Dataset Information

Proteomic analysis of experimental foodcrusts reveals discrepancies between food input and recovered protein signal

ABSTRACT: In order to investigate how representative the recoverable proteins from charred organic residues (foodcrust) are of the food mixture cooked to produce them, a protein-rich (salmon), lipid-rich (beef fat) and carbohydrate-rich (beetroot) food were mixed, cooked and analysed. The three ingredients were mixed in 20% increments, resulting in 21 different mixtures covering all combinations of the three foodstuffs. The mixtures were placed in ceramic vessels and heated nine times with samples taken after the first, fifth and ninth heating event. Then the vessels with foodcrust were buried for 52 days and sampled again after excavation. The extracted proteins indicate substantial disparities in the relative abundance of an ingredient in the food mixture and the percentage of identified proteins it contributed. In particular salmon proteins seem overrepresented in the recovered proteome, followed by beef fat and lastly beetroot. Additionally, we found that only a limited number of proteins could be identified after the burial and that only salmon and beetroot contributed to the after burial proteomes.

INSTRUMENT(S):

ORGANISM(S): Blank Sample Bos Taurus (bovine) Beta Vulgaris (sugar Beet) Salmo Salar (atlantic Salmon)

TISSUE(S): Root, Muscle, Adipose Tissue

SUBMITTER: Jan Dekker

LAB HEAD: Matthew James Collins

PROVIDER: PXD059930 | Pride | 2025-08-25

REPOSITORIES: Pride

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			Action	DRS
	20220906_D935_E10_5_R-calib.mzID.gz	Mzid
	20220906_D935_E10_5_R-calib.mzML	Mzml
	20220906_D935_E10_5_R.raw	Raw
	20220906_D935_E11_5R-calib.mzID.gz	Mzid
	20220906_D935_E11_5R-calib.mzML	Mzml

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Publications

An unclean slate, discrepancies between food input and recovered protein signal from experimental foodcrusts.

Dekker Joannes Adrianus Antonius JAA Hagan Richard R Collins Matthew M Hendy Jessica J

PloS one 20250822 8

Organic residues are a rich source of biomolecular information on ancient diets. In particular, foodcrusts, charred residues on ceramics, are commonly analysed for their lipid content and to a lesser extent protein in order to identify foods, culinary practices and material culture use in past populations. However, the composition of foodcrusts and the factors behind their formation are not well understood. Here we analyse proteomic data (available via ProteomeXchange with identifier PXD059930) ...[more]

PMID: 40845013

Similar Datasets

Project 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.

Project description:Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavarian). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA-levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two additional transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees. The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009). Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation. For one time point we had five microarrays and five dye-swaps for each of sun and shade leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.