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

From: 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

Sample Database searched Proteins detected Distinct peptides detected
2005 mesocarp MSDBa 1184 5679
2005 mesocarp Custom Vitis DB with weightingb and trimmingc 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
  1. aRelease 20063108, Hammersmith Campus of Imperial College London
  2. 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
  3. cPredicted tryptic peptides that were determined to likely be truncated were trimmed and removed from the custom peptide database