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.