Research article
Generation of a predicted protein database from EST data and application to iTRAQ analyses in grape (Vitis vinifera cv. Cabernet Sauvignon) berries at ripening initiation
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* Corresponding author: Steven T Lund stlund@interchange.ubc.ca
1 Wine Research Centre, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada
2 Bioinformatics Group, Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
3 University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
BMC Genomics 2009, 10:50 doi:10.1186/1471-2164-10-50
Published: 26 January 2009Additional files
Additional file 1:
Duplicated proteins and associated replication scores for exocarp 2004 technically replicated iTRAQ experiments. Ratiometric data are given in log2 scale.
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Additional file 2:
Duplicated proteins and associated replication scores for exocarp 2004 and exocarp 2005-1 biologically replicated iTRAQ experiments. Ratiometric data are given in log2 scale.
Format: XLS Size: 362KB Download file
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Additional file 3:
Proteins identified in all of the three iTRAQ data sets analyzed (exocarp 2004 (two technical replicates) and exocarp 2005-1) and tested for replication in expression trends along ripening initiation.
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Additional file 4:
Exocarp proteins listed for each K-means cluster along with corresponding log2-transformed ratiometric data for each protein entry. Exocarp proteins from the 2004, 2005-1, and 2005-2 datasets were combined into a single file. Duplicate entries were identified using an in-house script in the R environment with 'Custom ORF ID' as the search string. Then, ratiometric data at each of the three comparisons using 'green' as the reference stage were averaged prior to export for K-means cluster analyses.
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Additional file 5:
Mesocarp proteins listed for each K-means cluster along with corresponding log2-transformed ratiometric data for each protein entry. Mesocarp proteins from the 2004, 2005-1, and 2005-2 datasets were combined into a single file. Duplicate entries were identified using an in-house script in the R environment with 'Custom ORF ID' as the search string. Then, ratiometric data at each of the three comparisons using 'green' as the reference stage were averaged prior to export for K-means cluster analyses.
Format: XLS Size: 782KB Download file
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Additional file 6:
Protein isoforms detected in common between the exocarp and mesocarp (Additional files 4 and 5, respectively). A custom script written in the R environment was used to search for proteins common to the combined exocarp and mesocarp files using 'Custom ORF ID' as the search string.
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Additional file 7:
Protein isoforms detected only in exocarp samples. Proteins excluded from Additional file 6 that were detected in the combined exocarp file (Additional file 4) are shown.
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Additional file 8:
Protein isoforms detected only in mesocarp samples. Proteins excluded from Additional file 6 that were detected in the combined mesocarp file (Additional file 5) are shown.
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Additional file 9:
Protein source tissues and number of unique high confidence peptides per protein. Proteins presented in the Results and Discussion sections as well as in Figure 4 are shown. The source tissue for each protein hit shown in Column A corresponds to a ProteinPilot output file, which can be downloaded at http://www.landfood.ubc.ca/people/steven.lund webcite The number of unique > 95% confidence peptides determined by the ProteinPilot software for each protein is shown in Column E. Ratiometric data shown in Columns G, H, and I are relative to the green stage (Column F) and are not log2-transformed.
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Additional file 10:
Reference key for coding terms used in Column A (Cluster ORF ID) and Column B (Protein Annotation) in Additional files 1 through 8. The key is provided as a printable rapid reference for data mining in Additional files 1 through 8, as well as in the protein database available online, as shown in the Acknowledgments.
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