Fig. 4

Retention time and fragmentation accuracy of spectrum and chromatogram libraries. Scatterplots comparing retention times (RT) from the a DDA spectrum library and the b DIA chromatogram library to those from in a single HeLa DIA experiment. Each point represents a peptide, where blue peptides fit the retention time trend (green) within a Bayesian mixture model probability of 5% and red peptides are outliers (see Methods section for more details). c Delta RTs in the DDA spectrum library are 95% accurate to a window of 5.1 min, while d retention times in the chromatogram library are 95% accurate to 21 s. e The distribution of Pearson correlation coefficients between spectra in the DDA spectrum library and those detected from a single HeLa DIA experiment shows charge state bias, while f the distribution of correlation coefficients between spectra in the DIA chromatogram library and those from the same experiment shows much less bias