Table 1.
Comparison of four PNP identification approaches on various spectral datasets against the PNPdatabase with 5021 PNPs (1582 PNP families). Spectral networks were constructed using the GNPS interface (the Molecular Networking workflow2) with precursor and fragment ion tolerance set to 0.02 Da and all other parameters set to the default values. # PSMs stands for the number of identified PSMs, # variants stands for the number of identified PNP variants, and # PNPs (families) stands for the number of unique PNP identifications (PNP families). P−10, FDR0 and FDR5 stand for the number of identified PSMs, variants, unique PNPs or PNP families with P-value below 10−10, at 0%, and 5% False Discovery Rates, respectively. When processing SpectraCYANO, the SpecNets tool crashed after a week of execution, and the BruteForce approach crashed due to exceeding memory limit (25 GB RAM).
| Method | # PSMs | # variants | # PNPs (families) | ||||||
|---|---|---|---|---|---|---|---|---|---|
| P−10 | FDR0 | FDR5 | P−10 | FDR0 | FDR5 | P−10 | FDR0 | FDR5 | |
| SpectraPSEUD | |||||||||
| Standard | 1029 | 997 | 1029 | 42 | 36 | 42 | 42 (13) | 36 (12) | 42 (13) |
| SpecNets | 1837 | 1837 | 1837 | 164 | 164 | 164 | 41 (15) | 41 (15) | 41 (15) |
| BruteForce | 7545 | 261 | 3822 | 1042 | 60 | 479 | 436 (197) | 33 (13) | 242 (117) |
| VarQuest | 6055 | 224 | 6055 | 871 | 54 | 871 | 341 (148) | 30 (13) | 341 (148) |
|
| |||||||||
| SpectraSTREP1 | |||||||||
| Standard | 228 | 171 | 228 | 20 | 11 | 20 | 20 (10) | 11 (5) | 20 (10) |
| SpecNets | 337 | 265 | 337 | 57 | 37 | 57 | 20 (10) | 9 (3) | 20 (10) |
| BruteForce | 2648 | 57 | 841 | 1698 | 26 | 360 | 621 (293) | 6 (1) | 133 (69) |
| VarQuest | 2266 | 128 | 716 | 1397 | 51 | 287 | 496 (225) | 8 (3) | 95 (49) |
|
| |||||||||
| SpectraSTREP2 | |||||||||
| Standard | 85 | 85 | 85 | 13 | 13 | 13 | 13 (5) | 13 (5) | 13 (5) |
| SpecNets | 101 | 22 | 101 | 23 | 5 | 23 | 13 (5) | 4 (2) | 13 (5) |
| BruteForce | 258 | 25 | 31 | 134 | 8 | 11 | 95 (60) | 5 (2) | 7 (3) |
| VarQuest | 208 | 12 | 147 | 100 | 3 | 56 | 67 (45) | 1 (1) | 37 (25) |
|
| |||||||||
| SpectraCYANO | |||||||||
| Standard | 353 | 146 | 353 | 42 | 23 | 42 | 42 (20) | 23 (14) | 42 (20) |
| VarQuest | 3573 | 226 | 3573 | 2083 | 68 | 2083 | 702 (315) | 25 (14) | 702 (315) |
|
| |||||||||
| SpectraGNPS | |||||||||
| Standard | 14757 | 7464 | 14746 | 420 | 279 | 420 | 420 (143) | 279 (110) | 420 (143) |
| VarQuest | 379089 | 5661 | 179448 | 65204 | 1695 | 19619 | 2673 (835) | 675 (256) | 2025 (648) |