BioSunMS, a comprehensive software platform for submission, management, retrieval of sample and MS data, and clinical proteomics-related statistical analysis. BioSunMS integrated all functions into a user-friendly desktop  RCP application. Its architecture was composed of 5 parts.

• It had a Graphical User Interface written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plug-in architecture, which gave BioSunMS an advantage over other systems. It can be easily extended by incorporating new functions.
• It had a MySQL database, which contained all metadata, including patients’ general information, symptom description, laboratorial results and peaks from mass spectrometry.
• It had a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data.
• It was equipped with the software package R. The R package can be used for statistical calculations and MS peak process, such as peak extraction, t-test, classification, cluster analysis and et al.
• The libSVM Package was integrated into the BioSunMS system. It can be used for MS data-based sample classification and biomarker discovery.