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.