A Holistic Investigation of Protein Degradation during the Autolysis of Sea Cucumber (<i>Apostichopus japonicus</i>) Using a Peptidomics Strategy

Sea cucumber is a highly nutritious and commercially valuable marine resource but is prone to autolysis, which significantly deteriorates its quality. However, the protein changes associated with autolysis are insufficiently understood. This study aimed to elucidate the degradation patterns of structural proteins during autolysis from a holistic perspective. A portfolio of 2950 unique peptides derived from 69 structural proteins were detected by peptidomics analysis. The degradation of structural proteins was found to intensify predominantly after 24 h of autolysis. Fibrillar collagen degraded more rapidly than FACITs, and the degradation of muscle thin filaments was more severe compared to that of thick filaments. Tensilin was also implicated in the autolysis process. The terminal residues of released peptides displayed significant diversity, suggesting the involvement of a complex array of proteases in autolysis. This study advances the understanding of autolysis changes in sea cucumbers with a strategy of the postgenomics era.