We describe an integrated proteome database, termed Yonsei Proteome Research Center Proteome Database (YPRC‐PDB) which can store, retrieve and analyze various information including two‐dimensional electrophoresis (2‐DE) images and associated spot information that were obtained during studies of hepatocellular carcinoma (HCC). YPRC‐PDB is also designed to perform as a laboratory information management system that manages sample information, clinical background, conditions of both sample preparation and 2‐DE, and entire sets of experimental results. It also features query system and data‐mining applications, which are amenable to automatically analyze expression level changes of a specific protein and directly link to clinical information. The user interface is web‐based, so that the results from other laboratories can be shared effectively. In particular, the master gel image query is equipped with a graphic tool that can easily identify the relationship between the specific pathological stage of HCC and expression levels of a potential marker protein on the master gel image. Thus, YPRC‐PDB is a versatile integrated database suitable for subsequent analyses. The information in YPRC‐PDB is updated easily and it is available to authorized users on the World Wide Web (http://yprcpdb.proteomix.org/∼damduck/).