Figure 2.

Summary of peptide selection for targeted proteomics. Peptides were selected from three sources to obtain at least three peptides per protein: (i) those directly observed in the PDX discovery experiments, (ii) peptides available in-house from previous projects, and (iii) peptides from the online databases Peptide Atlas (http://www.peptideatlas.org/) and SRMAtlas (http://www.srmatlas.org/). For selection, peptides had to be between 7 and 25 amino acids in length, have a hydrophobicity score between 10 and 40, and have no more than one missed cleavage. A total of 1303 of the candidate biomarkers are represented by three or more peptides per protein; proteins with less than three peptides were keratins and IgGs.