Sourdough, yeast-fermented dough, and Lactobacillus-fermented dough were prepared with wheat flour, yeast, and Lactobacillus plantarum M616 and the protein degradation and the peptide formation patterns were studied via by SDS-PAGE, the changes in protein content were analyzed by Bradford method, and the formed peptide content was measured using HPLC. The results showed that yeast had almost no effect on the degradation of proteins in the dough. Lactobacillus plantarum M616 played a relatively important role in protein degraded during fermentation, demonstrated by the gradual decrease in the content of proteins during fermentation, which was the most obvious at 4~10 h. Additionally, the degradation of soluble proteins and of those with medium molecular weight was the most obvious. The content of gliadins increased first and then decreased at 0-10 h. The analysis of the content of peptides before and after fermentation indicted that L. plantarum M616 could promote the formation and accumulation of peptides in the dough.