Assessing the contribution of alternative splicing to proteome diversity in <it>Arabidopsis thaliana </it>using proteomics data

Abstract Background Large-scale analyses of genomics and transcriptomics data have revealed that alternative splicing (AS) substantially increases the complexity of the transcriptome in higher eukaryotes. However, the extent to which this complexity is reflected at the level of the proteome remains unclear. On the basis of a lack of conservation of AS between species, we previously concluded that AS does not frequently serve as a mechanism that enables the production of multiple functional proteins from a single gene. Following this conclusion, we hypothesized that the extent to which AS events contribute to the proteome diversity in Arabidopsis thaliana would be lower than expected on the basis of transcriptomics data. Here, we test this hypothesis by analyzing two large-scale proteomics datasets from Arabidopsis thaliana. Results A total of only 60 AS events could be confirmed using the proteomics data. However, for about 60% of the loci that, based on transcriptomics data, were predicted to produce multiple protein isoforms through AS, no isoform-specific peptides were found. We therefore performed in silico AS detection experiments to assess how well AS events were represented in the experimental datasets. The results of these in silico experiments indicated that the low number of confirmed AS events was the consequence of a limited sampling depth rather than in vivo under-representation of AS events in these datasets. Conclusion Although the impact of AS on the functional properties of the proteome remains to be uncovered, the results of this study indicate that AS-induced diversity at the transcriptome level is also expressed at the proteome level.