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Vendor specific software / Re: Problems while using Compound Discoverer 3.2
(1) I did some intensive tests on CD. The standard CD metabolomics workflow works pretty fine regarding RT alignment. Try to set high noise value. For instance, with our QE plus, we use 10e6 as noise threshold.
(2) If most of your peaks are not aligned, some unaligned peaks from different samples will of course be identified repeatedly. But also pay attention to structural isomers.
(3) Same could happen if most peaks are not aligned.
Wang