Diferentiate dda and dia

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Diferentiate dda and dia luzjpaulo25041  2022-01-26 07:11
 

Dear Skyline team,

I would like to ask if one could use Skyline to find out if a raw file was generated by dda or dia. I have a file that is supposed to be DDA but I fear it is not.

Best regards
Joao

 
 
Nick Shulman responded:  2022-01-26 07:20
Whenever I want to figure out what the isolation scheme of a raw file is, I use "SeeMS.exe" which you get when you install ProteoWizard.
You can install ProteoWizard from here:
https://proteowizard.sourceforge.io/download.html

When you open the raw file in SeeMS.exe, you can see a list of all of the spectra. The "Precursor Info" column will tell you which m/z was isolated for fragmentation, and the "Isolation Windows" column will tell you how wide of a window around that precursor was isolated.
If it's a DIA file, there will be a limited number of unique values in the Precursor Info column, and the Isolation Windows values will all be the width that you expect.
If it's a DDA file, then the numbers that you find in the Precursor Info column will almost all be unique, since they depend on exactly what m/z the mass spectrometer observed. The window widths in the Isolation Window column will typically be much smaller than you would see for a DIA experiment.
-- Nick