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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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2
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Uchida-Fukuhara Y, Shimamura S, Sawafuji R, Nishiuchi T, Yoneda M, Ishida H, Matsumura H, Tsutaya T. Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus. Sci Rep 2024; 14:5938. [PMID: 38467689 PMCID: PMC10928219 DOI: 10.1038/s41598-024-55779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition.
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Affiliation(s)
- Yoko Uchida-Fukuhara
- Department of Oral Morphology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8525, Japan.
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Rikai Sawafuji
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Takumi Nishiuchi
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Mt. Olive Hospital, Okinawa, 903-0804, Japan
| | - Hirofumi Matsumura
- School of Health Sciences, Sapporo Medical University, Hokkaido, 060-8556, Japan
| | - Takumi Tsutaya
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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3
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Végh EI, Douka K. SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. Bioinformatics 2024; 40:btae054. [PMID: 38337062 PMCID: PMC10918634 DOI: 10.1093/bioinformatics/btae054] [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: 06/19/2023] [Revised: 01/08/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data. RESULTS SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually. AVAILABILITY AND IMPLEMENTATION The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).
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Affiliation(s)
- Emese I Végh
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Archaeology, Environmental Changes, and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
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4
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Smith GM, Ruebens K, Zavala EI, Sinet-Mathiot V, Fewlass H, Pederzani S, Jaouen K, Mylopotamitaki D, Britton K, Rougier H, Stahlschmidt M, Meyer M, Meller H, Dietl H, Orschiedt J, Krause J, Schüler T, McPherron SP, Weiss M, Hublin JJ, Welker F. The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany. Nat Ecol Evol 2024; 8:564-577. [PMID: 38297138 DOI: 10.1038/s41559-023-02303-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Recent excavations at Ranis (Germany) identified an early dispersal of Homo sapiens into the higher latitudes of Europe by 45,000 years ago. Here we integrate results from zooarchaeology, palaeoproteomics, sediment DNA and stable isotopes to characterize the ecology, subsistence and diet of these early H. sapiens. We assessed all bone remains (n = 1,754) from the 2016-2022 excavations through morphology (n = 1,218) or palaeoproteomics (zooarchaeology by mass spectrometry (n = 536) and species by proteome investigation (n = 212)). Dominant taxa include reindeer, cave bear, woolly rhinoceros and horse, indicating cold climatic conditions. Numerous carnivore modifications, alongside sparse cut-marked and burnt bones, illustrate a predominant use of the site by hibernating cave bears and denning hyaenas, coupled with a fluctuating human presence. Faunal diversity and high carnivore input were further supported by ancient mammalian DNA recovered from 26 sediment samples. Bulk collagen carbon and nitrogen stable isotope data from 52 animal and 10 human remains confirm a cold steppe/tundra setting and indicate a homogenous human diet based on large terrestrial mammals. This lower-density archaeological signature matches other Lincombian-Ranisian-Jerzmanowician sites and is best explained by expedient visits of short duration by small, mobile groups of pioneer H. sapiens.
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Affiliation(s)
- Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- School of Anthropology and Conservation, University of Kent, Kent, UK.
| | - Karen Ruebens
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Elena Irene Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Pessac, France
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Klervia Jaouen
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Géosciences Environnement Toulouse (GET), Observatoire Midi-Pyrénées (OMP), Toulouse, France
| | - Dorothea Mylopotamitaki
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Kate Britton
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, Scotland
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Holger Dietl
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Jörg Orschiedt
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Shannon P McPherron
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
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5
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Mylopotamitaki D, Weiss M, Fewlass H, Zavala EI, Rougier H, Sümer AP, Hajdinjak M, Smith GM, Ruebens K, Sinet-Mathiot V, Pederzani S, Essel E, Harking FS, Xia H, Hansen J, Kirchner A, Lauer T, Stahlschmidt M, Hein M, Talamo S, Wacker L, Meller H, Dietl H, Orschiedt J, Olsen JV, Zeberg H, Prüfer K, Krause J, Meyer M, Welker F, McPherron SP, Schüler T, Hublin JJ. Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature 2024; 626:341-346. [PMID: 38297117 PMCID: PMC10849966 DOI: 10.1038/s41586-023-06923-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024]
Abstract
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany.
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Elena Irene Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Arev Pelin Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Karen Ruebens
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Bordeaux, France
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Huan Xia
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Jakob Hansen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - André Kirchner
- Department of Soil Protection and Soil Survey, State Authority for Mining, Energy and Geology of Lower Saxony (LBEG), Hannover, Germany
| | - Tobias Lauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology and Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Michael Hein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Ecology, Leuphana University, Lüneburg, Germany
- Historical Anthropospheres Working Group, Leipzig Lab, Leipzig University, Leipzig, Germany
| | - Sahra Talamo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Bologna University, Bologna, Italy
| | - Lukas Wacker
- Ion Beam Physics, ETH Zurich, Zurich, Switzerland
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Wang N, Xu Y, Tang Z, He C, Hu X, Cui Y, Douka K. Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China. Proc Biol Sci 2023; 290:20231129. [PMID: 37876197 PMCID: PMC10598447 DOI: 10.1098/rspb.2023.1129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150-10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37-20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.
