Label-free Quantitative Differential Proteomic Analysis of Large Yellow Croaker Cultured under Different Aquaculture Modes

Protein differences in large yellow croakers from different aquaculture patterns were investigated by label-free quantitative proteomics. Total muscle protein was extracted from large yellow croakers from common cage aquaculture and deep-water cage aquaculture, and identified and analyzed by high performance liquid chromatography-mass spectrometry (HPLC-MS). The raw data were processed using MaxQuant software to transform the signal peaks into matrix data for peptide/protein expression, followed by graphical visualization using the Perseus software. Differentially expressed proteins between the two aquaculture systems were selected by Student’s t test for gene functional classification, metabolic pathway enrichment and protein network interaction analysis, in which P < 0.05 was considered as statistically significant difference. The results showed that 6077 peptides, corresponding to 1232 proteins, were obtained through database alignment.of these proteins, 130 were significantly different between the two groups of large yellow croaker, with 76 being up-regulated proteins and 54 being down-regulated. The most up-regulated protein was TCP chaperone, and the most down-regulated protein was α-1(Ⅰ) chain collagen. Bioinformatics analysis demonstrated that the major differential proteins were heat shock protein, chaperones, globulin and collagen, and the environmental temperature may be the major factor causing significantly differential expression of large yellow croaker proteins.