Assay for Collagen Damage in the Food Industry

My PhD Project

Although thematically distant from the other applications, this one uses the same state-of-the-art technological solutions developed to address the analytical challenges associated with ancient protein analysis to deliver an accurate, convenient and effective assay of protein damage characterisation in industrial production. DEVRO is a world-leader in artificial sausage casing production. Artificial sausage casing is made of collagen usually derived from cattle and pig skin. During the sausage casing production process, collagen is subject to a series of harsh acidic and alkaline steps inducing permanent and irreversible biochemical damage in the collagen. DEVRO is interested in accurately characterising the amount and the type of damage in the collagen it processes, because this affects the final mechanical properties of its end product. Currently, DEVRO measures its collagen damage using a rudimentary ammonia assay, quantifying the amount of ammonia released as the product of deamidation of asparagine and glutamine in controlled acidic conditions. This assay has no resolution concerning the extent of each deamidation site and it is completely blind to other types of biochemical damage the production treatments can induce in collagen. PROJECT 9, will adapt the EvoSEP and Thermo Orbitrap technology for fast DIA tandem MS screening, 200 samples/day, of the damage products in the collagen DEVRO processes. A method for blind search of ancient protein damage was recently described by EC and JVO. The information generated during this phase will be integrated with the EvoSEP DIA tandem MS screening technology to deliver an accurate quality control assay DEVRO will routinely use to control the quality of its production.

Secondments

Secondment period of 3 months, during PhD year 1 and 2, at DEVRO PLC under Gordon Paul’s supervision to understand DEVRO’s industrial needs and to engineer the possible implementation of the methodology developed at University of Copenhagen in the DEVRO production plant.

Publications

Koenig, C., Bortel, P., Paterson, R. S., Rendl, B., Madupe, P. P., Troché, G. B., ... & Olsen, J. V. (2024). Automated high-throughput biological sex identification from archeological human dental enamel using targeted proteomics. Journal of Proteome Research, 23(11), 5107-5121.

Bortel, P., Piga, I., Koenig, C., Gerner, C., Martinez-Val, A., & Olsen, J. V. (2024). Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics. Molecular & Cellular Proteomics, 23(5).

Taurozzi, A. J., Rüther, P. L., Patramanis, I., Koenig, C., Sinclair Paterson, R., Madupe, P. P., ... & Cappellini, E. (2024). Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel. Nature Protocols, 1-32.

Warner, H., Franciosa, G., van der Borg, G., Coenen, B., Faas, F., Koenig, C., ... & van den Bogaart, G. (2024). Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation. Cell reports, 43(3).

Koenig, C., Martinez-Val, A., Naicker, P., Stoychev, S., Jordaan, J., & Olsen, J. V. (2023). Protocol for high-throughput semi-automated label-free-or TMT-based phosphoproteome profiling. STAR protocols, 4(3), 102536.

Madupe, P. P., Koenig, C., Patramanis, I., Rüther, P. L., Hlazo, N., Mackie, M., ... & Cappellini, E. (2023). Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus. bioRxiv, 2023-07.

Martínez-Val, A., Fort, K., Koenig, C., Van der Hoeven, L., Franciosa, G., Moehring, T., ... & Olsen, J. V. (2023). Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nature Communications, 14(1), 3599.

Koenig, C., Martinez‐Val, A., Franciosa, G., & Olsen, J. V. (2022). Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT‐based multiplexing. Proteomics, 22(19-20), 2100245.

Martinez-Val, A., Bekker-Jensen, D. B., Steigerwald, S., Koenig, C., Østergaard, O., Mehta, A., ... & Olsen, J. V. (2021). Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution. Nat Commun.

Takumi Tsutaya, Claire Koenig,  Enrico Cappellini, Scientific Reports(2019). Palaeoproteomic identification of breast milk protein residues from the archaeological skeletal remains of a neonatal dog.