Transition list issues

Transition list issues natalia goykhman  2022-02-13

Dear Skyline Team,

I have a few transition list issues (small molecules) that create a lot of busy work. I was hoping you could direct me to the relevant settings.
I’m working with Skyline, Windows 10 64-bit; the full transition list is attached.

Sometimes after a transition list is pasted (see tab All in the attached file), the M+1 Children in all analytes are unselected, and I have to select them manually (“2 Peaks” are pre-defined in the Full Scan Settings). I couldn’t figure out what exactly triggers this.
How can I make sure that the M+1 products are always automatically shown?

I have a transition list of 20 amino acids, some of them have labeled analogues.
I’d like to integrate the labeled and unlabeled analogues separately, since the unlabeled peaks are sometimes wider than the labeled ones (in biological samples).
When I put the labeled and unlabeled analogues under the same analyte name, their integration boundaries are synchronized, and I couldn’t find a way to unsynchronized them.
So, I separated the labeled and unlabeled analytes into different entries (see tab SeparateEntries in the attached file). However, when I paste this transition list into Skyline, the labeled compounds are automatically assigned an unlabeled mass as well, e.g., under Leu-13C I get both C6H13NO2 and C'6H13N'O2, and have to remove the unlabeled analog manually.

How can I prevent this automatic assignment of unlabeled m/z to the labeled compound?

When I use a transition list with separate entries for labeled and unlabeled compounds (see tab SeparateEntries in the attached file), there are 3 labeled compounds that are automatically converted to unlabeled, and I have to go and correct their formula manually.
I noticed it only happens to labeled compounds without any product ions: Ser-13C, Asp-13C, Cys2-13C.
How can prevent this from happening?

Thank you very much!

Brian Pratt responded:  2022-02-15

Hi Natalia,

Thanks for a very concise report with examples. I'm investigating, and will get back to you ASAP.

Thanks for using the Skyline support board,

Brian Pratt

Brian Pratt responded:  2022-02-15
To your first point, I've just added a Tip to the Skyline website that explains how this works.

Here's what it says (it sounds like the last bit is probably the important one in your case):

When you first import a transition list, Skyline will only show the most abundant isotope for precursors in the Targets window.

If you want to see others, there are a few settings that need to be adjusted in Transition Settings (via the Skyline Settings > Transition Settings... menu):

In the Filter tab, make sure the "Ion types" field includes the letter 'p' to indicate that you want to work with precursors.
In the Instrument tab, make sure the Min m/z and Max m/z values are suitable for the precursor m/z values you are interested in.
In the Full Scan tab, make sure the "Isotope Peaks" tab is set to something other than None.

Note that even if you have these values preserved in your settings from a previous run, you may have to visit the Transition Settings and make a slight change to your settings to provoke the creation of the additional precursor nodes in the Targets window. It doesn't matter which setting, and you can change it back again afterward, but this is necessary to reevaluate the contents of the Targets tree.
Brian Pratt responded:  2022-02-15
To the second and third points, that's a problem that's already fixed in the current Skyline-Daily. I'll make sure it's also corrected in the upcoming patch release for Skyline 21.2 as well.
natalia goykhman responded:  2022-02-16
Thank you very much, Brian!!!
I really appreciate it.