Proteomic based identification of cancer biomarkers: The LOCCANDIA integrated platform

Pancreatic cancer is the fourth leading cause of cancer death in the United States. Consequently, identification of clinically relevant biomarkers for the early detection of this cancer type is urgently needed. In recent years, proteomics profiling techniques combined with various data analysis methods have been successfully used to gain critical insights into processes and mechanisms underlying pathologic conditions, particularly as they relate to cancer. The LOCCANDIA (Lab-On-Chip based protein profiling for CANcer DIAgnosis) project is primarily concerned with validating the application of plasma protein profiling for early pancreatic cancer diagnosis by means of developing an innovative nano-technology based (lab-on-a-chip) platform integrated in a full proteomics analysis chain. This paper describes the integrated clinico-proteomic information management and analysis platform. In particular it focuses on discussing the underlying methodologies and technological aspects of key SW modules, i.e. the data preprocessing and profile reconstruction as well as the classification modules.