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Submitted on June 6, 2005
Revised on July 5, 2005
Accepted on July 11, 2005
Institute for Systems Biology, Seattle, WA 98103
Corresponding Author: nesvi{at}systemsbiology.org
The shotgun proteomics 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 paper we illustrate the difficulties of interpreting shotgun proteomics data, and discuss the need for common nomenclature and transparent informatics approaches. We also discuss related issues such as the state of protein sequence databases and their role in shotgun proteomics 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.
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