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Topic: Problems while using Compound Discoverer 3.2 (Read 77 times) previous topic - next topic

Problems while using Compound Discoverer 3.2

Dear all,

I have a question regarding the processing of MS metabolomics data recorded for cancer cell intracellular metabolites using a ZipChip electrophoresis unit coupled to a Q exactive Plus MS.

I am analyzing the data using Compound Discoverer 3.2 adopting an Untargeted Metabolomics workflow.

I have the following issues that I hope you can help me with:

1- Most of the obtained spectra cannot be aligned.

2- Some metabolites were identified twice or three times within the same spectra at different RT.

3- Many metabolites (especially amino acids) were identified separately and software cannot group them. For example, glutamic acid  was identified as four separate entries across all samples.

Thank you for taking the time to read this and I Look forward to your reply.


Re: Problems while using Compound Discoverer 3.2

Reply #1

(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.