Table 3.
Mean Counts of Ion Types in True Matches for Search Results Before and After Rescoringa
| unphosphorylated | phosphorylated | |||||
|---|---|---|---|---|---|---|
| both | rescore only | search only | both | rescore only | search only | |
| peptide length | 18.2 | 18.4 | 21.0 | 20.7 | 21.9 | 28.1 |
| # ions | 61.4 | 63.0 | 61.7 | 81.5 | 89.1 | 81.5 |
| unannotated | 22.0 | 32.1 | 30.1 | 30.3 | 42.0 | 36.7 |
| y ions | 18.5 | 14.8 | 15.0 | 26.6 | 26.2 | 24.2 |
| b ions | 8.9 | 5.9 | 6.2 | 11.7 | 8.0 | 10.1 |
| a ions | 1.7 | 1.3 | 0.9 | 1.3 | 1.3 | 0.6 |
| neutral loss | 4.3 | 2.7 | 3.2 | 16.4 | 16.0 | 13.4 |
| internal | 6.9 | 5.2 | 6.2 | 6.5 | 6.4 | 5.0 |
| immonium | 2.3 | 2.5 | 1.8 | 2.7 | 3.0 | 1.9 |
| parent | 1.1 | 1.2 | 1.6 | 2.4 | 2.3 | 2.9 |
| parent intensity | 191.6 | 204.9 | 369.1 | 197.9 | 199.1 | 295.1 |
a
“both” means true positive for both the sequence search and the rescoring, “rescore only” means true positive only after rescoring, and “search only” means true positive only before rescoring.