Merge two SRM together

support
Merge two SRM together nbekhti  2024-09-10 14:07
 

I have under my skyline file one same metabolite showing in two lines, and I would like to add the second transition into one same SRM
I tried adding transition, copy paste from another skyline file where they show up together, but the second transition is gray with no data when I do this.

How to fix that issue please?
Thanks
Nihel

 
 
Nick Shulman responded:  2024-09-10 14:25
It is not possible to add another Transition to a Precursor that is already in the document.
You have to create a new Transition List which has all of the transitions that you want in it, and insert that complete transition list using the "Edit > Insert > Transition List" menu item.

I am not sure I understand what you are saying about a transition being gray with no data. I do not see anything like that in your screenshot.
If you have other questions, it might be helpful if you sent us your Skyline document and raw files.

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.
The Share Document dialog also gives you the option of including the raw files, or you can zip them up and send them to us separately.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick
 
Nick Shulman responded:  2024-09-10 20:58
Actually, I was mistaken. You definitely can right-click on a Precursor in the Targets tree and add a new transition.
Now I definitely do not understand what you were asking but if you send us your files we will probably be able to figure it out.
-- Nick
 
nbekhti responded:  2024-09-13 05:51
Thank you Nick for the answers.
Here is the result when I test adding a new transition.
My apologies I'm not allowed to share the Skyline file for privacy reasons.
Thank you very much for helping me solve this issue
Nihel
 
Nick Shulman responded:  2024-09-13 07:17
After you add the second transition to that first precursor, you probably also have to tell Skyline to read the chromatograms again from the raw file.
You can do that using the "Reimport" button at "Edit > Manage Results".
Usually, with SRM chromatograms, Skyline copies all of the available chromatograms from the raw file into the .skyd file and when you add a new transition, it will immediately notice that there is a matching chromatogram available.
However, there are a few cases where not all of the SRM chromatograms end up in the .skyd file and a reimport would be necessary. One of those cases involves when there are two precursors in the Skyline document with the same m/z.

If doing a Reimport does not fix the problem, then the problem might be that your raw file really does have an available chromatogram with a Q3 value of 129.0420 and another chromatogram with the Q3 value of 84.9820, but their Q1 values are slightly different.
When Skyline is matching up chromatograms in the raw file to precursors and transitions in the Skyline document, the first thing that Skyline does is group the available chromatograms by the exact value of their Q1.
Then, for each group of chromatograms whose Q1 value is within the Method Match Tolerance M/Z (at "Settings > Transition Settings > Instrument; defaults to 0.055), Skyline finds the group which has the most Q3 values that match the product m/z's of the transitions under that precursor.
For this reason, if you had, for instance, a chromatogram with Q1/Q3 146.90/129.0420 and another chromatogram with Q1/Q3 146.92/84.9820, Skyline would never assign both of those chromatograms to a single precursor in the Skyline document because the Q1 values are slightly different.
-- Nick
 
nbekhti responded:  2024-09-18 07:36
Thank you very much Nick.
It doesn't work unfortunately for some reason, but I'll try to fix it when working on a new Skyline file.
Thanks again for taking the time
Nihel