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

Table 1 Comparison of numbers of high confidence peptides and proteins detected by ProteinPilot based on the amino acid sequence database searched.

Sample	Database searched	Proteins detected	Distinct peptides detected
2005 mesocarp	MSDB^a	1184	5679
2005 mesocarp	Custom Vitis DB with weighting^b and trimming^c	1424	10793
2005 exocarp	MSDB	1390	6915
2005 exocarp	Custom Vitis DB with weighting and trimming	1493	12945
2005 exocarp	Custom Vitis DB with trimming but no weighting	1447	12956
2005 exocarp	Custom Vitis DB with weighting but no trimming	1382	8845

^aRelease 20063108, Hammersmith Campus of Imperial College London
^bEST clustering weighted higher scores for ESTs derived from Cabernet Sauvignon in order to avoid the potential loss of SNPs specific to this cultivar during consensus sequence determination by the PCAP software
^cPredicted tryptic peptides that were determined to likely be truncated were trimmed and removed from the custom peptide database

ISSN: 1471-2164