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Affiliation(s)
- Naihui Wang
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, 72070 Tübingen, Germany
| | - Yang Xu
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Zhuowei Tang
- School of Archaeology, Jilin University, 130012 Changchun, People's Republic of China
| | - Cunding He
- China-Central Asia ‘the Belt and Road’ Joint Laboratory on Human and Environment Research, 710127 Xi'an, People's Republic of China
- School of Cultural Heritage, Northwest University, 710127 Xi'an, People's Republic of China
| | - Xin Hu
- Chongqing China Three Gorges Museum, 400013 Chongqing, People's Republic of China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Katerina Douka
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
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7
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Pan L, Ding C, Deng Y, Chen H, Yang H, Wang B, Zhou Y, Wang B. Microbial degradation mechanism of historical silk revealed by proteomics and metabolomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5380-5389. [PMID: 37812415 DOI: 10.1039/d3ay01033c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Archaeological silk undergoes destructive and irreversible changes during the natural process of decay. However, in-depth studies on the influence of this biological factor are still lacking. Here, a combination of proteomics and metabolomics is proposed for the first time to explore the interaction between bacteria and historical silk during biodegradation, which provides information on changes at the molecular level of proteins and bacterial metabolites. Morphological observation revealed biofilms produced by Stenotrophomonas maltophilia and Pseudomonas alcaligenes when cultured in the stationary phase and confirmed severe deterioration of silk. Proteomics showed that S. maltophilia had an unbiased effect on silk fibroin, indicating its ability to disrupt both heavy and light chains, as well as other proteins, while P. alcaligenes showed an affinity for more disordered proteins. Analysis of bacterial metabolites showed that overall activity reduction and significant accumulation of fatty acid and phenol metabolites occurred after silk addition, suggesting that the presence of silk may inhibit the activity of an individual strain. This study provides a new insight into the microbial degradation mechanism of archaeological silk.
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Affiliation(s)
- Lindan Pan
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Chuanmiao Ding
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Yefeng Deng
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Hao Chen
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Hailiang Yang
- Key Scientific Research Base of Textile Conservation, State Administration of Cultural Heritage, China National Silk Museum, Hangzhou 310002, China
| | - Biyang Wang
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
| | - Yang Zhou
- Key Scientific Research Base of Textile Conservation, State Administration of Cultural Heritage, China National Silk Museum, Hangzhou 310002, China
| | - Bing Wang
- Institute of Textile Conservation, Zhejiang Sci-Tech University, Hangzhou 310018, China.
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
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8
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Chocholova E, Roudnicky P, Potesil D, Fialova D, Krystofova K, Drozdova E, Zdrahal Z. Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus. J Proteome Res 2023; 22:3311-3319. [PMID: 37699853 PMCID: PMC10563166 DOI: 10.1021/acs.jproteome.3c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.
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Affiliation(s)
- Eva Chocholova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Pavel Roudnicky
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - David Potesil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Dana Fialova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Karolina Krystofova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Eva Drozdova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Zbynek Zdrahal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
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9
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Johnston E, Buckley M. Age-Related Changes in Post-Translational Modifications of Proteins from Whole Male and Female Skeletal Elements. Molecules 2023; 28:4899. [PMID: 37446562 DOI: 10.3390/molecules28134899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
One of the key questions in forensic cases relates to some form of age inference, whether this is how old a crime scene is, when in time a particular crime was committed, or how old the victim was at the time of the crime. These age-related estimations are currently achieved through morphological methods with varying degrees of accuracy. As a result, biomolecular approaches are considered of great interest, with the relative abundances of several protein markers already recognized for their potential forensic significance; however, one of the greatest advantages of proteomic investigations over genomics ones is the wide range of post-translational modifications (PTMs) that make for a complex but highly dynamic resource of information. Here, we explore the abundance of several PTMs including the glycosylation, deamidation, and oxidation of several key proteins (collagen, fetuin A, biglycan, serum albumin, fibronectin and osteopontin) as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts. We find that glycosylations lowered into adulthood but deamidation and oxidation increased in the same age range.
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Affiliation(s)
- Elizabeth Johnston
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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10
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Bray F, Fabrizi I, Flament S, Locht JL, Antoine P, Auguste P, Rolando C. Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry. Anal Chem 2023; 95:7422-7432. [PMID: 37130053 DOI: 10.1021/acs.analchem.2c03301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In the archaeological or paleontological field, PMF is known as zooarchaeology mass spectrometry (ZooMS) and is widely implemented to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to 10-fold the required bone sample amount (down to the milligram scale) and achieves robust deamidation value calculation in a high-throughput manner. These improvements rely on a 96-well plate samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious post-translational modification production, and PMF at high resolution using matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance (MALDI-FTICR) analysis. This method was applied to the identification of a hundred bones of herbivores from the Middle Paleolithic site of Caours (Somme, France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their osteomorphology, as well as to more challenging samples consisting of small or burned bone fragments. Deamidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.
