title: Proteomics studies confirm the presence of alternative protein isoforms on a large scale.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), C, Melchor Fernandez Almagro, Madrid 28029, Spain. mtress@cnio.es
authors.forename: Michael L
authors.initials: ML
authors.lastname: Tress
authors.forename: Bernd
authors.initials: B
authors.lastname: Bodenmiller
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D029721:Drosophila Proteins / Q000032:analysis* / Q000235:genetics*; D004331:Drosophila melanogaster; D049750:Genome, Insect; D010748:Phosphopeptides / Q000032:analysis; D020033:Protein Isoforms / Q000032:analysis / Q000235:genetics; D040901:Proteomics / Q000379:methods*
chemical_list: D029721:Drosophila Proteins; D010748:Phosphopeptides; D020033:Protein Isoforms