Schema of the workflow in construction of the predicted peptide database based upon Vitis spp. ESTs. Steps in EST selection (yellow), EST curation (orange), contig assembly (green), and translation, start methionine prediction, tryptic cleavage site prediction, and removal of predicted truncated N- and/or C-terminal peptides (blue) are shown. The in-house "GrapeGen" EST database was derived from the V. vinifera cv. Cabernet Sauvignon and Muscat Hamburg cDNAs . Where a CS EST was duplicated between the Genbank and in-house databases, the Genbank EST was removed and the EST from the in-house database, containing the phred scores, was used for clustering. CS = Cabernet Sauvignon ESTs; MH = Muscat Hamburg ESTs; Vv = Vitis vinifera; Wild = Vitis spp. ESTs other than V. vinifera. A key to the codes used in 'Cluster ORF ID' and 'Protein Annotation' in Additional files 1 through 8 is presented in Additional file 10 and may be printed out as a quick reference when examining the iTRAQ results; tissue types (i.e. CS_) are described in Methods and Additional file 10.