Palaeoproteomics to Unleash Studies on Human History

Auteurs: Jülide Kubat, Alessia Nava, Luca Bondioli, Christopher Dean, Clément Zanolli, Nicolas Bourgon, Anne-Marie Bacon, Fabrice Demeter, Beatrice Peripoli, Patrick Mahoney, Richard Albert, Ottmar Kullmer, Friedemann Schrenk, Wolfgang Müller
Publié dans: Nature Ecology and Evolution, Numéro Volume 7, 2023, ISSN 2397-334X
Éditeur: Nature Publishing Group
DOI: 10.21203/rs.3.rs-940427/v1

Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics

Auteurs: Anders H. Kverneland, Florian Harking, Joel Mario Vej-Nielsen, Magnus Huusfeldt, Dorte B. Bekker-Jensen, Inge Marie Svane, Nicolai Bache, Jesper V. Olsen
Publié dans: Molecular & Cellular Proteomics, Numéro 23, 2024, Page(s) 100790, ISSN 1535-9476
Éditeur: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2024.100790

Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics

Auteurs: Claire Koenig, Patricia Bortel, Ryan S. Paterson, Barbara Rendl, Palesa P. Madupe, Gaudry B. Troché, Nuno Vibe Hermann, Marina Martínez de Pinillos, María Martinón-Torres, Sandra Mularczyk, Marie Louise Schjellerup Jørkov, Christopher Gerner, Fabian Kanz, Ana Martinez-Val, Enrico Cappellini, Jesper V. Olsen
Publié dans: Journal of Proteome Research, 2024, ISSN 1535-3893
Éditeur: American Chemical Society
DOI: 10.1021/acs.jproteome.4c00557

Species identification of ivory and bone museum objects using minimally invasive proteomics

Auteurs: Catherine Gilbert, Vaclav Krupicka, Francesca Galluzzi, Aleksandra Popowich, Katell Bathany, Stéphane Claverol, Julie Arslanoglu, Caroline Tokarski
Publié dans: Science Advances, Numéro 10, 2024, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/sciadv.adi9028

Successive Protein Extraction Using Hydroxylamine to Increase the Depth of Proteome Coverage in Fresh, Forensic, and Archaeological Bones

Auteurs: Catherine Gilbert, Katell Bathany, Stéphane Claverol, Quentin Scanvion, Valery Hedouin, Benoit Bertrand, Caroline Tokarski
Publié dans: Analytical Chemistry, Numéro 96, 2024, Page(s) 3247-3252, ISSN 0003-2700
Éditeur: American Chemical Society
DOI: 10.1021/acs.analchem.3c02803

Human‐like enamel growth in <i>Homo naledi</i>

Auteurs: Patrick Mahoney, Gina McFarlane, Alberto J. Taurozzi, Palesa P. Madupe, Mackie C. O'Hara, Keneiloe Molopyane, Enrico Cappellini, John Hawks, Matthew M. Skinner, Lee Berger
Publié dans: American Journal of Biological Anthropology, Numéro 184, 2024, ISSN 2692-7691
Éditeur: John Wiley & Sons for the American Association of Biological Anthropologists
DOI: 10.1002/ajpa.24893

Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel

Auteurs: Alberto J. Taurozzi, Patrick L. Rüther, Ioannis Patramanis, Claire Koenig, Ryan Sinclair Paterson, Palesa P. Madupe, Florian Simon Harking, Frido Welker, Meaghan Mackie, Jazmín Ramos-Madrigal, Jesper V. Olsen, Enrico Cappellini
Publié dans: Nature Protocols, Numéro 19, 2024, Page(s) 2085-2116, ISSN 1754-2189
Éditeur: Nature Publishing Group
DOI: 10.1038/s41596-024-00975-3

Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo

Auteurs: Jülide Kubat, Ryan Paterson, Ioannis Patramanis, Graeme Barker, Fabrice Demeter, Arnaud Filoux, Ottmar Kullmer, Meaghan Mackie, Tomas Marques-Bonet, Nguyen Thi Mai Huong, Nguyen Anh Tuan, Sytha Pheng, Jessica Rippengal, Friedemann Schrenk, Viengkeo Souksavatdy, Lim Tze Tshen, Athiwat Wattanapituksakul, Wei Wang, Clément Zanolli, Enrico Cappellini, Anne-Marie Bacon
Publié dans: PLOS ONE, Numéro 18, 2023, Page(s) e0291308, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0291308

The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany

Auteurs: Geoff M. Smith, Karen Ruebens, Elena Irene Zavala, Virginie Sinet-Mathiot, Helen Fewlass, Sarah Pederzani, Klervia Jaouen, Dorothea Mylopotamitaki, Kate Britton, Hélène Rougier, Mareike Stahlschmidt, Matthias Meyer, Harald Meller, Holger Dietl, Jörg Orschiedt, Johannes Krause, Tim Schüler, Shannon P. McPherron, Marcel Weiss, Jean-Jacques Hublin, Frido Welker
Publié dans: Nature Ecology & Evolution, Numéro 8, 2024, Page(s) 564-577, ISSN 2397-334X
Éditeur: Nature Publishing Group
DOI: 10.1038/s41559-023-02303-6

Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses

Auteurs: Louise Le Meillour, Virginie Sinet-Mathiot, Ragnheiður Diljá Ásmundsdóttir, Jakob Hansen, Dorothea Mylopotamitaki, Gaudry Troché, Huan Xia, Jorsua Herrera Bethencourt, Karen Ruebens, Geoff M. Smith, Zandra Fagernäs, Frido Welker
Publié dans: iScience, Numéro 27, 2024, Page(s) 109432, ISSN 2589-0042
Éditeur: Cell Press
DOI: 10.1016/j.isci.2024.109432

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

Auteurs: Dorothea Mylopotamitaki, Marcel Weiss, Helen Fewlass, Elena Irene Zavala, Hélène Rougier, Arev Pelin Sümer, Mateja Hajdinjak, Geoff M. Smith, Karen Ruebens, Virginie Sinet-Mathiot, Sarah Pederzani, Elena Essel, Florian S. Harking, Huan Xia, Jakob Hansen, André Kirchner, Tobias Lauer, Mareike Stahlschmidt, Michael Hein, Sahra Talamo, Lukas Wacker, Harald Meller, Holger Dietl, Jörg Orschiedt, J
Publié dans: Nature, Numéro 626, 2024, Page(s) 341-346, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-023-06923-7

Palaeoproteomic identification of the original binder and modern contaminants in distemper paints from Uvdal stave church, Norway

Auteurs: Zahra Haghighi, Meaghan Mackie, Anne Apalnes Ørnhøi, Abigail Ramsøe, Tone Marie Olstad, Simon James Armitage, Christopher Stuart Henshilwood, Enrico Cappellini
Publié dans: Scientific Reports, Numéro 14, 2024, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-024-63455-4

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Auteurs: Ioannis Patramanis, Jazmín Ramos-Madrigal, Enrico Cappellini, Fernando Racimo
Publié dans: Peer Community Journal, Numéro 3, 2023, ISSN 2804-3871
Éditeur: PCI Organization
DOI: 10.24072/pcjournal.344

Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics

Auteurs: Patricia Bortel, Ilaria Piga, Claire Koenig, Christopher Gerner, Ana Martinez-Val, Jesper V. Olsen
Publié dans: Molecular & Cellular Proteomics, Numéro 23, 2024, Page(s) 100754, ISSN 1535-9476
Éditeur: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.mcpro.2024.100754

Hybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids

Auteurs: Ana Martínez-Val, Kyle Fort, Claire Koenig, Leander Van der Hoeven, Giulia Franciosa, Thomas Moehring, Yasushi Ishihama, Yu-ju Chen, Alexander Makarov, Yue Xuan, Jesper V. Olsen
Publié dans: Nature Communications, Numéro Volume 14, issue number 1, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1101/2022.12.19.520999

Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing

Auteurs: Claire Koenig, Ana Martinez-Val, Giulia Franciosa, Jesper V. Olsen
Publié dans: PROTEOMICS, Numéro Volume 22, issue number 19-20, 2022, Page(s) e2100245, ISSN 1615-9853
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202100245

Stable isotopes show Homo sapiens dispersed into cold steppes ~45,000 years ago at Ilsenhöhle in Ranis, Germany

Auteurs: Sarah Pederzani, Kate Britton, Manuel Trost, Helen Fewlass, Nicolas Bourgon, Jeremy McCormack, Klervia Jaouen, Holger Dietl, Hans-Jürgen Döhle, André Kirchner, Tobias Lauer, Mael Le Corre, Shannon P. McPherron, Harald Meller, Dorothea Mylopotamitaki, Jörg Orschiedt, Hélène Rougier, Karen Ruebens, Tim Schüler, Virginie Sinet-Mathiot, Geoff M. Smith, Sahra Talamo, Thomas Tütken, Frido Welker
Publié dans: Nature Ecology & Evolution, Numéro 8, 2024, Page(s) 578-588, ISSN 2397-334X
Éditeur: Nature Publishing Group
DOI: 10.1038/s41559-023-02318-z

Cofilin-Driven Nuclear Deformation Drives Dendritic Cell Migration through the Extracellular Matrix

Auteurs: Harry Warner, Giulia Franciosa, Guus van der Borg, Felix Faas, Claire Koenig, Rinse de Boer, René Classens, Sjors Maassen, Maksim Baranov, Shweta Mahajan, Deepti Dabral, Britt Coenen, Frans Bianchi, Niek van Hilten, Herre Jelger Risselada, Wouter H. Roos, Jesper Olsen, Laia Querol Cano, Geert van den Bogaart
Publié dans: Cell Reports, Numéro Volume 43, issue number 3, 2023, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1101/2023.07.10.548429

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

Auteurs: Ulises H. Guzman, Ana Martinez-Val, Zilu Ye, Eugen Damoc, Tabiwang N. Arrey, Anna Pashkova, Santosh Renuse, Eduard Denisov, Johannes Petzoldt, Amelia C. Peterson, Florian Harking, Ole Østergaard, Rasmus Rydbirk, Susana Aznar, Hamish Stewart, Yue Xuan, Daniel Hermanson, Stevan Horning, Christian Hock, Alexander Makarov, Vlad Zabrouskov, Jesper V. Olsen
Publié dans: Nature Biotechnology, 2024, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-023-02099-7

Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands

Auteurs: Joannes A. A. Dekker, Dorothea Mylopotamitaki, Annemieke Verbaas, Virginie Sinet-Mathiot, Samantha Presslee, Morgan L. McCarthy, Morten Tange Olsen, Jesper V. Olsen, Youri van den Hurk, Joris Brattinga, Frido Welker
Publié dans: Peer Community Journal, Numéro 4, 2024, ISSN 2804-3871
Éditeur: PCI Organization
DOI: 10.24072/pcjournal.451

Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification

Auteurs: Dorothea Mylopotamitaki, Florian S. Harking, Alberto J. Taurozzi, Zandra Fagernäs, Ricardo M. Godinho, Geoff M. Smith, Marcel Weiss, Tim Schüler, Shannon P. McPherron, Harald Meller, João Cascalheira, Nuno Bicho, Jesper V. Olsen, Jean-Jacques Hublin, Frido Welker
Publié dans: Scientific Reports, Numéro 13, 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-44885-y

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Auteurs: Ana Martinez-Val, Dorte B. Bekker-Jensen, Sophia Steigerwald, Claire Koenig, Ole Østergaard, Adi Mehta, Trung Tran, Krzysztof Sikorski, Estefanía Torres-Vega, Ewa Kwasniewicz, Sólveig Hlín Brynjólfsdóttir, Lisa B. Frankel, Rasmus Kjøbsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen & Jesper V. Olsen
Publié dans: Nature Communications, Numéro Volume 12, issue number 1, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