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Affiliation(s)
- Fabrice Bray
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - 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
| | - Jean-Luc Locht
- Inrap Hauts-de-France, 32, avenue de l'Étoile-du-Sud, Glisy 80440, France
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Pierre Antoine
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Patrick Auguste
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paléo, 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, 1-3 Allée Lavoisier, Villeneuve-d'Ascq F-59650, France
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11
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Silvestrini S, Lugli F, Romandini M, Real C, Sommella E, Salviati E, Arrighi S, Bortolini E, Figus C, Higgins OA, Marciani G, Oxilia G, Delpiano D, Vazzana A, Piperno M, Crescenzi C, Campiglia P, Collina C, Peresani M, Spinapolice EE, Benazzi S. Integrating ZooMS and zooarchaeology: New data from the Uluzzian levels of Uluzzo C Rock Shelter, Roccia San Sebastiano cave and Riparo del Broion. PLoS One 2022; 17:e0275614. [PMID: 36227961 PMCID: PMC9560625 DOI: 10.1371/journal.pone.0275614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
In this study we explore the potential of combining traditional zooarchaeological determination and proteomic identification of morphologically non-diagnostic bone fragments (ZooMS) collected from the Uluzzian levels of three Italian sites: Uluzzo C Rock Shelter, Roccia San Sebastiano cave, and Riparo del Broion. Moreover, we obtained glutamine deamidation ratios for all the contexts analysed during routine ZooMS screening of faunal samples, giving information on collagen preservation. We designed a selection protocol that maximizes the efficiency of the proteomics analyses by excluding particularly compromised fragments (e.g. from taphonomic processes), and that aims to identify new human fragments by favouring bones showing morphological traits more similar to Homo. ZooMS consistently provided taxonomic information in agreement with the faunal spectra outlined by traditional zooarchaeology. Our approach allows us to delineate and appreciate differences between the analysed contexts, particularly between the northern and southern sites, related to faunal, environmental, and climate composition, although no human remains were identified. We reconstructed the faunal assemblage of the different sites, giving voice to morphologically undiagnostic bone fragments. Thus, the combination of these analyses provides a more complete picture of the faunal assemblage and of the paleoenvironment during the Middle-Upper Palaeolithic transition in Italy.
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Affiliation(s)
- Sara Silvestrini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Federico Lugli
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Matteo Romandini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Cristina Real
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Eduardo Sommella
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Emanuela Salviati
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Simona Arrighi
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Unità di Ricerca di Preistoria e Antropologia, Università di Siena, Siena, Italy
| | - Eugenio Bortolini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Carla Figus
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | | | - Giulia Marciani
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Unità di Ricerca di Preistoria e Antropologia, Università di Siena, Siena, Italy
| | - Gregorio Oxilia
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Davide Delpiano
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
| | - Antonino Vazzana
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Marcello Piperno
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - Carlo Crescenzi
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Carmine Collina
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - Marco Peresani
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
- Istituto di Geologia Ambientale e Geoingegneria, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Enza Elena Spinapolice
- Dipartimento di Scienze dell’Antichità, Università degli Studi di Roma “La Sapienza”, Roma, Italy
| | - Stefano Benazzi
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
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12
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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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13
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Gianvincenzo FD, Peggie D, Mackie M, Granzotto C, Higgitt C, Cappellini E. Palaeoproteomics guidelines to identify proteinaceous binders in artworks following the study of a 15th-century painting by Sandro Botticelli's workshop. Sci Rep 2022; 12:10638. [PMID: 35739140 PMCID: PMC9226190 DOI: 10.1038/s41598-022-14109-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
Undertaking the conservation of artworks informed by the results of molecular analyses has gained growing importance over the last decades, and today it can take advantage of state-of-the-art analytical techniques, such as mass spectrometry-based proteomics. Protein-based binders are among the most common organic materials used in artworks, having been used in their production for centuries. However, the applications of proteomics to these materials are still limited. In this work, a palaeoproteomic workflow was successfully tested on paint reconstructions, and subsequently applied to micro-samples from a 15th-century panel painting, attributed to the workshop of Sandro Botticelli. This method allowed the confident identification of the protein-based binders and their biological origin, as well as the discrimination of the binder used in the ground and paint layers of the painting. These results show that the approach is accurate, highly sensitive, and broadly applicable in the cultural heritage field, due to the limited amount of starting material required. Accordingly, a set of guidelines are suggested, covering the main steps of the data analysis and interpretation of protein sequencing results, optimised for artworks.
