Figure 6. Precursor ion intensity affects peptide repeatability.

We examined the MS ion intensity of peptides from the Study 5 NCI-20 quintuplicates in three LTQ and three Orbitrap instruments. When a peptide was observed in multiple replicates, we recorded the median intensity observed. These graphs depict the distribution of intensities for peptides by the number of replicates in which they were identified. Peptides that were observed in only one replicate were considerably less intense than those appearing in multiple replicates. Orbitrap and LTQ instruments report intensities on different scales as reflected by the x-axes of the graphs.