Supplementary Figure 1: Comparison of converters.
From: Building high-quality assay libraries for targeted analysis of SWATH MS data
(a) Violin plots show the intrinsic fragment ion spectrum variability of three yeast sample injections converted with three DDA centroiding algorithms.
(b) Violin plots show how well the relative intensities of the six most intense fragment ions obtained by a certain centroiding algorithm compare to the relative intensities of the same six fragments in SWATH MS data.
The spectrum similarity was determined using the normalised spectral contrast angle as described by Toprak and co-workers41. N indicates the number of pairwise comparisons of fragment ion spectra for the same peptide precursors between each data file and S indicates the estimated level of dissimilarity obtained by comparing the experimental score distribution to the score distribution of a perturbation benchmark dataset (the lower S, the more similar the spectra).
(c) Depending on the centroiding algorithm implemented in the different peak pickers, the number of peptide and protein identifications from a database search vary slightly (after filtering for protein-level FDR=1%). The size of the circles is proportional to the number of identifications.
