Hi all,
I have been exploring MS-DIAL recently and I am wanting to learn optimising the parameters better. My question is for GCQTOF data, on MSDIAL - during peak detection how do I determine an accurate amplitude? Recommended is 1000, there's not a lot of guidance on the MS-DIAL manual explaining this in detail.
I am used to exploring my raw data in mzMine to determine noise level, in 1E2-5E5 sort of ranges. How does, or does it at all translate to how amplitude is decided?
Thank you
If you have some prior knowledge of features before hand, your best bet is to determine this in the vendor software. You just need to determine a suitable cutoff to call "noise" that you have some confidence is a lower intensity than a low-intensity biological peak. There is no right or wrong, one size fits all. You must examine your data before setting the MS-DIAL parameters because they may not be appropriate for every analysis.