Combination of FASP and fully automated 2D-LC-MS/MS allows in-depth proteomic characterization of mouse zymogen granules.

Zymogen granule (ZG) constituents play important roles in pancreatic injury and disease. In previous studies, proteomic analyses with rat zymogen granules were separated by two-dimensional gel electrophoresis or one-dimensional SDS-PAGE, followed by in-gel tryptic digestion. In order to overcome the disadvantage of in-gel digestion and to carry out further in-depth proteomic analysis of the zymogen granules, in this study, by combining a filter-aided sample preparation method and fully automated 2D-LC-MS/MS technique, 800 ZG proteins were identified with at least two unique peptides for each protein, 75% of which have not been previously reported. The identified proteins revealed broad diversity in protein identity and function. This is the largest dataset of ZG proteome, and also the first dataset of the mouse ZG proteome, which may help elucidate on the molecular architecture of ZGs and their functions.