Auteurs: Ryan S. Paterson, Meaghan Mackie, Alessio Capobianco, Nicola S. Heckeberg, Danielle Fraser, Fazeelah Munir, Ioannis Patramanis, Jazmín Ramos-Madrigal, Shanlin Liu, Abigail D. Ramsøe, Marc R. Dickinson, Chloë Baldreki, Marisa Gilbert, Raffaele Sardella, Luca Bellucci, Gabriele Scorrano, Fernando Racimo, Eske Willerslev, Kirsty E.H. Penkman, Jesper V. Olsen, Ross D.E. MacPhee, Natalia Rybczynski,
Publié dans: BioRxiv, 2024, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.06.07.597871

Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra

Auteurs: Petra Gutenbrunner, Pelagia Kyriakidou, Frido Welker and Jürgen Cox
Publié dans: bioRxiv, Numéro 6-Sep-21, 2021
Éditeur: The preprint server for biologi
DOI: 10.1101/2021.09.04.458985

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Auteurs: Ricardo Fong Zazueta, Johanna Krueger, David M. Alba, Xènia Aymerich, Robin M. D. Beck, Enrico Cappellini, Guillermo Carrillo Martín, Omar Cirilli, Nathan Clark, Omar E. Cornejo, Kyle Kai-How Farh, Luis Ferrández-Peral, David Juan, Joanna L. Kelley, Lukas F. K. Kuderna, Jordan Little, Joseph D. Orkin, Ryan S. Paterson, Harvinder Pawar, Tomas Marques-Bonet, Esther Lizano
Publié dans: BioRxiv, 2024, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.28.580462

Enamel proteins reveal biological sex and genetic variability within southern African<i>Paranthropus</i>

Auteurs: Palesa P. Madupe, Claire Koenig, Ioannis Patramanis, Patrick L. Rüther, Nomawethu Hlazo, Meaghan Mackie, Mirriam Tawane, Johanna Krueger, Alberto J. Taurozzi, Gaudry Troché, Job Kibii, Robyn Pickering, Marc Dickinson, Yonatan Sahle, Dipuo Kgotleng, Charles Musiba, Fredrick Manthi, Liam Bell, Michelle DuPlessis, Catherine Gilbert, Bernhard Zipfel, Lukas F. K. Kuderna, Esther Lizano, Frido Welker,
Publié dans: BioRxiv, 2023
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.03.547326

Oreopithecus bambolii: Does “Molecular Paleontology” can help us in better understanding such a peculiar fossil Ape?

Auteurs: Cieszynska W.K.C., Pandolfi L. & Rook L.
Publié dans: Paleodays 2021 Abstract Book, Numéro 2021,XXI Convegno della Società Paleontologica Italiana, live virtual edition, 2021, Page(s) p.35
Éditeur: Paleodays 2021. Abstract book del XXI Convegno della Società Paleontologica Italiana, live virtual edition
DOI: 10.5281/zenodo.4983943

Oreopithecus bambolii and its ecosystem: More than a century of research on a peculiar hominoid-bearing site

Auteurs: Cieszynska W.K.C., Pandolfi L. & Rook L.
Publié dans: Abstract book of the XVIII annual conference of the European Association of Vertebrate Palaeontologists, Numéro 5th-9th July 2021, 2021, Page(s) p.54
Éditeur: The European Association of Vertebrate Palaeontologists; Belvedere M., Díez Díaz V., Mecozzi B., Sardella R
DOI: 10.18563/pv.eavp2021

The feasibility of palaeoproteomics for studying ancient hominins from South Africa

Auteurs: Palesa Madupe, Nomawethu, Hlazo Patrick L. Rüther, Meaghan Mackie, Frido Welker, Jazmin Ramos Madrigal, Ioannis Patramanis, Fernando Racimo, Lauren Schroeder, Jesper V. Olsen, Rebecca R. Ackermann And, Enrico Cappellini
Publié dans: Journal of the American Association of Biological Anthropologists, Numéro 16 March 2022, 2022, Page(s) 112
Éditeur: AAPA ABSTRACTS
DOI: 10.1002/ajpa.24514

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