Ionisation bias undermines the use of matrix‐assisted laser desorption/ionisation for estimating peptide deamidation: Synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios

Simpson, Joanna; Fascione, M. A.; Bergström, Edmund T.; Wilson, Julie; Collins, Matthew J.; Penkman, Kirsty; Thomas‐Oates, Jane

doi:10.1002/rcm.8441

Cited by 8 publications

(3 citation statements)

References 28 publications

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“…We assessed the authenticity of the sequences by estimating the extent of deamidation. This is a rather crude but usually effective measure of the extent of overall degradation -not necessarily of age (Schroeter and Cleland, 2016;Simpson et al, 2019Simpson et al, , 2016Welker et al, 2016). In our case, we obtained results that were internally consistent: in EVA_C (heavily handled) all collagens appeared to be "ancient" and all keratins "modern", while in EVA_M16747 (not heavily handled but with a century-long post-excavation history), all collagens and all keratins appeared "ancient".…”

Section: Discussionsupporting

confidence: 67%

Never boring: Non-invasive palaeoproteomics of mummified human skin

Demarchi

Boano

Ceron

et al. 2020

Journal of Archaeological Science

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Section: Discussionsupporting

confidence: 67%

Never boring: Non-invasive palaeoproteomics of mummified human skin

Demarchi

Boano

Ceron

et al. 2020

Journal of Archaeological Science

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“…A recent study [Simpson et al, 2019] demonstrated that MALDI technique underestimates peptides with E in peptide mixtures containing Q and E substitutions that could potentially result in the systematic overestimation of q , i.e. remaining Q.…”

Section: Resultsmentioning

confidence: 99%

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

Nair

Palomo

Markussen

et al. 2022

Preprint

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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 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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“…A recent study (Simpson et al, 2019) demonstrated that MALDI technique underestimates peptides with E in mixtures containing Q and E substitutions that could potentially result in the systematic overestimation of q, i.e. remaining Q.…”

Section: Relative Rates Of Deamidationmentioning

confidence: 99%

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

Nair¹,

Palomo²,

Markussen³

et al. 2023

Peer Community Journal

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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 lowresolution 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.

show abstract

Ionisation bias undermines the use of matrix‐assisted laser desorption/ionisation for estimating peptide deamidation: Synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios

Cited by 8 publications

References 28 publications

Never boring: Non-invasive palaeoproteomics of mummified human skin

Never boring: Non-invasive palaeoproteomics of mummified human skin

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

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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