Comparing Targeted vs. Untargeted MS(2) Data-Dependent Acquisition for Peak Annotation in LC–MS Metabolomics

One of the most widely used strategies for metabolite annotation in untargeted LCMS is based on the analysis of MS(n) spectra acquired using data-dependent acquisition (DDA), where precursor ions are sequentially selected from MS scans based on user-selected criteria. However, the number of MS(n) spectra that can be acquired during a chromatogram is limited and a trade-off between analytical speed, sensitivity and coverage must be ensured. In this research, we compare four different strategies for automated MS(2) DDA, which can be easily implemented in the frame of standard QA/QC workflows for untargeted LC–MS. These strategies consist of (i) DDA in the MS working range; (ii) iterated DDA split into several m/z intervals; (iii) dynamic iterated DDA of (pre)selected potentially informative features; and (iv) dynamic iterated DDA of (pre)annotated metabolic features using a reference database. Their performance was assessed using the analysis of human milk samples as model example by comparing the percentage of LC–MS features selected as the precursor ion for MS(2), the number, and class of annotated features, the speed and confidence of feature annotation, and the number of LC runs required.