Proteomics-based analysis of functional proteins after fermentation of compound wheat embryo Chinese medicine

Abstract Compound probiotics were used to ferment compound wheat embryo Chinese medicine (CWECM) at 37 °C for a given period, and the fermentation end point was determined based on pH value. The full spectrum of the proteins within the fermentation supernatant was determined by ion mass spectrometry, and then the fermentation was analyzed by proteomics. The difference of functional protein of CWECM before and after fermentation was analyzed. Additionally, the changes in flavor peptides were examined. Our results indicated that when the fermentation was performed for 96 h, the pH value became stable over time, where it shifted from an initial 3.98 ± 0.04 to a stable 2.78 ± 0.04. Proteomic-based analysis of the fermentation supernatant indicated that the fermentation of the probiotics increased. The amount of functional proteome and protein within the supernatant increased from 60 proteomes and 136 proteins before fermentation to 70 proteomes and 149 proteins post fermentation. These proteins were primarily members of the Ubiquitin and Histone families. These families contain more specific peptides after fermentation, and the coverage was reduced. Analysis of the unique P0C512 protein after fermentation indicated that this protein is an unstable, 3D-effect columnar protein. We also found that probiotic fermentation can reduce the proportion of bitter peptides within fermentation broth from 47.49% to 36.98%, and the proportion of sweet peptides increased after fermentation from 35.29% to 51.01%. Based on our findings, we conclude that fermentation of CWECM by compound probiotics can reduce the pH of the CWECM solution, increase the number of functional proteomes and proteins, improve the taste of CWECM solutions, and improve the therapeutic efficacy of CWECM.