Applying Quantitative Proteomics for Evaluation of Protein Quality, Nutritional Value, and Extraction Methods in Side-Streams of Industrial Carrageenan Production from the Red Seaweed Eucheuma denticulatum (Spinosum)

As global focus on sustainable and zero-waste food protein production continues to increase, the search for alternative sources and side-stream valorization intensifies. The red seaweed Eucheuma denticulatum (Spinosum) could prove to be part of the solution in the Green Transition. Despite a modest protein content compared to other seaweed species and other alternative protein sources, the enormous quantities of Spinosum processed for hydrocolloid production, makes it a potential protein source by isolation of protein-rich side-stream.

In this work, we describe how the application of quantitative proteomics by LC-MS/MS is a highly valuable tool for characterization of protein extracts. In contrast to traditionally employed approaches for protein characterization in food science, proteomics provides protein-level identification and quantification, thereby providing a much deeper level of knowledge about the protein composition in the extracts. Moreover, by applying down-stream bioinformatic analysis of proteomics data, it is possible to predict a probable subcellular localization of the individual proteins. Through comparative analysis with quantitative transcriptomics data, proteomics, in combination with more traditional approaches, can be used to evaluate efficiency and selectivity in the applied extraction method – even in the case of species such as Spinosum, which are quite poorly characterized on the proteome level. Furthermore, we describe how novel bioinformatic algorithms can be applied for prediction of emulsifier and antioxidant peptides embedded in identified proteins. Using this bottom-up discovery approach, we identified and validated the functionality of several novel and potent peptides derived from abundant proteins in Spinosum extracts, thereby increasing their potential applicability and value. Finally, we describe how proteomics data can be used as a supplement to conventional amino acid analysis for evaluating nutritional value of the extracted protein.