How to set the same (matching) peak boundaries while integrating in Skyline

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How to set the same (matching) peak boundaries while integrating in Skyline MNezvedova  2022-01-20 03:03
 

Dear Sir or Madam,
sometimes it happens that when moving peak boundaries for light peptide, there is no change in peak boundaries for heavy peptide. So then they are not matching, and it makes the integration quite tricky. I couldn't find anything in the Skyline settings where this can be changed?

I appreciate your support,

Marketa

 
 
Nick Shulman responded:  2022-01-20 11:39
I am not sure that I understand your question.

Sometimes people have trouble choosing a new peak if there is not already a detected peak whose boundaries they can adjust with the mouse.
If you want to specify a brand new peak on the chromatogram graph, the way to do that is to point the mouse below the X-axis, and click and drag horizontally below the X-axis to specify the start and end points of the peak.

It sounds like you were asking something else.

Can you 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. You can upload larger files here:
https://skyline.ms/files.url

-- Nick
 
MNezvedova responded:  2022-01-24 00:22
Hi, yes, I was asking something different. I tried to show it in an example attached to this message.
There is no automatic change in the heavy peptide when I want to change the border for my light peptide. So it means that there are different integrated areas for light and heavy peptides.

Markéta
 
Nick Shulman responded:  2022-01-24 14:49
Markéta,

You would see the behavior that you are seeing if your heavy modifications had their "Relative Retention Time" set to something other than "Matching".
That is, if you go to:
Settings > Peptide Settings > Modifications
and push the "Edit List" button that is next to the Isotope Modifications
and then select one of those isotope modifications and press "Edit"
at the bottom of the Edit Isotope Modification dialog there's a dropdown which lets you specify the effect of the isotope modification on the peptide retention time. If you choose anything other than "Matching" then Skyline will allow you to set the heavy and light peak boundaries separately. If you set it to "Matching" then whenever you adjust the heavy or light peak boundaries, Skyline will adjust the other label type's peak boundaries at the same time.

Is that what's going on? If you still have questions you should probably send us your Skyline document ("File > Share" to create a .zip file).
-- Nick
 
MNezvedova responded:  2022-01-25 03:32
That was the problem! Yes, so thank you so much for your advice! :)

Have a nice day,

Markéta