Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00580.

• Statistics of water neutral loss peaks (Text S1); similarities of predicted spectra to the experimental spectra (Text S2); benchmarks of neutral loss peak generation and budding strategies (Text S3); collision energy (CE) calibration for the HeLa data set (Text S4); analysis of doubly phosphorylated peptides from HeLa cells (Text S5); optimization of CE value for Prosit and pDeep2, as well as phosphoRS parameters on the Syn-OF data set (Figure S1); statistics of water neutral loss peaks (Figure S2); dot product between the extracted peaks from the experimental spectra and the predicted spectra (Figure S3); DeltaDP results of matching the extracted peaks from the experimental spectra and the predicted spectra with different candidate phosphorylation sites (Figure S4); Phosphorylation site localization using MS/MS spectra predicted by pDeep2 with/without buddings (Figure S5); Phosphorylation site localization on Syn-OF, Syn-QE and Syn-TOF using different methods with neutral loss and budding (Figure S6); Localization results on the Syn-QE data set using different methods (Figure S7); Localization results on the Syn-TOF data set using different methods (Figure S8); Distributions of distance between the mislocated phosphorylation sites and the correct sites in Syn-OF using different methods (Figure S9); Optimization of CE value for pDeep2 on the HeLa data set (Figure S10); Phosphorylation site localization of doubly phosphorylated peptides from HeLa cells (Figure S11); LC–MS/MS datasets used in this study (Table S1); probability thresholds at 1% false localization rate (FLR) (Table S2) (PDF)

• Data Set S1: Phosphorylation site localization results on Syn-OF by Ascore and phosphoRS, as well as spectral matching using MS/MS spectra predicted by MS²PIP, Prosit, DeepMS2, and pDeep2 (XLSX)

• Data Set S2: Phosphorylation site localization results on Syn-OF using spectral matching by DeepMS2 with different neutral loss ratios (XLSX)

• Data Set S3: Phosphorylation site localization results on Syn-OF using spectral matching by DeepMS2 with different budding factors (XLSX)

• Data Set S4: Phosphorylation site localization results on Syn-OF using spectral matching by DeepMS2, MS²PIP, and Prosit with neutral loss generation and budding (XLSX)

• Data Set S5: Phosphorylation site localization results on Syn-QE by Ascore and phosphoRS, as well as spectral matching using MS/MS spectra predicted by MS²PIP, Prosit, DeepMS2, and pDeep2 (XLSX)

• Data Set S6: Phosphorylation site localization results on Syn-TOF by Ascore and phosphoRS, as well as spectral matching using MS/MS spectra predicted by MS²PIP, Prosit, DeepMS2, and pDeep2 (XLSX)

• Data Set S7: Phosphorylation site localization results on Syn-OF, Syn-QE, and Syn-TOF by phosphoRS combined with spectral matching (XLSX)

• Data Set S8: Phosphorylation site localization results for singly phosphorylated peptides from the HeLa data by phosphoRS, as well as phosphoRS combined with spectral matching (XLSX)

• Data Set S9: Phosphorylation site localization results for doubly phosphorylated peptides from the HeLa data by phosphoRS, as well as phosphoRS combined with spectral matching (XLSX)