Proteomics suggests that global protein expression studies can provide important clues for developing biomarkers and understanding tumor biology that cannot be obtained using other approaches. Proteomic studies, such as gelbased analyses and mass spectrometry-based analyses, have provided protein expression profiles that can be used to develop novel diagnostic and therapeutic biomarkers, allowing for the molecular classification of tumors. Recently, we used proteomic approaches to develop biomarkers for bone and soft tissue tumors and identified novel biomarkers for predicting the prognosis and chemosensitivity of bone and soft tissue tumors. Although the predictive power of these biomarkers has been confirmed in large validation studies, functional analyses of the biomarkers (proteins) remain to be conducted. In this article, we describe our proteomics methodology for identifying biomarkers and our approach to evaluating the functions of the biomarkers (proteins) and provide a few examples of our recent proteomic studies.