Fig. 3.
Accuracy between retention time prediction methods for peak groups extraction from SWATH-MS data files. A, The difference between observed and predicted retention time (ΔRT) of each of the confidently identified (FDR < 1%) peak groups defined by an RT-normalized assay library and extracted from a human, yeast, or mouse SWATH-MS run are compared between conditions where the assay library and SWATH-MS normalization were performed with synthetic iRT (SiRT) or common internal iRT (CiRT) normalization peptides. Data are presented as box and whisker plots, with the middle quartiles surrounding the median for the entire assay library represented by the box, whiskers showing the 95% data range and the upper and lower 2.5% of all values plotted as individual data points. B, Correlation between the intensity of a given peptide as determined by the SiRT or CiRT normalization procedure. Each dot represents the summed intensity of all transitions extracted for a given peptide peak group from the same raw file, with the only difference being the method of RT normalization. C, Distribution of matching and mis-matching peptide peak group intensities for the human (left) and yeast (middle) and mouse (right) derived samples. Pie charts depict overall distribution peptides with matching or mismatching intensity values between CiRT and SiRT aligned data sets. Horizontal bars show distribution of peptides among different categories explaining mismatched intensity values.