## 4 Conclusions  
There were significant differences in the composition of protein isolates and hydrolyses of roach and B. herring, extracted using different processes. In the case of both raw materials, the protein isolates produced using pH shift showed higher essential to non-essential amino acid ratios compared with enzymatically processed hydrolyses. Both the fatty acid composition and the lipid classes varied among the protein isolates produced by different processes, which was likely associated with both the removal and oxidation of lipids during the processes. The acidic pH shift resulted in an increase in the proportion of phospholipids compared with the raw material and was accompanied by a high proportion of PUFAs, and especially DHA. Alkali-extracted B. herring protein isolate contained a significantly higher proportion of FFAs and less TAGs compared with the raw material, acidic isolate and hydrolyses, and was also the most oxidized as indicated by protein carbonyls, PV, and volatile oxidation products. Enzymatically extracted protein hydrolyses from both roach and B. herring produced using Protamex, Neutrase, or Corolase were relatively similar (within the same raw material) in terms of lipid composition and showed lower lipid and protein oxidation compared with the protein isolates obtained from pH-shift processes. In the case of B. herring, protein hydrolysate produced using Neutrase had a higher PV and showed higher levels of some oxidation-related volatile compounds compared with the hydrolyses produced with Protamex and Corolase. Contradictory to most previous studies, the alkali-processed protein isolates of both roach and B. herring were more oxidized compared with acid-treated isolates. The contradictory findings could be related to species-related differences in the pH-dependent pro-oxidativity of hemoglobin.  
In terms of limiting oxidation, enzymatic hydrolysis was the more promising method for the valorization of proteins/peptides of both fish species, whereas extraction using pH shift was more favorable in terms of amino acid composition. However, the pH-shift process and enzymatic hydrolysis produce protein and peptide fractions with different molecular size and different functionalities, and since enzymatic fractionation produces hydrolysates, whereas pH shift does not hydrolyze the proteins to a large extent, the applications for protein isolates produced from these two processes are very different. Further research is needed to optimize the processing of B. herring and roach protein isolates and hydrolysates to limit the oxidation of lipids and proteins.  
The following are available online at [[https://www.mdpi.com/article/10.3390/foods11020230/s1](https://www.mdpi.com/article/10.3390/foods11020230/s1)]([https://www.mdpi.com/article/10.3390/foods11020230/s1](https://www.mdpi.com/article/10.3390/foods11020230/s1)), Figure S1: Schematic representation of the production of protein isolates and hydrolysates.  
Conceptualization, T.K., A.D., A.N., S.T., K.H. and B.Y.; methodology, T.K., A.D., A.P. and M.T.; formal analysis, T.K., A.D. and A.N.; investigation, T.K., A.D., A.N., A.P. and M.T.; resources, A.N. and K.H.; writing--original draft preparation, T.K. and A.D.; writing--review and editing, T.K., A.D., A.N., K.H. and B.Y.; visualization, T.K. and A.D.; supervision, S.T., K.H. and B.Y.; project administration, S.T. and B.Y.; funding acquisition, K.H. and B.Y. All authors have read and agreed to the published version of the manuscript.  
This work was funded by the Finnish Operational Programme of the European Maritime and Fisheries Fund (the Project \"Blue Welfare Network-Blue Products\", Project no. 33338), and personal working grants for [PERSON] from the Jenny and Antti Wihuri Foundation and the Finnish Cultural Foundation.  
Not applicable.  
The authors declare no conflict of interest.