Section: Archaeology
Topic: Archaeology

Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

10.24072/pcjournal.230 - Peer Community Journal, Volume 3 (2023), article no. e10.

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Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)2. During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this study, we propose a simple three-step workflow, developed as an R package called MALDIpqi(), to estimate deamidation in parchment derived collagen using low-resolution MALDI-TOF spectra. After pre-processing raw spectra, we used weighted least-squares linear regression to estimate Q deamidation levels from the convoluted isotopic envelope for seven collagen-peptide markers. Finally, we employed a linear mixed effect model to predict the overall deamidation level of a parchment sample termed Parchment Glutamine Index (PQI). To test the robustness of the workflow, we applied MALDIpqi() to previously published ZooMS data generated from almost an entire library of the Cistercian monastery at Orval Abbey, Belgium. In addition to reliably predicting PQI, we observed interesting patterns pertaining to parchment production. MALDIpqi() holds excellent potential for biocodicological and other archaeological studies involving collagen, such as bone, but we also foresee its application in the food and biomedical industry.  

Published online:
DOI: 10.24072/pcjournal.230
Type: Research article
Nair, Bharath 1; Palomo, Ismael Rodríguez 2; Markussen, Bo 3; Wiuf, Carsten 3; Fiddyment, Sarah 2; Collins, Matthew James 1, 2

1 Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen – Copenhagen, Denmark
2 McDonald Institute for Archaeological Research, University of Cambridge – Cambridge, United Kingdom
3 Department of Mathematical Sciences, University of Copenhagen – Copenhagen, Denmark
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     title = {Parchment {Glutamine} {Index} {(PQI):} {A} novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality {MALDI-TOF} data},
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Nair, Bharath; Palomo, Ismael Rodríguez; Markussen, Bo; Wiuf, Carsten; Fiddyment, Sarah; Collins, Matthew James. Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data. Peer Community Journal, Volume 3 (2023), article  no. e10. doi : 10.24072/pcjournal.230.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.archaeo.100019

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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