Data-independent acquisition-based SWATH-MS proteomics profiling to decipher the impact of farming system and chicken strain and discovery of biomarkers of authenticity in organic versus antibiotic-free chicken meat

In the literature, there is a paucity of methods and tools that allow the identification of biomarkers of authenticity to discriminate organic and non-organic chicken meat products. Shotgun proteomics is a powerful tool that allows the investigation of the entire proteome of a muscle and/or meat sample. In this study, a shotgun proteomics approach using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) has been applied for the first time to characterize and identify candidate biomarkers of authenticity in post-mortem chicken Pectoralis major muscles produced from organic and non-organic farming systems (antibiotic-free). The characterization was further performed within two chicken strains, these being Ross 308 and Ranger Classic. From the candidate protein biomarkers, bioinformatics enrichment analyses revealed significant differences in the muscle proteome between the two chicken strains, which may be related to their genetic background and rearing conditions. The results further provided novel insights on the potential pathways at interplay that are associated with the differences as a consequence of farming system of chicken strain, such as muscle contraction and energy metabolism. This study can pave the way to more in-depth investigations in proteomics applications to assess chicken meat authenticity and better understand the impact of farming systems on the chicken muscle and meat quality.