Fig. 3: Generation of DeepPhospho predicted libraries for DIA phosphoproteomics data mining.
From: DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation
a An experimental DDA library or direct DIA library can be converted to a predicted DDA library or a predicted DIA library by DeepPhospho. A predicted library can be also generated from public phosphoproteome or phosphosite databases, or external phosphoproteomics data. b Design of seven spectral libraries for the U2OS DIA data analysis. DDA/dDIA, experimental DDA or direct DIA library; predDDA/predDIA, predicted libraries converted from the DDA and DIA library; hPhosPepDB/hPhosSiteDB, predicted libraries built from public human phosphoproteome and phosphosite databases. Lib 3 to Lib 7 are comprised of two separate libraries. c Number of phosphopeptides and phosphosites identified using each library. Percentage of the total phosphopeptide or phosphosite number is shown for each predicted library relative to the project-specific DDA library (Lib 1). The proportions of shared identifications (IDs), gained IDs, lost IDs, and gap IDs yielded by Lib 2 to Lib 7 compared to Lib 1 are indicated in different color. Gap IDs are those present in Lib 1 yet absent in the DeepPhospho predicted libraries, thus they cannot be identified with the latter. d Library-specific FDR assessed using the target-decoy strategy. e % coefficient of variation (CV) of all phosphopeptide quantification between 10 replicates at each condition. Boxplot center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range. Source data for this figure are provided as a Source data file.
