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 126.96.36.1999, 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!