Tandem mass spectrometry protein identification on a PC grid

Zosso, D. and Podvinec, M. and Muller, M. and Aebersold, R. and Peitsch, M. C. and Schwede, T.. (2007) Tandem mass spectrometry protein identification on a PC grid. Studies in health technology and informatics, Vol. 126. pp. 3-12.

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Official URL: http://edoc.unibas.ch/dok/A5259304

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We present a method to grid-enable tandem mass spectrometry protein identification. The implemented parallelization strategy embeds the open-source x!tandem tool in a grid-enabled workflow. This allows rapid analysis of large-scale mass spectrometry experiments on existing heterogeneous hardware. We have explored different data-splitting schemes, considering both splitting spectra datasets and protein databases, and examine the impact of the different schemes on scoring and computation time. While resulting peptide e-values exhibit fluctuation, we show that these variations are small, caused by statistical rather than numerical instability, and are not specific to the grid environment. The correlation coefficient of results obtained on a standalone machine versus the grid environment is found to be better than 0.933 for spectra and 0.984 for protein identification, demonstrating the validity of our approach. Finally, we examine the effect of different splitting schemes of spectra and protein data on CPU time and overall wall clock time, revealing that judicious splitting of both data sets yields best overall performance.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Schwede)
05 Faculty of Science > Departement Biozentrum > Services Biozentrum > Research IT (Podvinec)
UniBasel Contributors:Podvinec, Michael and Schwede, Torsten
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:IOS Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:14 Sep 2012 06:50
Deposited On:22 Mar 2012 13:59

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