Table 1.
NOFI compared to Spectronaut in terms of sensitivity for interference detection. The comparison is based on the 806 fragment ions annotated as affected by interferences in the DC dataset. Once the Top-N number of fragment ions is selected for NOFI, the annotated interferences within the Top-N NOFIs are considered false negatives (FN) and the remaining ones are considered true positives (TP), since these interferences are effectively excluded for quantification. The “Top-N fragments” column is not applicable for Spectronaut.
| Algorithm | Top-N fragments | True positives | False negatives | Sensitivity |
|---|---|---|---|---|
| NOFI | 3 | 743 | 63 | 0.92 |
| 4 | 719 | 87 | 0.89 | |
| 5 | 686 | 120 | 0.85 | |
| 6 | 647 | 159 | 0.80 | |
| Spectronaut | NA | 613 | 193 | 0.76 |
Sensitivity = TP / (TP + FN).