PXD050001

PXD050001 is an original dataset announced via ProteomeXchange.

Title	Experimental Salmon, Deer and Chestnut Fresh, Cooked and Buried Foodcrust and Ceramic LC-MS/MS
Description	Proteomics has become a popular method for investigating diet and cuisine in well-preserved ancient food remains, and calcified deposits like dental calculus. However, foodcrusts (the typically charred residues on the surface of pottery) have not been extensively explored as a source of dietary proteins. We remain ignorant of the impact of cooking and burial on the protein extractome, and crucially, the extent to which palaeoproteomic extractomes actually reflect the composition of input ingredients and cuisines. Therefore, through cooking and burial experiments we investigate the impact of these processes on protein preservation in foodcrusts and accompanying ceramics. Here, we aim to identify proteins that persist throughout the cooking process and become embedded in foodcrusts and ceramics, as well as those that persist through six months burial in soil, using ‘typical’ Mesolithic ingredients of Cervus elaphus (red deer), Salmo salar (Atlantic salmon) and Castanea sativa (sweet chestnut). Specifically, we seek to understand why particular proteins persist through cooking and burial. Hence we examine a range of physiochemical properties which have been theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, with dietary proteins identified in all buried deer and salmon foodcrust replicates and most chestnut replicates, tentatively indicating that extraction of protein from ancient foodcrusts may be successful, while in contrast, dietary proteins were rarely identified in cooked or buried ceramics of any input ingredient. It was apparent that the input ingredient strongly influenced frequency of protein and peptide identifications, with chestnut surviving poorly compared to other ingredients, revealing that the detection of ingredients is biassed by the ingredients themselves. The results also reveal that degradation is not universal nor linear between proteins, indicating that protein physiochemical properties are at play. While certain properties appear to aid protein preservation such as hydrophobicity, none was seen to single-handedly explain why particular proteins/peptides survive in buried foodcrusts, with results indicating that certain properties act on protein preservation in complex ways requiring further investigation. These results have implications on archaeological analyses, by demonstrating the utility of foodcrusts as a good target sample for proteomics, while cautioning the interpretation of foodcrust extractomes: which should not be expected to reflect the initial input extractome.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_13:27:20.859.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD050001
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Miranda Evans
SpeciesList	scientific name: Cervus elaphus (Red deer); NCBI TaxID: 9860; scientific name: Castanea mollissima; NCBI TaxID: 60419; scientific name: Salmo salar (Atlantic salmon); NCBI TaxID: 8030;
ModificationList	2-pyrrolidone-5-carboxylic acid (Gln); acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-21 07:15:07	ID requested
⏵ 1	2025-05-06 13:27:21	announced

10.1098/rsos.240610;

Evans M, Hagan R, Boyd OJ, Bondetti M, Craig OE, Collins MJ, Hendy J, The impact of cooking and burial on proteins: a characterisation of experimental foodcrusts and ceramics. R Soc Open Sci, 11(9):240610(2024) [pubmed]

10.6019/PXD050001;

submitter keyword: ceramics,Palaeoproteomics, foodcrust

Jessica Hendy
contact affiliation	BioArCh, Department of Archaeology, University of York, United Kingdom
contact email	jessica.hendy@york.ac.uk
lab head
Miranda Evans
contact affiliation	University of Cambridge
contact email	miranda@palaeome.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050001
     1. Label: PRIDE project
     2. Name: Experimental Salmon, Deer and Chestnut Fresh, Cooked and Buried Foodcrust and Ceramic LC-MS/MS