modification of precursor m/z order in targets and results panels

modification of precursor m/z order in targets and results panels heuillet  2023-06-16 04:51

I use Skyline to process my MS data of 13C-fluxomics approaches. I study the 13C-incorporation inside my metabolites of interest.
In my transition list I associate different m/z to one compound. For example, for glutamate analysis I need to integrate:precursor,[M+1], [M+2], [M+3], [M+4], [M+5]. The number of m/z depends on the total number of carbon inside the molecule.
After loading my transition list, the order in the targets panel is not kept and the [M+1] is always the last m/z of the list for all metabolites.
How can I change that and put the [M+1] juste before the [M+2]?
thanks a lot,

Nick Shulman responded:  2023-06-16 08:43
Can you send us your Skyline document?
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.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:

I am not sure I understand your question. As far as I knew, Skyline always puts the M+1 precursor transition in between the monoisotopic and M+2 precursors and nothing could change this. I imagine things will be more clear after I see your Skyline document.

It might also be helpful if you could post a screenshot of what you are seeing.
-- Nick
heuillet responded:  2023-06-19 00:52
You can find attached my skyline project (zipfile) and a screenshot of what I obtain (red arrow: what I want to modify) and an extract of my transition list.
I hope it will be helpful.
thanks a lot,
Nick Shulman responded:  2023-06-19 11:11
I see that you have several different precursors for your molecules with different numbers of 13C atoms specified in the Precursor Adduct.
The "Isotope Label Type" of each of your precursors (including the one with zero 13C atoms) is "heavy".

If you want to control the order in which these precursors appear in the targets tree, I would recommend going to:
Settings > Molecule Settings > Labels
and push the "Edit List" button
and make it so that the label types you have are:

Then, when you import your transition list, make it so that your precursors with different numbers of 13C atoms had different values in the "Label Type" column in your transition list: the monoisotopic precursor should be "light", the one with one 13C should be "heavy", the one with two 13C's should be "heavy1", etc.
If you do that, then the precursors would be sorted the way you want in the Targets tree, because Skyline will look at the order of the label types in the "Settings > Molecule Settings > Label" page to decide what order label types should be displayed in.

Is this an experiment where you are looking for naturally occurring molecules which have some number of heavy carbon atoms, or did you actually synthesize these molecules with heavy labels?
If you just want to extract chromatograms for naturally occurring isotopes, you should instead go to:
Settings > Transition Settings > Full Scan
and change the "Isotope peaks included" settings so that Skyline adds precursor isotopes to the targets tree at the transition level.
This "Isotope peaks included" setting can only be used to add masses whose predicted abundance is at least 1% of the abundance of the most abundant mass, so you would not be able to use this setting to monitor 5 different masses for C4H6O4, but you would be able to monitor M+0 and M+1.
-- Nick
a rocher responded:  2023-07-20 01:37

I'm part of Maud's team.

We've tried all the possibilites :
For Label Type column :
1) Compound without 13C = light, Compound with one 13C = heavy, Compound with two 13C = heavy1, etc ...
2) Compound without 13C = heavy, Compound with one 13C = heavy1, Compound with two 13C = heavy2, etc ...

For Molecule Settings > Labels :
1) light, heavy, heavy1, ....
2) heavy, heavy1, heavy2, ....

Unfortunately none of these options work. We always have the compound labelled with one 13C at the end of the list in the targets tree.

You can find attached the different possibilites we've tried and the targets tree obtained in all cases.

Do you have any idea of the malfunction?

Thanks for your help
Nick Shulman responded:  2023-07-20 08:30

Can you send us your Skyline document?
In Skyline, you can use the menu item:
File > Share to create a .zip file containing your Skyline document.

If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here:

The "light" Isotope Label Type will always appear first in any list. You cannot do anything to control the position of "light" at "Settings > Molecule Settings > Labels > Edit List".
Make sure that you get everything in the correct order at "Settings > Molecule Settings > Labels" before you add any precursors to the document. If you change the position of an Isotope Label in that list, Skyline will usually delete all precursors from the document whose label position moved.

-- Nick
Brian Pratt responded:  2023-07-24 09:46
Hi Amandine,

This is a defect in how we sort adducts. I'm working on a fix - thanks for alerting us to the issue.

Best regards,

Brian Pratt
heuillet responded:  2023-12-10 23:57
do you plan to change the sorting of adduct for the next version of skyline? It is very important for use for our metabolomics data processing.
thanks a lot,
kind regards,
Brian Pratt responded:  2023-12-11 08:19
Yes, this is corrected in the current Skyline-Daily release.

Best regards,

Brian Pratt
samartinez3 responded:  2023-12-28 11:12
Hi Maud,

I was searching the site for help regarding this issue as I just came across it and stumbled on your post. I have found a way to solve the sorting issue, simply by exporting the transition list as a csv and using excel find/replace tool to replace the [MC13-H] which is the first carbon (13C-1) and changing it to [M1C13-H]. Then it automatically sorted in the correct order.

Brian Pratt responded:  2023-12-28 11:49
Hi Sara,

Thanks for being a helpful Skyline community member!

But this shouldn't be necessary any more - what version of Skyline are you using?


Brian Pratt
heuillet responded:  2024-01-08 05:05
Hi Brian, Hi sara,
Thanks you very much Sara for your help.

I am using the version. When I manually replace [MC13-H] with [M1C13-H] it's fine (but it's not an high throughput process...)
When i submit the attached transition list it doesn't work.

Maybe I didn't edit the transition list correctly to organize the order of the isotopologues.

Brian Pratt responded:  2024-01-08 10:35
Hi Maud,

This does work properly in Skyline-Daily (23.1.1), but not, as you have found, in Skyline 23.1.0.

Can you switch to Skyline-Daily?

By the way, while it is harmless to indicate the labels in the chemical formula, it is not necessary since that information is in the adduct description. That is,

Molecule List Name;Isotopologue;Molecule Name;Molecular Formula;Precursor m/z;Precursor Adduct;Precursor Charge;Explicit Retention Time

works just as well.