/acs.jproteome.7b00670] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
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30
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Mackie M, Hendy J, Lowe AD, Sperduti A, Holst M, Collins MJ, Speller CF. Preservation of the metaproteome: variability of protein preservation in ancient dental calculus. SCIENCE AND TECHNOLOGY OF ARCHAEOLOGICAL RESEARCH 2017; 3:74-86. [PMID: 29098079 PMCID: PMC5633013 DOI: 10.1080/20548923.2017.1361629] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/16/2017] [Indexed: 05/25/2023]
Abstract
Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.
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Affiliation(s)
- Meaghan Mackie
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Abigail D. Lowe
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Malin Holst
- BioArCh, Department of Archaeology, University of York, York, UK
- York Osteoarchaeology Ltd
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, UK
- EvoGenomics Section, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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31
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Sawafuji R, Cappellini E, Nagaoka T, Fotakis AK, Jersie-Christensen RR, Olsen JV, Hirata K, Ueda S. Proteomic profiling of archaeological human bone. ROYAL SOCIETY OPEN SCIENCE 2017; 4:161004. [PMID: 28680659 PMCID: PMC5493901 DOI: 10.1098/rsos.161004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/09/2017] [Indexed: 05/18/2023]
Abstract
Ancient protein analysis provides clues to human life and diseases from ancient times. Here, we performed shotgun proteomics of human archeological bones for the first time, using rib bones from the Hitotsubashi site (AD 1657-1683) in Tokyo, called Edo in ancient times. The output data obtained were analysed using Gene Ontology and label-free quantification. We detected leucocyte-derived proteins, possibly originating from the bone marrow of the rib. Particularly prevalent and relatively high expression of eosinophil peroxidase suggests the influence of infectious diseases. This scenario is plausible, considering the overcrowding and unhygienic living conditions of the Edo city described in the historical literature. We also observed age-dependent differences in proteome profiles, particularly for proteins involved in developmental processes. Among them, alpha-2-HS-glycoprotein demonstrated a strong negative correlation with age. These results suggest that analysis of ancient proteins could provide a useful indicator of stress, disease, starvation, obesity and other kinds of physiological and pathological information.
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Affiliation(s)
- Rikai Sawafuji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Nakagami, Okinawa 903-0215, Japan
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ster Voldgade 5–7, 1350 Copenhagen, Denmark
| | - Tomohito Nagaoka
- Department of Anatomy, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511, Japan
| | - Anna K. Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ster Voldgade 5–7, 1350 Copenhagen, Denmark
| | - Rosa Rakownikow Jersie-Christensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Kazuaki Hirata
- Department of Anatomy, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- School of Medicine, Hangzhou Normal University, No.58, Haishu Road, Cangqian, Yuhang District, Hangzhou, Zhejiang 311121, People’s Republic of China
- Author for correspondence: Shintaroh Ueda e-mail:
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Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein. J Proteome Res 2017; 16:920-932. [PMID: 28111950 PMCID: PMC5401637 DOI: 10.1021/acs.jproteome.6b00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Caroline J. DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy P. Cleland
- Department of Chemistry, University of Texas-Austin, Austin, Texas 78712, United States
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul M. Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics, San Carlos, California 94070, United States
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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Schroeter ER, DeHart CJ, Schweitzer MH, Thomas PM, Kelleher NL. Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics. PeerJ 2016; 4:e2603. [PMID: 27812413 PMCID: PMC5088622 DOI: 10.7717/peerj.2603] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 11/22/2022] Open
Abstract
Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Caroline J DeHart
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Paul M Thomas
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Neil L Kelleher
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
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Surmik D, Boczarowski A, Balin K, Dulski M, Szade J, Kremer B, Pawlicki R. Spectroscopic Studies on Organic Matter from Triassic Reptile Bones, Upper Silesia, Poland. PLoS One 2016; 11:e0151143. [PMID: 26977600 PMCID: PMC4792425 DOI: 10.1371/journal.pone.0151143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/24/2016] [Indexed: 11/19/2022] Open
Abstract
Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted "blood vessels" showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the "blood vessels" was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment.
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Affiliation(s)
- Dawid Surmik
- Faculty of Earth Science, University of Silesia, Będzińska 60, 41–200, Sosnowiec, Poland
- Park of Science & Human Evolution, 1 Maja 10, 46–040, Krasiejów, Poland
| | - Andrzej Boczarowski
- Faculty of Earth Science, University of Silesia, Będzińska 60, 41–200, Sosnowiec, Poland
- Park of Science & Human Evolution, 1 Maja 10, 46–040, Krasiejów, Poland
| | - Katarzyna Balin
- A. Chełkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40–007, Katowice, Poland
- Silesian Centre for Education and Interdisciplinary Research, 75 Pułku Piechoty 1A, 41–500, Chorzow, Poland
| | - Mateusz Dulski
- Silesian Centre for Education and Interdisciplinary Research, 75 Pułku Piechoty 1A, 41–500, Chorzow, Poland
- Institute of Material Science, University of Silesia, 75 Pułku Piechoty 1A, 41–500, Chorzow, Poland
| | - Jacek Szade
- A. Chełkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40–007, Katowice, Poland
- Silesian Centre for Education and Interdisciplinary Research, 75 Pułku Piechoty 1A, 41–500, Chorzow, Poland
| | - Barbara Kremer
- Institute of Paleobiology, Polish Academy of Science, Twarda 51/55, 00–818, Warszawa, Poland
| | - Roman Pawlicki
- Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31–034, Kraków, Poland
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35
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Schroeter ER, Cleland TP. Glutamine deamidation: an indicator of antiquity, or preservational quality? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:251-255. [PMID: 26689157 DOI: 10.1002/rcm.7445] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Much credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens. METHODS We re-evaluated the relationship between glutamine deamidation and geologic time by examining previously published data from five recent mass spectrometry studies of archeaological fossils. Deamidation values recovered for fossils were graphed against their reported chronologic age using WebPlotDigitizer. RESULTS The experimental data that has been produced from fossil material to date show that the extent of glutamine deamidation does not correspond to the absolute age of the specimens being examined, but rather show extreme variation between specimens of similar age and taxonomic affinity. CONCLUSIONS Because deamidation rates and levels can be greatly affected by numerous chemical and environmental factors, we propose that glutamine deamidation is better suited as an indicator of preservational quality and/or environmental conditions than a mark of the endogeneity or authenticity of ancient proteins.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12182, USA
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Cleland TP, Schroeter ER, Zamdborg L, Zheng W, Lee JE, Tran JC, Bern M, Duncan MB, Lebleu VS, Ahlf DR, Thomas PM, Kalluri R, Kelleher NL, Schweitzer MH. Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis. J Proteome Res 2015; 14:5252-62. [PMID: 26595531 DOI: 10.1021/acs.jproteome.5b00675] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.
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Affiliation(s)
| | | | - Leonid Zamdborg
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | | | - Ji Eun Lee
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States.,Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - John C Tran
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics , San Carlos, California 94070, United States
| | - Michael B Duncan
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Valerie S Lebleu
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center , Houston, Texas 77054, United States
| | - Dorothy R Ahlf
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Raghu Kalluri
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center , Houston, Texas 77054, United States.,Department of Biological Chemistry and Molecular Pharmacology and Harvard-MIT Division of Health Sciences and Technology, Harvard University , Cambridge, Massachusetts 02139, United States
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Mary H Schweitzer
- North Carolina Museum of Natural Sciences , Raleigh, North Carolina 27601, United States
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