%0 Conference Paper
%B HealthGrid 2007
%D 2007
%T Grid-based Analysis of Tandem Mass Spectrometry Data in Clinical Proteomics
%A Quandt, Andreas
%A Hernandez, Patricia
%A Kunzst, Peter
%A Pautasso, Cesare
%A Tuloup, Marc
%A Appel, Ron
%C Geneva, Switzerland
%K Grid Workflows, SwissPIT
%X Biomarker detection is one of the greatest challenges in Clinical Proteomics. Today, great hopes are placed into tandem mass spectrometry (MS/MS) to discover potential biomarkers. MS/MS is a technique that allows large scale data analysis, including the identi?cation, characterization, and quanti?cation of molecules. Especially the identi?cation process, that implies to compare experimental spectra with theoretical amino acid sequences stored in specialized databases, has been subject for extensive research in bioinformatics since many years. Dozens of identi?cation programs have been developed addressing different aspects of the identi?cation process but in general, clinicians are only using a single tools for their   data analysis along with a single set of speci?c parameters. Hence, a signi?cant proportion of the experimental spectra do not lead to a con?dent identi?cation score due to inappropriate parameters or scoring schemes of the applied analysis soft-   ware. The swissPIT (Swiss Protein Identi?cation Toolbox) project was initiated to provide the scienti?c community with an expandable multi-tool platform for automated and in-depth analysis of mass spectrometry data. The swissPIT uses multiple   identi?cation tools to automatic analyze mass spectra. The tools are concatenated as analysis work?ows. In order to realize these calculation-intensive work?ows we are using the Swiss Bio Grid infrastructure. A ?rst version of the web-based front-   end is available (http://www.swisspit.cscs.ch) and can be freely accessed after requesting an account. The source code of the project will be also made available in the near future.