Retention time prediction based proteomic analysis on proteins from glycolysis/gluconeogenesis pathway of E. coli

Several studies on the prediction of the LC retention time of tryptic peptides have been applied on protein identification for the proteomic analyses. In this study a proteomic method was developed based on prediction of retention time of chromatography and mass to charge value. With the conversion of normalized elution time into predicted retention time, tryptic peptides of E. coli cytosol were analyzed by RPLC-ESI-MS/MS with the preferred precursor ion list generated from glycolysis/gluconeogenesis pathway. Totally 8 of the 25 targeted proteins were identified with the method of precursor ion selected MS/MS detection, comparing to the 5 proteins identified with automatic MS/MS detection. The new method shows improvement on both the number and the quality of the MS/MS detection of targeted peptides. The average absolute deviation of predicted RT and observed RT is 3.5 minutes, which indicates the acceptable application to the further proteomic analysis.