Pea (Pisum sativum) is one of the most abundant and inexpensive alternate sources of protein. Pea proteins have a good distribution of essential amino acids, but they contain relatively low amounts of sulfur-containing amino acids (methionine and cysteine) and tryptophan in comparison to cereal crops. Pea isolate samples from different time-points during fermentation with Aspergillus oryzae, were used for shotgun mass spectrometry (LC-MS/MS) analysis to identify the proteome matrix changes.