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Affiliation(s)
| | - D Peggie
- National Gallery Scientific Department, London, UK
| | - M Mackie
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - C Granzotto
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Conservation and Science, Art Institute of Chicago, Chicago, IL, USA
| | - C Higgitt
- National Gallery Scientific Department, London, UK
| | - E Cappellini
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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14
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Palmyrene Polychromy: Investigations of Funerary Portraits from Palmyra in the Collections of the Ny Carlsberg Glyptotek, Copenhagen. HERITAGE 2022. [DOI: 10.3390/heritage5020063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The current study is the first comprehensive investigation of the polychromy of Palmyrene funerary portraits. It presents the technical examinations of six portraits (ca. 150–250 CE) from the collection of the Ny Carlsberg Glyptotek, illustrating the marvellous splendour of the cultural heritage of ancient Palmyra. The six portraits were examined with various analytical methods, including microscopy, ultraviolet-induced visible fluorescence imaging and visible light-induced infrared luminescence imaging, X-ray fluorescence spectroscopy, scanning electron microscopy coupled to energy-dispersive X-ray spectroscopy, and Fourier transform infrared spectroscopy. Finally, two samples were collected for liquid chromatography–tandem mass spectrometry to obtain the amino acid sequence information. Various pigments were detected in the polychromy including lapis lazuli, pyromorphite, mimetite, yellow ochre, red ochre, a red lake, lead carbonate, zinc oxide, bone black, and charcoal black. The proteinaceous binding medium was identified as collagen-based and possibly also keratin-based animal glue. The examinations of the Palmyrene portraits in the Ny Carlsberg Glyptotek have proven that these artefacts, despite their current uniform, white appearance, originally presented themselves in a wealth of colours. This is illustrated by the digital reconstructions carried out of two of the examined portraits, which show how the original painting of these portraits would have given them an entirely different expression from what we see today.
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15
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Ntasi G, Palomo IR, Marino G, Piaz FD, Sirano F, Cappellini E, Birolo L, Petrone P. Molecular signatures written in bone proteins of 79 AD victims from Herculaneum and Pompeii. Sci Rep 2022; 12:8401. [PMID: 35624181 PMCID: PMC9142588 DOI: 10.1038/s41598-022-12042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
An extensive proteomic analysis was performed on a set of 12 bones of human victims of the eruption that in AD 79 rapidly buried Pompeii and Herculaneum, allowing the detection of molecular signatures imprinted in the surviving protein components. Bone collagen survived the heat of the eruption, bearing a piece of individual biological history encoded in chemical modifications. Here we show that the human bone proteomes from Pompeii are more degraded than those from the inhabitants of Herculaneum, despite the latter were exposed to temperatures much higher than those experienced in Pompeii. The analysis of the specimens from Pompeii shows lower content of non-collagenous proteins, higher deamidation level and higher extent of collagen modification. In Pompeii, the slow decomposition of victims' soft tissues in the natural dry-wet hydrogeological soil cycles damaged their bone proteome more than what was experienced at Herculaneum by the rapid vanishing of body tissues from intense heat, under the environmental condition of a permanent waterlogged burial context. Results herein presented are the first proteomic analyses of bones exposed to eruptive conditions, but also delivered encouraging results for potential biomarkers that might also impact future development of forensic bone proteomics.
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Affiliation(s)
- Georgia Ntasi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Ismael Rodriguez Palomo
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gennaro Marino
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Department of Humanities, University Suor Orsola Benincasa, Naples, Italy
| | - Fabrizio Dal Piaz
- Department of Medicine, Surgery and Dentistry, University of Salerno, Fisciano, Salerno, Italy
| | | | - Enrico Cappellini
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy. .,Task Force Di Ateneo "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, Naples, Italy.
| | - Pierpaolo Petrone
- Task Force Di Ateneo "Metodologie Analitiche per la Salvaguardia dei Beni Culturali", University of Naples Federico II, Naples, Italy.,Department of Advanced Biomedical Sciences, Departmental Section of Legal Medicine, Anatomy and Histology, University of Naples Federico II, Naples, Italy
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16
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Bonicelli A, Di Nunzio A, Di Nunzio C, Procopio N. Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks. J Proteome Res 2022; 21:1285-1298. [PMID: 35316604 PMCID: PMC9087355 DOI: 10.1021/acs.jproteome.1c00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Indexed: 01/30/2023]
Abstract
Bone is a hard biological tissue and a precious reservoir of information in forensic investigations as it retains key biomolecules commonly used for identification purposes. Bone proteins have recently attracted significant interest for their potential in estimating post-mortem interval (PMI) and age at death (AAD). However, the preservation of such proteins is highly dependent on intrinsic and extrinsic factors that can hinder the potential application of molecular techniques to forensic sciences. The present study aims at investigating the effects that two commonly used types of burial practices (entombment and inhumation) have on bone protein survival. The sample consists of 14 exhumed individuals from cemeteries in Southern Italy with different AADs (29-85 years) and PMIs (1-37 years). LC-MS/MS analyses show that 16 proteins are better preserved under the entombed conditions and 4 proteins are better preserved under the inhumed conditions, whereas no clear differences are detected for post-translational protein modifications. Furthermore, several potential "stable" protein markers (i.e., proteins not affected by the burial environment) are identified for PMI and AAD estimation. Overall, these results show that the two burial environments play a role in the differential preservation of noncollagenous proteins, confirming the potential of LC-MS/MS-based proteomics in forensic sciences.
