Issue with loading transition list with deuterium as H'1 in formula for newer Skyline version

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Issue with loading transition list with deuterium as H'1 in formula for newer Skyline version j3 menzel  2022-11-12
 

Hi Skyline team,

I'd like to ask, whether the notation for heavy atoms has changed recently?
I used to enter deuterium into transition lists as H' (one deuterium being H'1), which worked fine for Skyline (64-bit) 21.1.0.278.
I can still use this older Skyline version without problems, but the newest one shows an error when trying to load such transition lists.
The error message I get is:

Failed reading the file C:... .csv. The given key was not present in the dictionary.

The same transition list without any H' is loading fine in the latest Skyline version.
Is there a way I can generate transition lists with deuterium containing precursors and products that will work in all versions of Skyline?

Thanks,

Phil

 
 
Nick Shulman responded:  2022-11-13
Can you send us your transition list CSV file?
I don't think we intentionally made any change to the way that "H'" is interpreted in transition lists, so any behavior change you are seeing is likely just a bug.
-- Nick
 
j3 menzel responded:  2022-11-13
Hi Nick,

thanks for the quick response. I would certainly be able to fix this little issue myself - actually, only the transition lists fail to read into Skyline, when they contain H'0.
If I create one that contains only H'1, then it is imported fine in the latest Skyline version. This seems to be a change from previous versions, but it's not a problem as I can just delete any instance of H'0 from my target lists and then also use the new Skyline versions from now on. In case you wanted to test this, I have attached the transition lists, but otherwise all good.

Thanks again to the whole Skyline team for the quick support on any issues!
Kind regards,
Phil
 
Nick Shulman responded:  2022-11-14
I can tell you that this change and behavior has something to do with this fix that we applied a few months ago:
https://github.com/ProteoWizard/pwiz/pull/1945

It has to do with preserving the order of elements in the formula when we are removing isotopes from the chemical formula (i.e. replacing "H'" with "H"). There is a bit of a logic error in our code, which causes it to choke in this case.
We will try to fix this in a future update of Skyline-Daily.

Thanks for reporting this issue.
-- Nick
 
Brian Pratt responded:  2022-11-16
Just confirming that the issue isn't with H' per se - it's with H'0 (that's a zero, not an Oxygen). We used to handle that, but it was pretty much by accident since declaring an atom with count zero is a pretty unusual way to write a chemical formula. At any rate, we will once again deal with it gracefully in the next Skyline-Daily. Thanks for the heads up!

Brian Pratt