Proteomic Applications in Aquaculture and Fish Welfare

Proteomics has emerged as a transformative approach in aquaculture research, offering a comprehensive perspective on protein expression, modification and interaction within cultured species. By profiling the proteome under varying environmental, nutritional and husbandry conditions, researchers can identify biomarkers of stress, disease susceptibility and growth performance. Such biomarkers inform both selective breeding programmes and real-time health monitoring, enabling early intervention in the face of pathogenic challenges or suboptimal welfare. Additionally, proteomic tools facilitate the characterisation of allergenic proteins and the assessment of muscle quality, supporting consumer safety and product authenticity. Recent technological advances in mass spectrometry, bioinformatics and sample preparation have increased the sensitivity and throughput of analyses, making high-resolution proteome profiling feasible in routine aquaculture operations. Overall, proteomics contributes to a deeper mechanistic understanding of fish physiology and welfare, guiding the development of more sustainable and welfare-oriented practices in the global aquaculture industry.

Research from Nature Portfolio

Recent studies have employed high-resolution mass spectrometry to characterise the muscle proteome of coldwater trout species. In one analysis of Himalayan snow trout, liquid chromatography–tandem mass spectrometry combined with label-free quantification revealed sex- and weight-specific changes in over 230 muscle proteins. Differentially regulated proteins were linked to skeletal muscle development, energy metabolism and innate immunity, reflecting seasonal growth dynamics and environmental adaptation. The insights gained offer potential biomarkers for monitoring physiological status and optimizing feeding regimes in coldwater aquaculture.

Proteomic Applications in Aquaculture and Fish Welfare publication trend

The graph below shows the total number of articles in proteomic applications in aquaculture and fish welfare across all publications each year (not limited to Nature Index journals).

Technical terms

Proteomics: The large-scale study of the full complement of proteins expressed by an organism, tissue or cell under specific conditions.

Liquid chromatography–tandem mass spectrometry (LC–MS/MS): An analytical technique that separates peptides by chromatography and identifies them by sequential mass analysis.

Label-free quantification (LFQ): A mass spectrometry approach to measure relative protein abundance without the use of isotopic or chemical labels.

Biomarker: A measurable molecule whose presence, absence or change in level indicates a biological condition or process.

Environmental protein (eProtein): Proteins released into environmental samples (for example, water) that reflect the physiological state of organisms.

References

1. LC–MS/MS based characterisation and differential expression of proteins in Himalayan snow trout, Schizothorax labiatus using LFQ technique. Scientific Reports (2023).
2. Integrating omics technologies for improved quality and safety of seafood products. Aquaculture and Fisheries (2023).
3. Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare research. BMC Genomics (2020).
4. Unveiling Aquatic Organism Health Through eProteins: A Contemporary Perspective. Research Ideas and Outcomes (2024).