Supplementary Figure 3: Boxplots of the shape measure (log_L_R), SNR, and RT difference
From: moFF: a robust and automated approach to extract peptide ion intensities
Boxplots of shape measure (log_L_R), SNR, and RT difference between input peak RT and peak apex RT as identified by moFF, across all CPTAC study 6 runs. The majority of peaks across these 45 runs display a symmetrical shape (log_L_R close to 0) and consistently high SNRs. Replicates within each of the labs (designated by a set of three consecutive numbers: 1, 2 and 3 for lab 1; 4, 5 and 6 for lab 2; 7, 8 and 9 for lab 3) show quite consistent median RT difference, while more variation can be seen between labs. The samples (designated by capital letter A, B, C, D, E) have less of an effect, with different samples showing consistent median RT differences for a given lab.
