Duplicate transitions

Duplicate transitions hober  2021-02-22

I regularly perform screening of peptides where I look for all potential +1 and +2 product ions from the different precursors I have selected. However, I often end up with cases where there are multiple identical precursor ion-product ion pairs, e.g. a b3 ion with the same m/z as a y3 ion and so forth.
This is unfortunately not limited to identical m/z, but also includes product ions with small differences in m/z that after rounding by the MS control software end up with the same m/z.

Would it be possible to implement something similar to the "Remove Repeated Peptides", but for transitions in Skyline?

Nick Shulman responded:  2021-02-22
Can you send us your Skyline document?
I am not sure whether we would be able to implement this feature, but it would be good to be able to take a look at a real world scenario where it would be useful.

Why do you want to get rid of these transitions? How are they causing problems? SRM method taking too long?

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. Otherwise, you can upload it here:

One tricky thing about trying to implement "remove duplicates" with a sort of "fuzzy matching" is that this fuzzy matching is not transitive. That is, you might have three transitions: 400.01, 400.03, and 400.05 and you tell Skyline that duplicate transitions are within 0.03 of each other. In the end, Skyline might leave you with just the transition 400.03, or it might remove that one transition and leave you with 400.01 and 400.05.
-- Nick
hober responded:  2021-07-13
Dear Nick,
Sorry for taking so long before getting back to you.
I've found a suitable case where this issue is triggered, where the b3+ and b5++ have the same m/z.

Not surprisingly, it works exporting the transition list and then tidying up the transitions to get rid of duplicated ones, but it trips up the method export which refuses to export methods where duplicated transitions exist.

Hope this sheds some light on the issue.