Table 1. Statistics of three iTRAQ quantitative proteomic experiments.
| iTRAQ quantitative proteomic experiment | Number of proteins identified | FDR (%)a | Percentage of iTRAQ-labeled peptides (%) | Number of qualified peptidesb | Percentage of quantified proteins (%) |
| Duplicate experiment | 296 | 2.14 | 99.67 | 1,159 | 93.92 |
| Small-scale experiment | 277 | 3.51 | 99.72 | 1,185 | 98.56 |
| Large-scale experiment | 2,659 | 2.22 | 99.53 | 28,894 | 94.55 |
a
FDR (false discovery rate) was calculated by the formula: D/R×100%, where D and R are the number of matches above identity threshold determined by searching decoy and real databases, respectively.
b
Qualified peptides are peptides satisfying all the four criteria (see Methods for details) and were used for protein quantitation.