Hi, I am trying to search for significantly different compounds after a treatment via an untargerted metabolomics approach.
The RAW file was processed and annotated by Compound Discoverer software.
After setting the suitable parameters, there still mutliple hit of the same compound with a slight different at retention time. For example, I have two cholines that have high confidence score.
Because I need to trace the choline in other experiment, how can I know which choline is the real one?
Run choline in your system to find out its correct retention time. Eventually, you need to develop your own in-house library for those compounds you would like to trace based on your own LC-MS system
Thank you very much. The thing is I have tried running a few pure compounds as standards to check the retention time.
The same exact compound will have a (slightly) different retention time for every LCMS run.
So I though I would just average the intensity of that particular metabolite that having different retention time.
Is that the correct way to do?