Abstract: Objective To compare the advantages and disadvantages of full scan acquisition (FSA) mode and data dependent acquisition (DDA) mode for untargeted metabolomic analysis. Methods Qualitative and quantitative results of two acquisition methods were compared by using a standard mixture of 9 metabolites and human urine sample. Results In the analysis of standard sample, the metabolite abundance in FSA mode was about 2.36 times higher than that in DDA mode (P＜0.05), the CV of metabolites abundance ranged from 2.14% to 11.20% in DDA mode and from 0.81% to 6.35% in FSA mode. In the analysis of urine sample, there was no statistical difference in the number of spectra and metabolite feature between FSA mode and DDA mode. When injecting 1, 2 and 4 μL, the number of metabolites identified by FSA mode was 9.5％, 1.9％ and 10％ higher than those identified by DDA mode, respectively. And the median CV of metabolite abundance analyzed by FSA(7.1％,3.0％ and 2.6％)was significantly lower than that by DDA(10.3％, 7.0% and 6.5%). When injecting 1, 2 and 4 μL,with the increase of abundance, the median CV of metabolite abundance in DDA mode was 1.3-1.7,1.7-1.8 and 1.4-1.9 times higher than that in FSA mode (P＜0.05), and with the increase of peak width, the median CV of DDA mode was 1.5-1.8, 1.7-2.1 and 2.0-2.2 times higher than that of FSA mode (P＜0.05). Conclusions FSA mode requires high system stability, it is suitable for fast and small-scale sample analysis; DDA mode has lower requirement for system stability, and is convenient and time-saving, which can be used for long-time and large-scale sample analysis.

Key words: untargeted metabolomics, full scan acquisition(FSA), data dependent acquisition(DDA)