Supplementary Figure 4: Comparison of Prosit and MS2PIP.
From: Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
Subsets of the ProteomeTools holdout are used in this figure. None of the peptides and spectra in this dataset were used to train or test Prosit’s fragment intensity model. In boxplots, outliers are not shown, whiskers indicate 1.5 interquartile range (IQR), and black horizontal lines indicate median values. For reference, a spectral angle of 0.9 and 0.7 are indicated. (a) Benchmark of Prosit’s (green) and MS2PIP’s (orange) fragment ion intensity prediction compared to the experimental ProteomeTools spectrum respectively. Data is split by peptide length on a random subset of the ProteomeTools holdout dataset. (b) Same as (a) but split by precursor charge. (c) Same as (a) but split by collision energy. (d) Comparison of Prosit’s and MS2PIP’s fragment ion intensity prediction limited to spectra acquired at NCE 35 of the holdout set. Orange dots denote peptides that were (likely) part of MS2PIPs training data.
