Importing results does not show peaks (which I know are there)

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Importing results does not show peaks (which I know are there) barryh  2021-01-12
 

Hello there,

I am creating a very simple project for absolute quantitation, I selected my one and only peptide then I imported the file with the results (and while uploading I can visualize the peaks at around 2.5 min) and then when it is done importing the results the chromatogram window shows from 0 to 1.2 min and shows that there are NO peaks (See attached screenshot). I have tried everything to zoom out of that region and see the 2.5 min peaks (LC method is 6 minutes long) and I can't seem to find a successful way. Any advice would be greatly appreciated.

Thank you very much!

 
 
Nick Shulman responded:  2021-01-12
When you see the "No product ion chromatograms found" it means that there are some chromatograms, but they are MS1 chromatograms, and you have told Skyline to only show you MS2 chromatograms.

You should right-click on the chromatogram graph and choose "Transitions > All". I believe you have selected the option "Transitions > Products".

It is also possible that something else is going wrong. If "Transitions > All" does not fix it, you can send us your Skyline document.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise you can upload it here:
https://skyline.ms/files.url

-- Nick
 
barryh responded:  2021-01-12
Nick,

Thank you so much for your prompt reply. I tried that and still nothing. Here is the file attached.

HHB!
 
Nick Shulman responded:  2021-01-12
The product ions that you have chromatograms for are the singly charged y6+, y7+ and y8+ ions, but those fragment ions do not appear in your Targets tree.

The reason that Skyline did not add those ions to your Targets tree is that "1" is not included in the Ion Charges list at "Settings > Transition Settings > Filter".

You can add those fragment ions to your Targets tree by right-clicking on the precursor "886.9827++" and choosing "Pick Children".
You will have to click on the filter button on the child picker window in order for Skyline to show you the fragment ions which are being filtered out.
After you have unselected the filter button, you will see that there is a green dot next to y6, y7 and y8, so you will know that those are the ions you should add.

Another way to get those fragment ions into your document would be to go to:
Settings > Transition Settings > Filter
and make it so that "1" is contained in the Ion Charges list.
-- Nick
 
barryh responded:  2021-01-12
Nick,

That's great, no wonder I couldn't see it. Thank you for all the help!!!!

HHB!