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Affiliation(s)
- Andrea Bonicelli
- Forensic
Science Research Group, Faculty of Health and Life Sciences, Applied
Sciences, Northumbria University, NE1 8ST Newcastle
Upon Tyne, United Kingdom
| | - Aldo Di Nunzio
- Chemical
Sciences Department, University of Naples
Federico II, 80126 Naples, Italy
| | - Ciro Di Nunzio
- Legal
Medicine Department, University of Catanzaro
Magna Graecia, 88100 Germaneto, Italy
| | - Noemi Procopio
- Forensic
Science Research Group, Faculty of Health and Life Sciences, Applied
Sciences, Northumbria University, NE1 8ST Newcastle
Upon Tyne, United Kingdom
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17
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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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18
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Boudier-Lemosquet A, Mahler A, Bobo C, Dufossée M, Priault M. Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation. Methods 2021; 200:3-14. [PMID: 34843979 DOI: 10.1016/j.ymeth.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/17/2022] Open
Abstract
Our current knowledge on protein deamidation results from a journey that started almost 100 years ago, when a handful of researchers first described the non-enzymatic "desamidation" of glutamine, and the effect of different anions on the catalytic rate of the reaction. Since then, the field has tremendously expended and now finds outreach in very diverse areas. In light of all the recent articles published in these areas, it seemed timely to propose an integrated review on the subject, including a short historical overview of the landmark discoveries in the field, highlighting the current global positioning of protein deamidation in biology and non-biology fields, and concluding with a workflow for those asking if a protein can deamidate, and identify the residues involved. This review is essentially intended to provide newcomers in the field with an overview of how deamidation has penetrated our society and what tools are currently at hand to identify and quantify protein deamidation.
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Affiliation(s)
| | - Adrien Mahler
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Claude Bobo
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Mélody Dufossée
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Muriel Priault
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France.
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19
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The degradation of intracrystalline mollusc shell proteins: A proteomics study of Spondylus gaederopus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140718. [PMID: 34506968 DOI: 10.1016/j.bbapap.2021.140718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/20/2021] [Accepted: 08/31/2021] [Indexed: 11/23/2022]
Abstract
Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a "molecular clock" for geochronological applications. But despite seventy years of ancient protein research, the fundamental aspects of diagenesis-induced changes to protein structures and sequences remain elusive. In this study we investigate the degradation of intracrystalline proteins by performing artificial degradation experiments on the shell of the thorny oyster, Spondylus gaederopus, which is particularly important for archaeological research. We used immunochemistry and tandem mass tag (TMT) quantitative proteomics to simultaneously track patterns of structural loss and of peptide bond hydrolysis. Powdered and bleached shell samples were heated in water at four different temperatures (80, 95, 110, 140 °C) for different time durations. The structural loss of carbohydrate and protein groups was investigated by immunochemical techniques (ELLA and ELISA) and peptide bond hydrolysis was studied by tracking the changes in protein/peptide relative abundances over time using TMT quantitative proteomics. We find that heating does not induce instant organic matrix decay, but first facilitates the uncoiling of cross-linked structures, thus improving matrix detection. We calculated apparent activation energies of structural loss: Ea (carbohydrate groups) = 104.7 kJ/mol, Ea (protein epitopes) = 104.4 kJ/mol, which suggests that secondary matrix structure degradation may proceed simultaneously with protein hydrolysis. While prolonged heating at 110 °C (10 days) results in complete loss of the structural signal, surviving peptide sequences were still observed. Eight hydrolysis-prone peptide bonds were identified in the top scoring shell sequence, the uncharacterised protein LOC117318053 from Pecten maximus. Interestingly, these were not the expected "weak" bonds based on published theoretical stabilities calculated for peptides in solution. This further confirms that intracrystalline protein degradation patterns are complex and that the overall microchemical environment plays an active role in protein stability. Our TMT approach represents a major stepping stone towards developing a model for studying protein diagenesis in biomineralised systems.
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20
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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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21
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Trends in deamidation across archaeological bones, ceramics and dental calculus. Methods 2021; 200:67-79. [PMID: 34450289 DOI: 10.1016/j.ymeth.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 08/14/2021] [Indexed: 11/23/2022] Open
Abstract
The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.
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22
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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23
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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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24
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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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25
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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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26
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On the standardization of ZooMS nomenclature. J Proteomics 2020; 235:104041. [PMID: 33160104 DOI: 10.1016/j.jprot.2020.104041] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/14/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes. With new researchers beginning to use the method, it is imperative that a user-friendly, standardized approach be established. A major barrier has been the often haphazard and changing nomenclature used to label peptide markers necessary for taxonomic identification. Consistent, reliable, and easy-to-understand nomenclature is key to the growth of ZooMS, particularly as the reference library continues to expand. We propose a new set of standardized guidelines for peptide markers based on their position in the type I collagen sequence from the beginning of the highly conserved, helical region. Since this region has no insertions or deletions over a wide range of taxonomic groups, the proposed nomenclature system can be used reliably and consistently across all vertebrate taxa. We propose to label ZooMS peptide markers with the gene, followed by the position of the first and last amino acid of the marker from the start of the helical region. SIGNIFICANCE STATEMENT: We propose a standardized nomenclature system for ZooMS peptide markers that provides consistent labels across multiple, broad taxonomic groups. This system unambiguously locates the marker peptides in the type I collagen sequence, avoids duplication of marker names, and facilitates the creation of large ZooMS databases which can include all vertebrates.
