Intestinal Proteomic Study of Cottonseed Protein–Based Diets in Channel Catfish (Ictalurus punctatus)

Cotton meal is a major by-product of cotton processing and is rich in protein, with a crude protein content exceeding 40%, making it one of the most valuable plant-based protein sources for livestock and poultry compound feeds. However, the effects of cottonseed concentrate protein (CPC) as a replacement for fishmeal on the growth performance and metabolic processes of Ictalurus punctatus remain insufficiently understood. Elucidating how CPC-supplemented diets influence fish immunity and metabolism is of significant research interest, as it may support the identification of alternative protein sources for aquafeeds, reduce feed costs, and improve economic efficiency in aquaculture.In this study, proteomic sequencing was performed on gut tissues of fish fed diets in which fishmeal was partially replaced with CPC to investigate diet-induced protein expression changes. A total of 4,774 UniProt entries were identified, encompassing 5,595 proteins and 34,535 peptide fragments across 25 functional classifications. Peptides containing 10 amino acid residues were the most abundant, representing approximately 11% of the total peptide length, with most peptide segments distributed between 7 and 25 amino acids.Comparative analysis revealed 173 differentially expressed proteins, including 160 upregulated and 13 downregulated proteins. Functional annotation showed that 60 proteins were assigned to COG categories, 5 to Swiss-Prot and GO, 172 to KEGG pathways, and 124 to KOG classifications. These differentially expressed proteins were primarily associated with amino acid transport and metabolic processes. Dephenolized cottonseed protein is particularly rich in essential amino acids, especially lysine and cystine, at levels higher than those found in many other plant-derived protein sources. This amino acid composition may influence the expression and activity of amino acid transporter proteins, thereby modulating amino acid transport and metabolism in fish.Overall, this study provides a valuable proteomic resource and a scientific foundation for the development and utilization of cotton meal protein as a sustainable alternative protein source in aquaculture feeds.