Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data
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 parchm...
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2023-01-01
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| Series: | Peer Community Journal |
| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.230/ |
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| author | Nair, Bharath Palomo, Ismael Rodríguez Markussen, Bo Wiuf, Carsten Fiddyment, Sarah Collins, Matthew James |
| author_facet | Nair, Bharath Palomo, Ismael Rodríguez Markussen, Bo Wiuf, Carsten Fiddyment, Sarah Collins, Matthew James |
| author_sort | Nair, Bharath |
| collection | DOAJ |
| description | 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.
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| format | Article |
| id | doaj-art-9f60dff0f2414d679bf3b0bc7b293fef |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-9f60dff0f2414d679bf3b0bc7b293fef2025-02-07T10:16:50ZengPeer Community InPeer Community Journal2804-38712023-01-01310.24072/pcjournal.23010.24072/pcjournal.230Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF dataNair, Bharath0https://orcid.org/0000-0002-1897-4132Palomo, Ismael Rodríguez1https://orcid.org/0000-0001-5313-9709Markussen, Bo2https://orcid.org/0000-0001-7793-9620Wiuf, Carsten3https://orcid.org/0000-0002-1302-4445Fiddyment, Sarah4https://orcid.org/0000-0002-8991-2318Collins, Matthew James5https://orcid.org/0000-0003-4226-5501Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen – Copenhagen, DenmarkMcDonald Institute for Archaeological Research, University of Cambridge – Cambridge, United KingdomDepartment of Mathematical Sciences, University of Copenhagen – Copenhagen, DenmarkDepartment of Mathematical Sciences, University of Copenhagen – Copenhagen, DenmarkMcDonald Institute for Archaeological Research, University of Cambridge – Cambridge, United KingdomGlobe Institute, Faculty of Health and Medical Sciences, University of Copenhagen – Copenhagen, Denmark; McDonald Institute for Archaeological Research, University of Cambridge – Cambridge, United KingdomParchment 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.230/ |
| spellingShingle | 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 |
| title | Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data |
| title_full | Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data |
| title_fullStr | Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data |
| title_full_unstemmed | Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data |
| title_short | Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data |
| title_sort | parchment glutamine index pqi a novel method to estimate glutamine deamidation levels in parchment collagen obtained from low quality maldi tof data |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.230/ |
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