openBIS for Proteomics was developed within the SystemsX.ch project PhosphoNetX to manage protein identification as well as protein quantification data. Protein identifications resulting from TPP (the Trans-Proteomic Pipeline) are imported as protXML files and displayed in a tabular Protein Viewer. Within this Protein Viewer custom queries have been integrated for the quantification data for a set of pre-defined treatment conditions. The current proteomics setup has further been configured to query the relational proteomics database via structured query language (SQL). Either predefined or custom SQL queries can be run.
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