Integration and analysis of high content omics data have been critical to the investigation of molecule interactions (e.g., DNA–protein, protein–protein, chemical–protein) in biological systems. Human proteomic strategies that provide enriched information on cell surface proteins can be utilized for repurposing of drug targets and discovery of disease biomarkers. Although several published resources have proved useful to the analysis of these interactions, our newly developed web-based platform Targets-search has the capability of integrating multiple types of omics data to unravel their association with diverse molecule interactions and disease. Here, we describe how to use Targets-search, for the integrated and systemic exploitation of surface proteins to identify potential drug targets, which can further be used to analyze gene regulation, protein networks, and possible biomarkers for diseases and cancers. To illustrate this process, we have taken data from Ewing’s sarcoma to identify surface proteins differentially expressed in Ewing’s sarcoma cells. These surface proteins were then analyzed to determine which ones were known drug targets. The information suggested putative targets for drug repurposing and subsequent analyses illustrated their regulation by the transcription factor EWSR1.