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Analysis and validation of proteomic data generated by tandem mass spectrometry

Nature Methods volume 4, pages 787–797 (2007)Cite this article

Abstract

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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Figure 1: Peptide identification by MS/MS database searching.
Figure 2: Statistical analysis of large-scale datasets of peptide assignments.
Figure 3: Quantitative proteomics workflows.

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Acknowledgements

This work was supported in part by US National Institutes of Health (NIH) National Cancer Institute Grant R01 CA126239 to A.I.N. and with federal funds from the National Heart, Lung, and Blood Institute of the NIH under contract no. N01-HV-28179 to R.A.

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Authors and Affiliations

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

    Alexey I Nesvizhskii

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

    Olga Vitek

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

    Ruedi Aebersold

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

    Ruedi Aebersold

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Correspondence to Ruedi Aebersold.

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Nesvizhskii, A., Vitek, O. & Aebersold, R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4, 787–797 (2007). https://doi.org/10.1038/nmeth1088

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