Error loading isotopic peaks from transition list

Error loading isotopic peaks from transition list laura corveleyn  2023-09-11 06:27


I encountered an error when trying to import a transition list (which I exported from another Skyline project); it is not extracting the isotopic peaks. I tried looking into the transition settings, but I couldn't find any restrictions there for the isotopic peaks. I added the Skyline file and transition list in the attachment. Could you help me with this?

Thank you!


Brian Pratt responded:  2023-09-11 10:59

I think the issue is that Skyline isn't expecting to be told about the precursor isotopes, it expects to calculate those on its own.

If you edit out those lines with [M+1] and [M+2] I think you'll find it works just fine.

But I will add an issue to deal with this more gracefully in future.

Thanks for using the Skyline support board!

Brian Pratt

Nick Shulman responded:  2023-09-11 14:18
The question often comes up, "After I have imported a transition list, how can I automatically add all of usual precursor transitions".

You can use the "Auto-select all Transitions" checkbox on the "Refine > Advanced" dialog, and that will give you all the precursor transitions, but it also will probably make changes to the other transitions that you have in your document.

So, what you actually have to do is:
1. Go to "Settings > Transition Settings > Filter" and make sure that the settings there will not exclude any of the transitions that are currently in your document.
I see that the settings there say to use all y, b ions from ion 1 to last ion, with the ion charges of 1.
You have a few charge 2 transitions in your document, so you should change the "Ion charges" textbox to say "1, 2".

2. Use the "Transitions" report in the Document Grid and type something into every cell in the "Transition Note" column (you can type something into the first cell, select the entire column of cells and then use the "Fill Down" right-click menu item).

3. Go to "Refine > Advanced" and check the checkbox next to "Auto-select all ... Transitions".
All of the appropriate precursor transitions will have been added to the document, but also a lot of other transitions will also have been added.

4. On the Transitions report on the Document Grid, show only rows where "Transition Note" is blank and "Fragment Ion" does not start with "precursor".

5. Select all the rows in the Document Grid and use the red "X" button on the Document Grid toolbar to delete all the selected Transitions.

-- Nick
laura corveleyn responded:  2023-09-12 00:25
Hi Brian and Nick,

Thank you for the quick response! I tried the auto-select all transitions and it worked fine! I had unique transitions for some peptides, but it didn't change that.