Palaeoproteomics to Unleash Studies on Human History

Deliverables

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Publications

Dietary strategies of Pleistocene Pongo sp. and Homo erectus on Java (Indonesia)

Author(s): 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
Published in: Nature Ecology and Evolution, Issue Volume 7, 2023, ISSN 2397-334X
Publisher: 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

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

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

Author(s): Catherine Gilbert, Vaclav Krupicka, Francesca Galluzzi, Aleksandra Popowich, Katell Bathany, Stéphane Claverol, Julie Arslanoglu, Caroline Tokarski
Published in: Science Advances, Issue 10, 2024, ISSN 2375-2548
Publisher: 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

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

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

Author(s): 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
Published in: American Journal of Biological Anthropology, Issue 184, 2024, ISSN 2692-7691
Publisher: 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

Author(s): 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
Published in: Nature Protocols, Issue 19, 2024, Page(s) 2085-2116, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-024-00975-3

Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo

Author(s): 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
Published in: PLOS ONE, Issue 18, 2023, Page(s) e0291308, ISSN 1932-6203
Publisher: 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

Author(s): 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
Published in: Nature Ecology & Evolution, Issue 8, 2024, Page(s) 564-577, ISSN 2397-334X
Publisher: Nature Publishing Group
DOI: 10.1038/s41559-023-02303-6

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

Author(s): 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
Published in: iScience, Issue 27, 2024, Page(s) 109432, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2024.109432

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

Author(s): 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
Published in: Nature, Issue 626, 2024, Page(s) 341-346, ISSN 0028-0836
Publisher: 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

Author(s): Zahra Haghighi, Meaghan Mackie, Anne Apalnes Ørnhøi, Abigail Ramsøe, Tone Marie Olstad, Simon James Armitage, Christopher Stuart Henshilwood, Enrico Cappellini
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-63455-4

PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Author(s): Ioannis Patramanis, Jazmín Ramos-Madrigal, Enrico Cappellini, Fernando Racimo
Published in: Peer Community Journal, Issue 3, 2023, ISSN 2804-3871
Publisher: PCI Organization
DOI: 10.24072/pcjournal.344

Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics

Author(s): Patricia Bortel, Ilaria Piga, Claire Koenig, Christopher Gerner, Ana Martinez-Val, Jesper V. Olsen
Published in: Molecular & Cellular Proteomics, Issue 23, 2024, Page(s) 100754, ISSN 1535-9476
Publisher: 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

Author(s): 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
Published in: Nature Communications, Issue Volume 14, issue number 1, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2022.12.19.520999

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

Author(s): Claire Koenig, Ana Martinez-Val, Giulia Franciosa, Jesper V. Olsen
Published in: PROTEOMICS, Issue Volume 22, issue number 19-20, 2022, Page(s) e2100245, ISSN 1615-9853
Publisher: 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

Author(s): 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
Published in: Nature Ecology & Evolution, Issue 8, 2024, Page(s) 578-588, ISSN 2397-334X
Publisher: Nature Publishing Group
DOI: 10.1038/s41559-023-02318-z

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

Author(s): 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
Published in: Cell Reports, Issue Volume 43, issue number 3, 2023, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1101/2023.07.10.548429

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

Author(s): 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
Published in: Peer Community Journal, Issue 4, 2024, ISSN 2804-3871
Publisher: PCI Organization
DOI: 10.24072/pcjournal.451

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

Author(s): 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
Published in: Scientific Reports, Issue 13, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-44885-y

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Author(s): 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
Published in: Nature Communications, Issue Volume 12, issue number 1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

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

Author(s): Cieszynska W.K.C., Pandolfi L. & Rook L.
Published in: Paleodays 2021 Abstract Book, Issue 2021,XXI Convegno della Società Paleontologica Italiana, live virtual edition, 2021, Page(s) p.35
Publisher: 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

Author(s): Cieszynska W.K.C., Pandolfi L. & Rook L.
Published in: Abstract book of the XVIII annual conference of the European Association of Vertebrate Palaeontologists, Issue 5th-9th July 2021, 2021, Page(s) p.54
Publisher: 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

Author(s): 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
Published in: Journal of the American Association of Biological Anthropologists, Issue 16 March 2022, 2022, Page(s) 112
Publisher: AAPA ABSTRACTS
DOI: 10.1002/ajpa.24514

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

Author(s): Petra Gutenbrunner, Pelagia Kyriakidou, Frido Welker and Jürgen Cox
Published in: bioRxiv, Issue 6-Sep-21, 2021
Publisher: The preprint server for biologi
DOI: 10.1101/2021.09.04.458985

Deliverables

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