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Chromatogram Information Unavailable Message csb548  2024-03-05 08:51
 

Dear Support Team,

I am new to using Skyline and I am trying to create a workflow to enable rapid peptide identifications in my samples (the samples I am performing the test on have already been analyzed through Mascot, and the peptides I am targeting have been identified in all of the samples). My data is DDA-timsTOF HT data. When I try to import my data, I keep being met with a "chromatographic information unavailable" message. I'm not sure what it is I am doing wrong so any help would be appreciated!

I should also note, these samples have not undergone any digestion.

I have attached some Skyline files and some written instructions I was writing as I was making the document in Skyline to keep track of everything.

Thanks,
Charllotte
 
 
Nick Shulman responded:  2024-03-05 09:03
If you want to extract chromatograms from DDA data, you actually have to also tell Skyline to extract chromatograms from the MS1 data as well.
That is, you need to go to:
Settings > Transition Settings > Full Scan
and choose something for "MS1 filtering Isotope peaks included" section.
And you should also go to "Settings > Transition Settings > Filter" and change "Ion Types" to something which includes the letter "p", such as "y, p".

After you have done that you can tell Skyline to extract chromatograms again by using the "Reimport" button at "Edit > Manage Results".

Chromatograms extracted from DDA data do not look very good because they have long straight lines that connect the places where a matching precursor happens to have been selected for fragmentation.
We added the "DDA" acquisitions method so that you would have something to click on in order to see MS2 spectra, but, unfortunately, it only works if you have also told Skyline to extract MS1 chromatograms (I should fix this).

By the way, if you have any more questions, the best way to send a Skyline document to someone else is to use the menu item:
File > Share

This menu item will create a .zip file containing your Skyline document and supporting files including extracted chromatograms, spectral libraries, background proteome.
If that .zip file is less than 50MB you can attach it to this support request. Larger files can always be uploaded here:
https://skyline.ms/files.url
-- Nick
 
csb548 responded:  2024-03-05 09:49
Thank you! That seems to have worked now.

Charllotte