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Topic: Will the data of LC-MS be removed (Read 224 times) previous topic - next topic

Will the data of LC-MS be removed

Dear everyone,
       Two sets of data, one metabolite only exists in one of them. In the peak alignment result, will mass spectrum information of the metabolite be preserved?

      Looking forward to your answers.

      All the best.

Re: Will the data of LC-MS be removed

Reply #1
It depends on your alignment settings.

I suppose, you have these two datasets as groups. If you put 0 to Alignment/N% detected in at least one group, your feature for sure will make it to the list.

Again, how your data are actually organized? # of groups, biological or measurement replicates, etc...

Re: Will the data of LC-MS be removed

Reply #2

Thank you very much for your help.

How should I set the alignment parameters? Please explain in detail because I have just started to use this software.

Our experiment was divided into two groups (normal group and model group), UPLC-Q/TOF-MS was used to collect data. We want to find out the difference metabolites (the difference in quality, not in quantity) between the two groups through MS-DIAL software.

Re: Will the data of LC-MS be removed

Reply #3
> Our experiment was divided into two groups (normal group and model group), UPLC-Q/TOF-MS was used to collect data.

Do you have biological or measurement replicates for each sample in your group or it is simply X measurements, each from different specimen?

Re: Will the data of LC-MS be removed

Reply #4
it is simply X measurements, each from different specimen. There are 10 samples in each group

Re: Will the data of LC-MS be removed

Reply #5
It does not depend on software, it's common issue - what do you want to see as a feature and how robust it should be.

Then i would set Peak count filter to and N% detected in at least one group in initial evaluation to 0%, or better - do chromatogram similarity heatmap in something like R/XCMS, then Peak count to 0 and N% detected to 80%.

Again, you urgently need pooled QC for such investigation.

Re: Will the data of LC-MS be removed

Reply #6
Thank you very much for your help !