There are now thousands of known bioactive compounds in vivo. However, we thought that most of their target proteins, immediately bound to the compounds and perturbation of their activities by other methods also exhibited similar bio-activity in vivo, are still unclear. Therefore we now focus on our effort for identification of specific binding proteins to known bioactive compounds such as drugs using affinity resins bearing them because we believed that some of them could be new drug targets. Sensitive analysis of specific binding proteins in SDS-PAGE gel and reliability of LC-MS/MS system were vital for performing our project. We here show 1) development of a cutting-apparatus for preparation of pieces of acrylamide-gel including specific binding protein, 2) optimization of pre-treatment system for effective reduction of carry-over samples in a stacking-column in LC-MS/MS system, and 3) optimization of experimental condition of in-gel digestion without calcium ion, from our efforts to optimize our system for sensitive identification of proteins using a LC-MS/MS system.