Table 3.
Summary of yeast search results without prior peptide FDR filtering at various glycan FDR levels
| Glycan FDR (%) | Glycan FDR only glycoPSMs | NeuAc PSMs | NeuGc PSMs | Fucose PSMs | Other non-east PSMs | Raw entrapment rate (%) | Adjusted entrapment rate (%) |
|---|---|---|---|---|---|---|---|
| 1 | 14,052 | 1 | 0 | 50 | 1178 | 8.7 | 0.09 |
| 0.5 | 11,291 | 1 | 0 | 13 | 424 | 3.9 | 0.04 |
| 0.1 | 5171 | 0 | 0 | 0 | 41 | 0.8 | 0.008 |
The combined yeast and mouse (1670) glycan list was used for the MSFragger search. In total, 33,450 potential glycoPSMs were supplied to PTM-Shepherd with no peptide FDR filter. PSMs matched to entrapment glycans are shown for each FDR level along with raw and adjusted entrapment rates.