Updated project metadata. This study aimed at performing the quantitative proteomics analysis of gut tissue, one of Labeo rohita, one of the important aquaculture fish species. Data was acquired using high resolution mass spectrometry followed by Label free quantification. After performing statistical analysis, a panel of differentially expressed proteins were identified which include extracellular matrix proteins, cytoskeletal proteins, immune related proteins and metabolic enzymes. This analysis revealed important signaling pathways and protein-protein interaction networks which could help in understanding disease pathogenesis. The data acquired in the study would provide a basis for further omics research and can help in elucidating biological processes in healthy or diseased fish.