Supplementary Figure 3: Optimization of the asymmetric isolation window by analyses of tryptic HeLa digests.
From: EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification
(a) Abundance of the M+1 isotopic peak in MS/MS scans relative to the monoisotopic precursor ion as a function of the isolation window offset for an isolation width of 0.4 Th and only doubly charged precursor ions (N=4,413) (b) As above but only for triply charged precursor ions (N=2,182). (c) Abundance of the isolated precursor ion in MS/MS scans relative to its abundance when isolated without offset and an 1.4 Th window width (N=5468) (d) RawOvFtT in MS/MS scans relative to the RawOvFtT values with an isolation width of 1.4 Th and without an offset (N=5468) (e) Number of identified MS/MS scans relative to the number of identified MS/MS scans with an 1.4 Th isolation window width and without an offset (N=3). The center bars indicate the mean values an error bars show the standard deviation. Boxplot elements: center line = median, lower and upper box limits = first and third quartiles, whiskers = maximum 1.5x inter-quartile range.
