In the post-genome-sequence era, both the amount and the variety of proteome data are rapidly increasing due to the progress of protein identification methods such as mass-spectrometry (MS), high-throughput liquid chromatography. To manage a wide variety of enormous data and control the quality of the analysis results, IT platform for proteomics data is necessary for the researchers. We have developed a proteomics solution system which consists of a sample management system by using barcode tracing, a MS spectrum data archiving system, a proteome analysis result management system, a data mining system of related papers from literature databases and so on. This IT platform can facilitate proteomics researchers exploring relationships between sample resource information, MS data and identification results. We have proposed an XML format, HUP-ML (Human Proteome Markup Language), for proteomics databases, and for exchanging proteome data. HUP-ML can describe the preparation parameters as well as the results of 2D gel electrophoresis analysis / LC analysis by adopting a proteome-analysis-oriented data model, which would make proteome data comparable and reproducible. HUP-ML involves such information as sample preparation, 2D gel electrophoresis conditions, spot identification results, amino acid sequences. We provide the editor with graphical user interface (GUI) to create and utilize XML formatted proteomics data. In addition, we developed the database of human kidney glomerulus proteome using by 2-DE analysis. The database is accessible through the Internet and it exemplifies the way of proteome data exchange by using the XML format and its contribution to collaboration between researchers.
