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

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Palaeoproteomic analysis of skeletal proteomes is used to provide taxonomic identifications for an increasing number of archaeological specimens. The success rate depends on a range of taphonomic factors and differences in the extraction protocols employed. By analyzing 12 archaeological bone specimens from two archaeological sites, we demonstrate that reducing digestion duration from 18 to 3 hours has no measurable impact on the obtained taxonomic identifications. Peptide marker recovery, COL1 sequence coverage, or proteome complexity are also not significantly impacted. Although we observe minor differences in sequence coverage and glutamine deamidation, these are not consistent across our dataset. A 6-fold reduction in digestion time reduces electricity consumption, and therefore CO2 emission intensities. We furthermore demonstrate that working in 96-well plates further reduces electricity consumption by 60%, in comparison to individual microtubes. Reducing digestion time therefore has no impact on the taxonomic identifications, while reducing the environmental impact of palaeoproteomic projects.
OriginalsprogEngelsk
Artikelnummer109432
TidsskriftiScience
Vol/bind27
Udgave nummer4
Antal sider17
ISSN2589-0042
DOI
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
This research has been made possible through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, grant agreement no. 948365 , awarded to F.W. F.W. and J.H.B. are supported by VILLUM FONDEN (no. 40747 ). L.L.M. and V.S.-M. were supported by a Fyssen Foundation postdoctoral fellowship (2021–2023 and 2023–2025, respectively). L.L.M. and Z.F. are supported by the European Union ’ Horizon Europe research and innovation program under the Marie Skłodowska-Curie grant agreements no. 1220891001 (ICARHUS) and 101106627 (PROMISE), respectively. F.W. and J.H. were supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 956351 (ChemArch). D.M. received support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 861389 (PUSHH). G.M.S. is funded by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie scheme (no. 101027850 ). Archaeological research at La Draga is made possible through the project “Landscape modelization and resource management in the transition to farming in northeaster Iberia” (PID2019-109254GB-C21), funded by the Agencia Estatal de Investigación (Spain), and “La Draga i la neolitització al NE de Catalunya, formació i dinàmiques d’ocupació del jaciment'' funded by Departament de Cultura de la Generalitat de Catalunya . We furthermore thank the Museu Arqueològic Comarcal de Banyoles for access to facilities and specimens. We thank J.-J. Hublin, D. Zhang, M. Saña and J. Olsen for access to materials. We also thank R.K. Heikkilä and E. Demey for assistance with the MALDI-ToF run at the ESPCI (Paris, France).

Funding Information:
This research has been made possible through funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, grant agreement no. 948365, awarded to F.W. F.W. and J.H.B. are supported by VILLUM FONDEN (no. 40747). L.L.M. and V.S.-M. were supported by a Fyssen Foundation postdoctoral fellowship (2021–2023 and 2023–2025, respectively). L.L.M. and Z.F. are supported by the European Union’ Horizon Europe research and innovation program under the Marie Skłodowska-Curie grant agreements no. 1220891001 (ICARHUS) and 101106627 (PROMISE), respectively. F.W. and J.H. were supported by the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 956351 (ChemArch). D.M. received support from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 861389 (PUSHH). G.M.S. is funded by the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie scheme (no. 101027850). Archaeological research at La Draga is made possible through the project “Landscape modelization and resource management in the transition to farming in northeaster Iberia” (PID2019-109254GB-C21), funded by the Agencia Estatal de Investigación (Spain), and “La Draga i la neolitització al NE de Catalunya, formació i dinàmiques d'ocupació del jaciment'' funded by Departament de Cultura de la Generalitat de Catalunya. We furthermore thank the Museu Arqueològic Comarcal de Banyoles for access to facilities and specimens. We thank J.-J. Hublin, D. Zhang, M. Saña and J. Olsen for access to materials. We also thank R.K. Heikkilä and E. Demey for assistance with the MALDI-ToF run at the ESPCI (Paris, France). L.L.M. V.S.-M. Z.F. and F.W. designed the study. J.H. R.D.A. G.T. and F.W. conducted experiments. V.S.-M. R.D.A. J.H. D.M. X.H. J.H.B. and Z.F. conducted data analyses. G.M.S. K.R. Z.F. and F.W. contributed reagents, software or granted access to instruments. L.L.M. V.S.-M. Z.F. and F.W. wrote a first draft of the paper with input of all the authors. The authors declare no competing interests.

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© 2024 The Author(s)

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