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Opening DIA for small molecules ((bbCID (MS/MS) and MS)) from Bruker impact II

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Opening DIA for small molecules ((bbCID (MS/MS) and MS)) from Bruker impact II mohamed kaddah  2023-01-03 19:54
 

I am trying to open bbCID (MS/MS) and MS from Bruker, it is a type of DIA. I applied this method for degradation of pharmaceutical compound (small molecule). What is the procedure, how I can insert the range not a list of masses?

Can I inspect the data manually? is the step seeing the precursor and products overlayed available? can I use the software to extract specific ions during by inspection?
 
 
Nick Shulman responded:  2023-01-03 20:00
I am not sure that I understand your question.

If you would like to look at the spectra in your mass spec data file, then you can use a program called "SeeMS.exe" which is part of ProteoWizard. You can install ProteoWizard from here:
https://proteowizard.sourceforge.io/

If you want to use Skyline, you really do need to tell Skyline the precursor and product m/z's of all of the transitions that you want Skyline to extract chromatograms for.
You might find helpful some of the "Small Molecule" tutorials on the Skyline tutorial page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials

-- Nick