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Originally published In Press as doi:10.1074/mcp.R500012-MCP200 on July 11, 2005.
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Molecular & Cellular Proteomics 4:1419-1440, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Tutorial

Interpretation of Shotgun Proteomic Data

The Protein Inference Problem*

Alexey I. Nesvizhskii{ddagger},§ and Ruedi Aebersold{ddagger},¶

From the {ddagger} Institute for Systems Biology, Seattle, Washington 98103 and Institute for Molecular Systems Biology, ETH-Zurich, CH-8093 Zurich, Switzerland

The shotgun proteomic strategy based on digesting proteins into peptides and sequencing them using tandem mass spectrometry and automated database searching has become the method of choice for identifying proteins in most large scale studies. However, the peptide-centric nature of shotgun proteomics complicates the analysis and biological interpretation of the data especially in the case of higher eukaryote organisms. The same peptide sequence can be present in multiple different proteins or protein isoforms. Such shared peptides therefore can lead to ambiguities in determining the identities of sample proteins. In this article we illustrate the difficulties of interpreting shotgun proteomic data and discuss the need for common nomenclature and transparent informatic approaches. We also discuss related issues such as the state of protein sequence databases and their role in shotgun proteomic analysis, interpretation of relative peptide quantification data in the presence of multiple protein isoforms, the integration of proteomic and transcriptional data, and the development of a computational infrastructure for the integration of multiple diverse datasets.

§ To whom correspondence should be addressed: Inst. for Systems Biology, 1441 N. 34th St., Seattle, WA 98103. Tel.: 206-732-1245; Fax: 206-732-1299; E-mail: nesvi{at}systemsbiology.org


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