Removing Redundant Transitions

Removing Redundant Transitions eajarett  2022-11-28 14:07


I am trying to exclude all redundant transitions in a DIA assay library from quantitation. I was able to export all transitions and manually determine which ones were identical with others based on their molecule list name, precursor m/z, precursor charge, product m/z, and fragment ion.

I tried manually deleting all transitions in my DIA assay library and reimporting the "mixed transition list" containing only the non-redundant transitions, but this didn't work. Is there a better way to exclude the redundant transitions from quantitation?

Thank you so much!

Nick Shulman responded:  2022-11-28 14:13
Could you send us your Skyline document? I do not think I understand your question, but if I could see your Skyline document it might make more sense.

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 and spectral libraries.

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

Also, if you could send us a screenshot of what you are asking about that might also help.
-- Nick
eajarett responded:  2022-11-28 14:41
Thanks so much for your quick response! I attached the Skyline document and a screenshot here that hopefully makes the problem clearer. I study histone PTMs, so my DIA assay library includes many copies of the same histone peptides, just containing different modifications. An example of this is in the attached screenshot. With this being the case, there are a lot of transitions in the DIA assay library that I cannot distinguish between peptides. For example, b5 highlighted in the screenshot could belong to either of the peptides shown in the screenshot. For this reason, I would like to uncheck this transition for "quantitative." Is there an automatic way to do this?
eajarett responded:  2022-11-28 14:47
Nick Shulman responded:  2022-11-28 16:05
It sounds like you might have tried to attach your file to a support request, but nothing actually got attached.
This often seems to happen if the file you are attaching is larger than the 50MB limit.
You can upload larger files here:

Usually, people decide which transitions have interference by having multiple technical replicates, rather than trying to predict which transitions are going to have the same retention time and precursor window as some other thing in the sample. The transitions with interference are likely to have larger CVs across the replicates, because the thing that is interfering is likely to vary more across the replicates in terms of how much it interferes with the measured signal.

I am supposed to implement some features in a future version of Skyline which will help you figure out which transitions have interference like that, and either remove them from the document or mark them as non-quantitative. I am not sure what the best way to do this with the current version of Skyline is. There might be something useful on the "Results" tab of "Refine > Advanced", or there might be something useful with "View > Peak Areas > CV Histogram".

Some people use other tools to decide which are the most quantitative transitions. One popular tool which we are planning on copying some features from is EncyclopeDIA:

-- Nick
bobxiong responded:  2023-12-24 12:14
Hi All,

The ion redundancy issue has been brought up more than once on this forum, but it has not yet resulted in a universal off-the-shelf solution (Skyline team please correct me if I am wrong). I believe that Skyline stated in the past that SRMCollider was on the to-do list of external tools to be integrated in Skyline. To make a long story short, if you want to have a list of peptides ranked by potentially interfering transitions derived from the background proteome, I invite you to take a look at ProteinQuantSRM-Dx

Ion redundancy evaluation is based on calculated retention time and indistinguishable precursor/product ions (.e.g. within +/- 0.5 amu on a triple quadrupole mass spectrometer).

Happy Holidays!

Bob Xiong

Founder, ProteinQuantSRM-Dx