1
|
Hansen J, Sierra A, Mata S, Gassiot Ballbè E, Rey Lanaspa J, Welker F, Saña Seguí M, Clemente Conte I. Combining traceological analysis and ZooMS on Early Neolithic bone artefacts from the cave of Coro Trasito, NE Iberian Peninsula: Cervidae used equally to Caprinae. PLoS One 2024; 19:e0306448. [PMID: 38985699 PMCID: PMC11236160 DOI: 10.1371/journal.pone.0306448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024] Open
Abstract
Few studies have combined the analysis of use-wear traces, traceology, and the proteomic taxonomic identification method Zooarchaeology by Mass Spectrometry (ZooMS). Traceology provides information on the usage, in this case, of bone artefacts, while ZooMS allows for taxonomic identifications where diagnostic features are otherwise gone. The approaches therefore offer complementary information on bone artefacts, allowing for insights into species selection strategies in bone tool manufacture and their subsequent use. Here we present a case study of 20 bone artefacts, mainly bone points, from the Early Neolithic cave site of Coro Trasito located on the southern slope of the Central Pyrenees. Hitherto, studies on Early Neolithic bone artefacts from the Iberian Peninsula have suggested based on morphological assessments that Ovis aries/Capra hircus constituted the majority of the bone material selected for bone tool production. However, the taxonomic identification in this study suggests that, at this site, Cervidae was selected equally to that of O. aries/C. hircus. Furthermore, bone artefacts made from Cervidae specimens seem to be utilised in a wider range of artefact types compared to O. aries/C. hircus. Coro Trasito's bone artefact species composition is probably site-specific to some degree, however, morphological assessments of bone artefacts might not be representative and could be biased towards certain species. Therefore, research on bone artefacts' usage could possibly gain new insights by implementing ZooMS in combination with traceology.
Collapse
Affiliation(s)
- Jakob Hansen
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Sierra
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sergi Mata
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | | | - Javier Rey Lanaspa
- Departamento de Educación, Cultura y Deporte, Diputación General de Aragón, Zaragoza, Aragón, Spain
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Maria Saña Seguí
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Ignacio Clemente Conte
- Departamento de Arqueología y Antropología, Institución Milá y Fontanals de Estudios en Humanidades (IMF), del Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Barcelona, Spain
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Bonicelli A, Mickleburgh HL, Chighine A, Locci E, Wescott DJ, Procopio N. The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics. eLife 2022; 11:e83658. [PMID: 36583441 PMCID: PMC9803353 DOI: 10.7554/elife.83658] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.
Collapse
Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
| | - Hayley L Mickleburgh
- Amsterdam Centre for Ancient Studies and Archaeology (ACASA) – Department of Archaeology, Faculty of Humanities, University of AmsterdamAmsterdamNetherlands
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Alberto Chighine
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Emanuela Locci
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Daniel J Wescott
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Brandt LØ, Taurozzi AJ, Mackie M, Sinding MHS, Vieira FG, Schmidt AL, Rimstad C, Collins MJ, Mannering U. Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade. PLoS One 2022; 17:e0270040. [PMID: 35895633 PMCID: PMC9328512 DOI: 10.1371/journal.pone.0270040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/02/2022] [Indexed: 11/18/2022] Open
Abstract
Fur is known from contemporary written sources to have been a key commodity in the Viking Age. Nevertheless, the fur trade has been notoriously difficult to study archaeologically as fur rarely survives in the archaeological record. In Denmark, fur finds are rare and fur in clothing has been limited to a few reports and not recorded systematically. We were therefore given access to fur from six Danish high status graves dated to the Viking Age. The fur was analysed by aDNA and palaeoproteomics methods to identify the species of origin in order to explore the Viking Age fur trade. Endogenous aDNA was not recovered, but fur proteins (keratins) were analysed by MALDI-TOF-MS and LC-MS/MS. We show that Viking Age skin clothing were often composites of several species, showing highly developed manufacturing and material knowledge. For example, fur was produced from wild animals while leather was made of domesticates. Several examples of beaver fur were identified, a species which is not native to Denmark, and therefore indicative of trade. We argue that beaver fur was a luxury commodity, limited to the elite and worn as an easily recognisable indicator of social status.
Collapse
Affiliation(s)
- Luise Ørsted Brandt
- The GLOBE Institute, University of Copenhagen, København K, Denmark
- * E-mail:
| | | | - Meaghan Mackie
- The GLOBE Institute, University of Copenhagen, København K, Denmark
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, København K, Denmark
| | | | | | | | | | | | | |
Collapse
|
6
|
Are We Betting on the Wrong Horse? Insignificant Archaeological Leather Fragments Provide the First Evidence for the Exploitation of Horsehide in Renaissance Denmark. HERITAGE 2022. [DOI: 10.3390/heritage5020053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Large archaeological, organic materials can be difficult to preserve, conserve, and store in their entirety, which is why prioritisation is often necessary. Priority is generally given to recognisable objects rather than smaller fragments. Nevertheless, for archaeological leather, exactly such insignificant fragments can provide new information on the diversity of species exploited. In this pilot study, we use a Citizen Science approach for the first time to identify archaeological leather fragments using the protein-based method Zooarchaeology by Mass Spectrometry (ZooMS). By inviting the public to participate in archaeological research, the project’s first 52 samples, including both recognisable and unidentifiable objects, were analysed. We show that the participants not only generated good data, but also contributed to current knowledge by identifying two hitherto undescribed animal species for leather in medieval and Renaissance Copenhagen. The finding of deer suggests that Copenhagen citizens now and then had access to game through the nobility and the finding of horse suggests that the unclean status of horses was sometimes overlooked to exploit its hide. Our findings are promising for more identifications and the new knowledge the project will generate. The study calls into question how we prioritise and assign value to cultural heritage materials.
Collapse
|
7
|
Welker F. Editorial. J Proteomics 2021; 253:104460. [PMID: 34955453 DOI: 10.1016/j.jprot.2021.104460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Frido Welker
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|