Figure 3.

Validating SEPs with targeted mass spectrometry. Analysis of PRR3-SEP by Skyline and subsequent MRM targeted LC–MS identifies additional peptides from this SEP. The tryptic peptide (blue box) that was detected in the original shotgun proteomics experiment led to the initial identification of the PRR3-SEP. To identify additional peptides from PRR3-SEP, we used Skyline to predict MRM transitions for four tryptic peptides from PRR3-SEP, and this information is fed into a targeted LC–MS experiment. This experiment identified peptides for two out of the four peptides and provided an additional two peptides (red and purple boxes) to validate this PRR3-SEP.