Table 2. For other PTMs, performance comparison of different methods on S/T/Y sites at the high (Sp = 99.0%) and median stringency level (Sp = 95.0%).
| PTMs | Methods | Sp (%) | Sn (%) | Pre (%) | Acc (%) | Sp (%) | Sn (%) | Pre (%) | Acc (%) |
|---|---|---|---|---|---|---|---|---|---|
| S: O-GlcNAc | Proposed | 99.0 (threshold: 7.6e−4) | 24.3 | 66.3 | 93.4 | 95.0 (threshold: 6.1e−4) | 50.6 | 45.1 | 91.7 |
| O-GlcNAcScan | 99.0 | 16.1 | 56.5 | 92.7 | 95.0 | 32.5 | 34.5 | 90.3 | |
| O-GlcNAcPRED | 99.0 | 11.1 | 47.4 | 92.4 | 95.0 | 22.6 | 26.8 | 89.5 | |
| YinOYang | 99.0 | 3.29 | 21.1 | 91.8 | 95.0 | 10.3 | 14.3 | 88.6 | |
| T: O-GlcNAc | Proposed | 99.0 (threshold: 4.4e−3) | 28.5 | 71.2 | 93.3 | 95.0 (threshold: 1.8e−3) | 75.1 | 56.9 | 93.4 |
| O-GlcNAcScan | 99.0 | 10.9 | 48.6 | 91.8 | 95.0 | 33.0 | 37.3 | 90.0 | |
| O-GlcNAcPRED | 99.0 | 4.85 | 29.6 | 91.4 | 95.0 | 15.8 | 21.6 | 88.5 | |
| YinOYang | 99.0 | 3.03 | 20.8 | 91.2 | 95.0 | 11.5 | 7.74 | 88.2 | |
| Y: Nitration | Proposed | 99.0 (threshold: 2.2e−2) | 10.3 | 93.2 | 48.8 | 95.0 (threshold: 1.3e−2) | 53.1 | 93.2 | 71.3 |
| iNitro-Tyr | 99.0 | 15.8 | 94.9 | 51.9 | 95.0 | 40.2 | 91.2 | 64.0 | |
| GPS-YNO2 | 99.0 | 2.82 | 78.9 | 44.6 | 95.0 | 16.2 | 80.7 | 50.4 | |
| Y: Sulfation | Proposed | 99.0 (threshold: 1.2e−2) | 90.8 | 93.9 | 93.9 | 95.0 (threshold: 3.8e−3) | 98.9 | 77.1 | 95.9 |
| GPS-TSP | 99.0 | 33.7 | 85.2 | 89.5 | 95.0 | 67.4 | 69.4 | 90.9 | |
| Sulfinator | 99.0 | 4.76 | 39.4 | 85.1 | 95.0 | 35.2 | 54.3 | 86.3 | |
| SulfoSite | 99.0 | 24.9 | 80.9 | 88.2 | 95.0 | 45.8 | 60.9 | 87.8 |