Comparative shotgun proteomics analysis of wheat gluten proteins digested by various peptidases

In this study, nine wheat cultivars were digested with five different peptidases or combinations. Large differences already occurred in the number of identified peptides. With 4115 peptides, trypsin resulted in by far the most peptide identifications, followed by thermolysin with 1421 peptides. However, this no longer applied at protein level. Although most metabolic protein groups (673) were identified with trypsin, this did not apply to gluten proteins of which around 130 gluten protein groups were identified with each peptidase. The ω-gliadins were detected with all peptidases except trypsin. A relative quantification of the gluten protein groups and comparison with quantitative RP-UHPLC-UV results showed that there was the greatest overlap after thermolysin digestion. Otherwise, there was not much overlap between the relatively quantified LC-MS/MS data of the different peptidases.