Figure 2. Basis of deconvolution approach.

(a) MS² isolation window shapes for Agilent 6520 QTOF. Using a larger MS² isolation window increases the likelihood of isolating more than 1 precursor in the collision cell for MS² analysis, but also improves the relative intensity of ions transmitted. Representative (b) MS² at 0 V and (c) MS² at 20 V data used for deconvolution over a 30 second chromatographic window. Each box in the plots represents a single scan. Peak intensity is denoted by color, with bright red representing the most intense peaks. The blue brackets indicate the position of the 9 Da MS² isolation window used. Ion intensities that are high and low in alternating scans (i.e., bright red followed by light red) are ions that are included and excluded respectively with shifts in the position of the MS² isolation window. Our deconvolution approach is based on identifying matching patterns in the MS² plots at 0 and 20 V. An example of a matched precursor and associated fragment is shown with arrows.