Biology subjects

Engels, I.

Publications and source records attributed to Engels, I..

3 recordsLinked to original sources

bioRxiv2026

Palaeoproteomic deconvolution of physical and genetic collagen mixtures

Species identification in palaeoproteomics relies on genome-derived protein sequences which are often poor-quality, and lacks tools to cope with multi-species samples. Here, we address both challenges through the analysis of physical and genetic mixtures. Species that are absent from our database are considered a genetic mixture, i.e. a patchwork of peptides from closely related species. Inversely, various overlapping peptide stretches allow us to resolve complex physical mixtures. This is benchmarked by analysing physical mixtures of modern bone fragments, including genetic mixtures. We illustrate the impact of our approach via a rapid and high-throughput analysis of >2500 bone fragments, revealing the Eemian-era faunal environment around Scladina Cave, including the first Palaeoloxodon antiquus identified at this site. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/732552v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@a33296org.highwire.dtl.DTLVardef@4e4b85org.highwire.dtl.DTLVardef@402290org.highwire.dtl.DTLVardef@9d35b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Palaeoproteomics reveals bovine carcass processing with 6,000-year-old flint tools

Lithic tools are the most abundant cultural artefacts found at prehistoric archaeological sites. Through their study, we can understand essential activities such as hunting, processing of animal carcasses and plant materials, and working of resources such as ochre and bone, as well as broader technological and cultural practices. For the first time, proteomics was applied alongside use-wear and optical microscopy residue analyses, enabling the identification of bovine, plant, and human proteins on faceted tools from the Mesolithic-Neolithic site of Bazel-Sluis, Belgium. This retrieval of identifiable protein from an area with poor organic preservation demonstrates wide-reaching potential for archaeological research, opening a new avenue of investigation into prehistoric lifeways and adding to the growing corpus of evidence accessible through palaeoproteomics. A workflow for future analyses is suggested, based on our integrated sampling strategy requiring no additional tool manipulations.

paleontology↗

bioRxiv2024

ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation

LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse datasets containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. ClassiCOL embraces and even extends this ambiguity using a novel isoBLAST approach. The exhaustive set of potential peptide candidates created in this way is then used to retain or reject different potential paths at each taxonomic branching point down to the taxonomic level attainable with the sample information, always allowing for potential mixtures in the process. As an end point, all considered ambiguity is graphically represented with a clear prioritization of the species in the sample. Using public as well as in-house data, we demonstrate the performance of this universal postprocessing approach on different instruments and explore the possibility of identifying genetic as well as sample mixtures. Diet reconstruction from 40,000 year old cave hyena coprolites illustrates the exciting potential of this approach. TeaserClassiCOL is a postprocessing tool that allows for more accurate species classification from LC-MS/MS measurements of collagen.

bioinformatics↗