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27
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Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia. Sci Rep 2020; 10:16674. [PMID: 33028848 PMCID: PMC7541484 DOI: 10.1038/s41598-020-73542-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022] Open
Abstract
The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for molecular phylogenetic reconstructions of ancient fauna previously thought to be unreachable using ancient DNA.
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28
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Lanigan LT, Mackie M, Feine S, Hublin JJ, Schmitz RW, Wilcke A, Collins MJ, Cappellini E, Olsen JV, Taurozzi AJ, Welker F. Multi-protease analysis of Pleistocene bone proteomes. J Proteomics 2020; 228:103889. [DOI: 10.1016/j.jprot.2020.103889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
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29
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Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature 2020; 581:299-302. [DOI: 10.1038/s41586-020-2259-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
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30
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A 14C chronology for the Middle to Upper Palaeolithic transition at Bacho Kiro Cave, Bulgaria. Nat Ecol Evol 2020; 4:794-801. [DOI: 10.1038/s41559-020-1136-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022]
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31
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Vilanova C, Porcar M. Art-omics: multi-omics meet archaeology and art conservation. Microb Biotechnol 2020; 13:435-441. [PMID: 31452355 PMCID: PMC7017809 DOI: 10.1111/1751-7915.13480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/10/2019] [Indexed: 11/30/2022] Open
Abstract
Multi-omics can informally be described as the combined use of high-throughput techniques allowing the characterization of complete microbial communities by the sequencing/identification of total pools of biomolecules including DNA, proteins or metabolites. These techniques have allowed an unprecedented level of knowledge on complex microbial ecosystems, which is having key implications in land and marine ecology, industrial biotechnology or biomedicine. Multi-omics have recently been applied to artistic or archaeological objects, with the goal of either contributing to shedding light on the original context of the pieces and/or to inform conservation approaches. In this minireview, we discuss the application of -omic techniques to the study of prehistoric artworks and ancient man-made objects in three main technical blocks: metagenomics, proteomics and metabolomics. In particular, we will focus on how proteomics and metabolomics can provide paradigm-breaking results by unambiguously identifying peptides associated with a given, palaeo-cultural context; and we will discuss how metagenomics can be central for the identification of the microbial keyplayers on artworks surfaces, whose conservation can then be approached by a range of techniques, including using selected microorganisms as 'probiotics' because of their direct or indirect effect in the stabilization and preservation of valuable art objects.
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Affiliation(s)
- Cristina Vilanova
- Darwin Bioprospecting Excellence SLCatedrático Agustín Escardino, 946980PaternaSpain
| | - Manuel Porcar
- Darwin Bioprospecting Excellence SLCatedrático Agustín Escardino, 946980PaternaSpain
- Institute for Integrative Systems BiologyISysBio (Universitat de València‐CSIC)Parc Científic de la Universitat de ValènciaC. Catedràtic José Beltrán 246980PaternaSpain
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32
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Abstract
Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam samples derived originally from sperm whales (Physeter macrocephalus). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.
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Affiliation(s)
- Ruairidh Macleod
- Section for EvoGenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.,Homerton College, University of Cambridge, Hills Road, Cambridge CB2 8PH, UK
| | - Mikkel-Holger S Sinding
- Section for EvoGenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.,Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Morten Tange Olsen
- Section for EvoGenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark
| | - Matthew J Collins
- Section for EvoGenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.,McDonald Institute for Archaeological Research, Department of Archaeology and Anthropology, University of Cambridge, West Tower, Downing Street, Cambridge CB2 3ER, UK
| | - Steven J Rowland
- Biogeochemistry Research Centre, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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33
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Sinet-Mathiot V, Smith GM, Romandini M, Wilcke A, Peresani M, Hublin JJ, Welker F. Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy). Sci Rep 2019; 9:12350. [PMID: 31451791 PMCID: PMC6710433 DOI: 10.1038/s41598-019-48706-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Collagen type I fingerprinting (ZooMS) has recently been used to provide either palaeoenvironmental data or to identify additional hominin specimens in Pleistocene contexts, where faunal assemblages are normally highly fragmented. However, its potential to elucidate hominin subsistence behaviour has been unexplored. Here, ZooMS and zooarchaeology have been employed in a complementary approach to investigate bone assemblages from Final Mousterian and Uluzzian contexts at Fumane cave (Italy). Both approaches produced analogous species composition, but differ significantly in species abundance, particularly highlighted by a six fold-increase in the quantity of Bos/Bison remains in the molecularly identified component. Traditional zooarchaeological methods would therefore underestimate the proportion of Bos/Bison in these levels to a considerable extent. We suggest that this difference is potentially due to percussion-based carcass fragmentation of large Bos/Bison bone diaphyses. Finally, our data demonstrates high variability in species assignment to body size classes based on bone cortical thickness and fragment size. Thus, combining biomolecular and traditional zooarchaeological methods allows us to refine our understanding of bone assemblage composition associated with hominin occupation at Fumane.
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Affiliation(s)
- Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matteo Romandini
- University of Bologna, Department of Cultural Heritage, Ravenna, Italy.,University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Marco Peresani
- University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy.
