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Topic: Can MS2 of Pools just be used for identification? (Read 3170 times) previous topic - next topic

Can MS2 of Pools just be used for identification?

Does MSDial support an iterative exclusion DDA Q-TOF workflow where a pooled sample is used to generate a series of MS2 data files  by iterative exclusion DDA and each individual sample is analyzed by MS1 only. The DDA files are only used for identification and the MS1 files are used to look for fold changes.
 

Re: Can MS2 of Pools just be used for identification?

Reply #1 –
I'm pretty sure you can. MS2's as QCs. Remove the 'include' check next to them. Set the unknowns to groups you want to compare. Run the data.

You may have to play around a bit with it. You can do that by going back to 'file property setting' & changing things as needed.

Re: Can MS2 of Pools just be used for identification?

Reply #2 –
I did try assigning them as QC's in the file property dialog after peak detection, alignment etc., and the MS2 samples bar did disappear but the fold changes did not change and I suspect the fold change calc uses the MS2 samples bar when it is the largest bar. BTW, I assume the fold change is the largest bar height divided by the lowest bar height (?).