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Is there a way to import search results from compound discoverer?

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Is there a way to import search results from compound discoverer? licky lck  2025-03-21 05:05
 

Hi,

I would like to use skyline to quantify my compound discoverer search results. Unfortunately, the ".cdresult" file cannot be imported into skyline just like the ".pdresult" from proteome discoverer. I know that there is a way to do so, at least to import the MS2 spectra into skyline with the included transition list. Could you please help me out?

Ps: I tried to import a file to skyline as annotation file, but skyline tells me that I am missing a column called "elementlocator".

Thanks a lot,
Chengkang
 
 
Nick Shulman responded:  2025-03-21 05:23
Skyline does not know how to read .cdresult files.

The CSV file that you have attached is similar to what you would import into Skyline with the "File > Import > Transition List" menu item.
However, in Skyline, a Transition List must have one fragment ion per line.
Your CSV files has all of the transitions for a particular molecule on the same line with the different Product m/z values specified in separate columns each named "Fragment".
Would it be possible for you to create a transition list file which looks like what Skyline is expecting?

You can learn more about importing transition lists into Skyline in the Small Molecule Targets tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule

-- Nick
 
licky lck responded:  2025-03-23 04:26
Thanks a lot Nick, I will give it a try.