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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34
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Simpson JP, Fascione M, Bergström E, Wilson J, Collins MJ, Penkman KE, Thomas‐Oates J. Ionisation bias undermines the use of matrix-assisted laser desorption/ionisation for estimating peptide deamidation: Synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1049-1057. [PMID: 30908787 PMCID: PMC6594239 DOI: 10.1002/rcm.8441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI). METHODS We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)). RESULTS When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed. CONCLUSIONS MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.
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Affiliation(s)
| | | | - Ed Bergström
- Department of ChemistryUniversity of YorkYorkUK
- Centre of Excellence in Mass SpectrometryUniversity of YorkYorkUK
| | - Julie Wilson
- Department of ChemistryUniversity of YorkYorkUK
- Department of MathematicsUniversity of YorkYorkUK
| | | | | | - Jane Thomas‐Oates
- Department of ChemistryUniversity of YorkYorkUK
- Centre of Excellence in Mass SpectrometryUniversity of YorkYorkUK
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35
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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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36
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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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37
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Shevchenko A, Schuhmann A, Thomas H, Wetzel G. Fine Endmesolithic fish caviar meal discovered by proteomics in foodcrusts from archaeological site Friesack 4 (Brandenburg, Germany). PLoS One 2018; 13:e0206483. [PMID: 30485287 PMCID: PMC6261446 DOI: 10.1371/journal.pone.0206483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/12/2018] [Indexed: 01/19/2023] Open
Abstract
The role of aquatic resources in ancient economies and paleodiet is important for understanding the evolution of prehistorical societies. Charred food remains from ancient pottery are valuable molecular evidence of dietary habits in antiquity. However, conventional archaeometric approaches applied in their analysis lack organismal specificity, are affected by abundant environmental contaminants, do not elucidate food processing recipes and are limited in the inland regions where diverse dietary resources are available. We performed proteomics analysis of charred organic deposits adhered on early ceramics from Mesolithic-Neolithic inland site Friesack 4 (Brandenburg, Germany). One of pots—a small coarse bowl radiocarbon dated to the end of the 5th millennium BC—was attributed to Endmesolithic pottery. Proteomics of foodcrust from this vessel identified fine carp roe meal and revealed details of a prehistorical culinary recipe. Ancient proteins were unequivocally distinguished from contemporary contaminants by computing deamidation ratios of glutamine residues. These data paint a broader picture of the site-specific exploitation of aquatic resources and contribute to better understanding of the dietary context of Neolithic transition in European inland.
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Affiliation(s)
- Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Andrea Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Günter Wetzel
- Brandenburgisches Landesamt für Denkmalpflege und Archaeologisches Landesmuseum (BLDAM), Aussenstelle Cottbus, Germany
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38
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Procopio N, Chamberlain AT, Buckley M. Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine. J Proteome Res 2018; 17:1000-1013. [PMID: 29356547 DOI: 10.1021/acs.jproteome.7b00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomic analyses are becoming more widely used in archeology not only due to the greater preservation of proteins in ancient specimens than DNA but also because they can offer different information, particularly relating to compositional preservation and potentially a means to estimate biological and geological age. However, it remains unclear to what extent different burial environments impact these aspects of proteome decay. Teeth have to date been much less studied than bone but are ideal to explore how proteins decay with time due to the negligible turnover that occurs in dentine relative to bone. We investigated the proteome variability and deamidation levels of different sections of molar teeth from archeological bovine mandibles as well as their mandibular bone. We obtained a greater yield of proteins from the crown of the teeth but did not find differences between the different molars analyzed within each mandible. We also obtained the best variety of protein from a well-preserved mandible that was not the youngest one in terms of chronological age, showing the influence of the preservation conditions on the final proteomic outcome. Intriguingly, we also noticed an increase in abundance levels of fetuin-A in biologically younger mandibles as reported previously, but the opposite trend in tooth dentine. Interestingly, we observed higher glutamine deamidation levels in teeth from the geologically oldest mandible despite it being the biologically youngest specimen, showing that the archeological age strongly impacts on the level of deamidations observed, much more so than biological aging. This indicates that the glutamine deamidation ratio of selected peptides may act as a good predictor of the relative geochronological age of archeological specimens.
