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Proteomics studies confirm the presence of alternative protein isoforms on a large scale

Michael L Tress1*, Bernd Bodenmiller2, Ruedi Aebersold2345 and Alfonso Valencia1

Author Affiliations

1 Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, Madrid 28029, Spain

2 Institute of Molecular Systems Biology, ETH, Wolfgang-Pauli-Str., 8093 Zurich, Switzerland

3 Institute for Systems Biology, Seattle, WA 98103, USA

4 Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland

5 Faculty of Science, University of Zurich, 8057 Zurich, Switzerland

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Genome Biology 2008, 9:R162  doi:10.1186/gb-2008-9-11-r162

Published: 18 November 2008



Alternative splicing of messenger RNA permits the formation of a wide range of mature RNA transcripts and has the potential to generate a diverse spectrum of functional proteins. Although there is extensive evidence for large scale alternative splicing at the transcript level, there have been no comparable studies demonstrating the existence of alternatively spliced protein isoforms.


Recent advances in proteomics technology have allowed us to carry out a comprehensive identification of protein isoforms in Drosophila. The analysis of this proteomic data confirmed the presence of multiple alternative gene products for over a hundred Drosophila genes.


We demonstrate that proteomics techniques can detect the expression of stable alternative splice isoforms on a genome-wide scale. Many of these alternative isoforms are likely to have regions that are disordered in solution, and specific proteomics methodologies may be required to identify these peptides.