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

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)
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?



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,
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:

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