Fruit bagging is a very effective method for study of fruit qualities and anthocyanin synthesis. The characterization of differentially expressed proteins that were isolated from both bagged and normal fruit skin tissue is apparently an essential parameter for understanding the effect of shading on fruit qualities and to understand the mechanism of fruit coloring in Pyrus communis. Proteome maps of both bagged and normal P. communis 'Placer' fruit skin were obtained by performing two-dimensional electrophoresis analysis and compared to assess the extent to which protein distribution differed in pear skin. The comparative analysis showed 38 differentially expressed proteins between the two samples: with three protein spots up-regulated and 35 down-regulated in the bagged fruit. Differentially expressed protein spots were subjected to matrix-assisted laser desorption ionization time of flight (MALDI-TOF) analysis and the data compared to that of known proteins to deduce their possible functions. Of these, 21 protein spots were identified and classified into functional classes. These identified proteins were mainly involved in photosynthesis, signal transduction, energy pathway, protein folding and assembly, and carbohydrate and acidity metabolisms, and were under-expressed in bagged fruit skins. This work provides a first characterization of the proteome changes in response to fruit bagging treatment in red pears.