Stable isotope tracing experiments: Is is possible to change the order of isotopologues in the peak area replicate comparison?

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Stable isotope tracing experiments: Is is possible to change the order of isotopologues in the peak area replicate comparison? Michi  2020-08-27
 

Dear Skyline team,

Thank you so much for all your effort, I don't know what I would do without Skyline anymore. I recently discovered that you also implemented new plots for the peak area replicate comparison that allows you to directly see the labeling patterns when doing stable isotope tracing experiments in the format I'm used to. It works very well for small metabolites. However, when looking at compounds with more than 10 carbons, the ordering of isotopologues is not by mass, but alphanumeric?, i.e. it shows the M-H, then the M10C13-H, M11C13-H,...., and only at the end the M1C13-H, M2C13-H, etc.

Is there an option to sort these differently? I need to export the data to do natural isotope abundance correction and plot the different isotopologues as fractions afterwards anyway, but it would be very helpful to see them in the right order in Skyline already. It is currently confusing if you don't look very closely and realize how they are ordered.

I attached an example.

Thanks,
Michi

 
 
Nick Shulman responded:  2020-08-27
If you want to monitor more than one heavy form of your molecule, instead of giving them all the Label Type "heavy", we recommend that you go to:
Settings > Molecule Settings > Labels
and add a bunch more label types, such as "heavy", "heavy1", "heavy2", "heavy3", etc...

"light" always has to be the first label type, but you have control over the ordering of the heavy labels.

I realize that might make things more complicated than the way that you are doing, but there are a lot of places where Skyline wants to be able to assume that every precursor can be uniquely identified by its label type and charge.

Another thing that seems to work is, when you are adding transitions, instead of specifying that the adduct is:
[M2C13-H]
you could add a "0" so it sorts correctly:
[M02C13-H]

-- Nick
 
Michi responded:  2020-08-27
Thank you for your help Nick!

Adding the "0" works great for what we need. However, I will also keep the different label types in mind.

Thanks,
Michi