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Affiliation(s)
- Noemi Procopio
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Andrew T Chamberlain
- School of Earth and Environmental Sciences, The University of Manchester , Stopford Building, 99 Oxford Road, Manchester M13 9PG, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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39
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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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40
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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: 23] [Impact Index Per Article: 3.3] [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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41
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Dominguez-Vega E, De Vijlder T, Romijn EP, Somsen GW. Capillary electrophoresis-tandem mass spectrometry as a highly selective tool for the compositional and site-specific assessment of multiple peptide-deamidation. Anal Chim Acta 2017; 982:122-130. [PMID: 28734351 DOI: 10.1016/j.aca.2017.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/06/2017] [Accepted: 06/11/2017] [Indexed: 12/20/2022]
Abstract
Site-specific mapping of multiple deamidations in peptides is a challenging analytical task. In this work, capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) is presented as a high-resolution tool for the detailed characterization of these subtle modifications in peptides. The 4.5-kDa peptide drug TRI-1144, which contains five closely-positioned potential deamidation sites, was selected as model compound. TRI-1144 was exposed to acidic conditions and/or elevated temperatures for 1-14 h. Stressed samples were analyzed using a background electrolyte (BGE) of 150 mM ammonium formate (pH 6.0) in combination with a capillary coated with a bilayer of Polybrene-dextran sulfate. Separation of deamidated and deacetylated TRI-1144 species, including several positional isomers, was greatly enhanced by adding up to 40 vol% of acetonitrile-isopropanol (87.5:12.5, v/v) to the BGE, allowing reliable determination of the number of deamidations/deacetylations per degradation product. Collision-induced dissociation MS/MS was conducted on the separated peptide components in order to reveal the exact position of deamidation on the peptide chain. Obtained fragment ions showed overlapping isotopic distributions in their MS/MS spectra resulting from the comigration of different isomeric deamidated species. Comparison of theoretical and measured isotope distributions for specific y ions of peptide fragments yielded the identity and relative abundance of isomeric deamidated products. The developed CE-MS/MS methodology was used for the highly selective evaluation of TRI-1144 stability under different stress conditions, providing detailed qualitative and semi-quantitative degradation maps of the peptide drug.
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Affiliation(s)
- Elena Dominguez-Vega
- Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | - Thomas De Vijlder
- Pharmaceutical Development and Manufacturing Sciences, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Edwin P Romijn
- Pharmaceutical Development and Manufacturing Sciences, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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42
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Gallart-Palau X, Serra A, Sze SK. LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics. J Vis Exp 2017. [PMID: 28448026 DOI: 10.3791/55626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in human pathology and other biochemical contexts. In order to perform characterization of protein deamidation, we have recently developed a novel long-length electrostatic repulsion-hydrophilic interaction chromatography-tandem mass spectrometry (LERLIC-MS/MS) method which can separate the glutamine (Gln) and asparagine (Asn) isoform products of deamidation from model compounds to highly complex biological samples. LERLIC-MS/MS is, therefore, the first shotgun proteomics strategy for the separation and quantification of Gln deamidation isoforms. We also demonstrate, as a novelty, that the sample processing protocol outlined here stabilizes the succinimide intermediate allowing its characterization by LERLIC-MS/MS. Application of LERLIC-MS/MS as shown in this video article can help to elucidate the currently unknown molecular arrays of protein deamidation. Additionally, LERLIC-MS/MS provides further understanding of the enzymatic reactions that encompass deamidation in distinct biological backgrounds.
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Affiliation(s)
- Xavier Gallart-Palau
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University
| | - Aida Serra
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University
| | - Siu Kwan Sze
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University;
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43
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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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44
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Affiliation(s)
- Noemi Procopio
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Michael Buckley
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
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45
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Vinciguerra R, De Chiaro A, Pucci P, Marino G, Birolo L. Proteomic strategies for cultural heritage: From bones to paintings. Microchem J 2016. [DOI: 10.1016/j.microc.2015.12.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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46
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Cleland TP, Schroeter ER, Schweitzer MH. Biologically and diagenetically derived peptide modifications in moa collagens. Proc Biol Sci 2016; 282:20150015. [PMID: 25972464 DOI: 10.1098/rspb.2015.0015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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47
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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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48
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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49
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Boles GC, Coates RA, Berden G, Oomens J, Armentrout PB. Experimental and Theoretical Investigations of Infrared Multiple Photon Dissociation Spectra of Glutamine Complexes with Zn2+ and Cd2+. J Phys Chem B 2015; 119:11607-17. [DOI: 10.1021/acs.jpcb.5b06528] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia C. Boles
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Rebecca A. Coates
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, NL-6525 ED Nijmegen, The Netherlands
- Van‘t
Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P. B. Armentrout
- Department
of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112, United States
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50
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Solazzo C, Wilson J, Dyer JM, Clerens S, Plowman JE, von Holstein I, Walton Rogers P, Peacock EE, Collins MJ. Modeling Deamidation in Sheep α-Keratin Peptides and Application to Archeological Wool Textiles. Anal Chem 2013; 86:567-75. [DOI: 10.1021/ac4026362] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline Solazzo
- BioArCh, Biology
(S Block), Wentworth Way, University of York, York YO10 5DD, U.K
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
| | - Julie Wilson
- Department
of Mathematics, University of York, York YO10 5YW, U.K
- Department
of Chemistry, University of York, York YO10 5YW, U.K
| | - Jolon M. Dyer
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
- Biomolecular Interaction
Centre, School of Biological Sciences, University of Canterbury, Private Bag
4800, Christchurch 8140, New Zealand
- Riddet Institute, Massey University, Private
Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Clerens
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
| | - Jeffrey E. Plowman
- Proteins
and Biomaterials, AgResearch Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand
| | | | | | - Elizabeth E. Peacock
- NTNU
University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Department
of Conservation, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Matthew J. Collins
- BioArCh, Biology
(S Block), Wentworth Way, University of York, York YO10 5DD, U.K
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