Figure 1.

Evaluation of the missing data for the labeled CPTAC data set shows (A) a marginal negative correlation between the mean log₂ abundance (before normalization to the reference pool) and the percentage of missing data and (C) that within a 4-plex experiment that the majority of peptides are either all present or all absent for the three nonreference samples. For a similar unlabeled CPTAC data set it is observed that (B) there is a similar negative correlation between log₂ abundance (before normalization) and missing data, but for (D) sampling of data in a 4-plex manner yields varying probabilities across the number that will be present or absent.