Supplementary Figure 15: Target-decoy analysis of Prosit and MS2PIP.
From: Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
(a) Comparison of the spectral angles of MS2PIP predictions to spectral angles of Prosit predictions for target (green) and decoy (orange) peptide spectrum matches generated by Andromeda. A random subset of 10,000 PSMs from the Bekker-Jensen tryptic dataset are shown. The PSM for peptide LVDCLSR is analysed in (c). (b) As in (a), but on a random subset of 10,000 PSMS from the Bekker-Jensen chymotrypsin dataset. (c) Analysis of a PSM for which Prosit’s prediction has a lower spectral angle than MS2PIP’s prediction. The PSM is highlighted in (a). Top: Prosit prediction compared to 12 experimental ProteomeTools spectra. Middle: Prosit prediction compared to the experimental spectrum from Bekker-Jensen. Bottom: MS2PIP prediction compared to the experimental spectrum from Bekker-Jensen. SA and R state spectral angle and Pearson correlation, respectively.
