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Nature Methods - 4, 787 - 797 (2007)
Published online: 27 September 2007; | doi:10.1038/nmeth1088

Analysis and validation of proteomic data generated by tandem mass spectrometry

Alexey I Nesvizhskii1, Olga Vitek2 & Ruedi Aebersold3, 4

1  University of Michigan, Department of Pathology and Center for Computational Medicine and Biology, Ann Arbor, Michigan 48105, USA.

2  Purdue University, Departments of Statistics and Computer Science, West Lafayette, Indiana 47107, USA.

3  Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8093 Zurich, Switzerland and Faculty of Sciences, University of Zurich, CH-8006 Zurich, Switzerland.

4  Institute for Systems Biology, Seattle, Washington 98103, USA.

Correspondence should be addressed to Ruedi Aebersold rudolf.aebersold@imsb.biol.ethz.ch

The analysis of the large amount of data generated in mass spectrometry–based proteomics experiments represents a significant challenge and is currently a bottleneck in many proteomics projects. In this review we discuss critical issues related to data processing and analysis in proteomics and describe available methods and tools. We place special emphasis on the elaboration of results that are supported by sound statistical arguments.

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Nature Methods
ISSN: 1548-7091
EISSN: 1548-7105
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