Seaweeds are regarded as a sustainable source of food protein, but protein extraction is severely impaired by the complex extracellular matrix. In this work, we investigated the protein-level effects of enzymatic extraction upstream of carrageenan extraction for the industrial red seaweed . Combination of quantitative proteomics and bioinformatic prediction of subcellular localization was shown to have immense potential for process evaluation; even in the case of poorly annotated species such as Applying cell wall degrading enzymes markedly improved the relative recovery of intracellular proteins compared to treatment with proteolytic enzymes or no enzymatic treatment. Moreover, results suggest that proteomics data may prove useful for characterizing amino acid composition and that length-normalization is a viable approach for relative protein quantification in non-specific analysis. Importantly, the extracts were abundant in proteins, which contained both previously verified and novel, potential bioactive peptides, highlighting their potential for application as functional food ingredients.