Hi, I did untargeted metabolite profiling by using Thermo, and used mzcloud as well as chemspider for putative annotation. I wonder how to deal with duplicated features. Should I use them all for multivariate analysis or is it better to remove the duplicates beforehand? If I need to remove the duplicates, what parameters do you use to decide which hit to be used?
For example, I got four hits of metabolite “X” with 2–3 min difference in retention time, and all similarity matching of more than 90%
Thank you