For the following libraries a parallel reaction monitoring (PRM) approach was used to measure the synthetic peptides. Subsequently, the raw files were searched in various MaxQuant runs, separated based on the heavy labeled amino acid modification to keep the search space within reasonable limits. The search results were loaded into Skyline to visualize and manually validate the identified peaks. Then, synthetic MS2 spectra were exported from Skyline and used as a library in the SRM experiments.
Source files used to build the following libraries are available at https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?identifier=PASS01234. Spectral library generation is described in the associated publication: High-Throughput Assessment of Kinome-wide Activation States.