This study investigated the use of ultrafiltration for sustainable protein recovery and the treatment of shrimp washing wastewater (SWW). Three ultrafiltration membranes with molecular weight cut-offs of 5, 10, and 50 kDa were tested using a combined ultrafiltration–diafiltration process (UF-DF). The performance of each membrane was assessed based on protein recovery efficiency, chemical oxygen demand (COD) reduction, turbidity, fouling behavior, and cleaning efficiency. The 5 kDa membrane showed superior performance, achieving over 90% protein and COD rejection and producing the highest protein-enriched retentate. It also exhibited the lowest fouling index and best cleaning recovery, confirming its suitability for protein concentration and wastewater treatment. This research highlights UF-DF as a promising, eco-efficient technology for valorizing seafood processing effluents by recovering high-value proteins and reducing environmental discharge loads.

The identification of phosphopeptides is currently a challenge when they are part of a complex matrix of peptides, such as a milk protein enzymatic hydrolysate. This challenge increases with both the number of phosphorylation sites on the phosphopeptides and their amino acid length. Here, this paper reports a four-phase strategy from an enzymatic casein hydrolysate before a mass spectrometry analysis in order to enhance the identification of phosphopeptides and phosphosites: (i) the control protein hydrolysate, (ii) a two-step enzymatic dephosphorylation of the latter, allowing for the almost total dephosphorylation of peptides, (iii) a one-step enzymatic dephosphorylation, allowing for the partial dephosphorylation of the peptides and (iv) an additional endoGluC enzymatic hydrolysis, allowing for the cleavage of long-size peptides into shorter ones. The reverse-phase high-pressure liquid chromatography–tandem mass spectrometry (RP-HPLC-MS/MS) analyses of hydrolysates that underwent this four-phase strategy allowed for the identification of 28 phosphorylation sites (90%) out of the 31 referenced in UniprotKB/Swiss-Prot (1 June 2021), compared to 17 sites (54%) without the latter. The alpha-S2 casein phosphosites, referenced by their similarity in the UniProt database, were experimentally identified, whereas pSer148, pThr166 and pSer187 from a multiphosphorylated long-size kappa-casein were not. Data are available via ProteomeXchange with identifier PXD027132.