Skip to main content
Topic: Peak detection: Amplitude calc (Read 2164 times) previous topic - next topic

Peak detection: Amplitude calc

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

Re: Peak detection: Amplitude calc

Reply #1
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.