Lipid Creator No longer Exporting to Skyline

Lipid Creator No longer Exporting to Skyline wlstutts  2021-06-24


After upgrading Skyline Daily, I have lost functionality in Lipid Creator for exporting to Skyline. See attached error message. Any help resolving this issue would be appreciated!

Nick Shulman responded:  2021-06-24
We usually ask people to contact the developers of the external tool directly. The support page for the Lipid Creator external tool is here:

If you post your question on that page, it will be the first question posted there. I do not know how quickly you will get a response, but it's always nice to start an active support community on the external tool support pages.

I can also take a look at the problem if you would like. I do not know how to use Lipid Creator so you would have to send me your files and tell me what you did so that I can reproduce the problem.

If your files are less than 50MB you can attach them to this support request. Otherwise you can upload them here:
-- Nick
nils hoffmann responded:  2021-06-24
Hi there,
we are tracking this issue here:
Please check that issue for details and for the current status of our investigation into the root cause.

We only started noticing this issue with the latest Skyline release (21.1).
This may be related to the new transition list import features in Skyline. @Nick Were there any internal changes to the column names or the expected format?

We are using the SkylineToolClient#InsertSmallMoleculeTransitionList method with a csv string argument.

Brian Pratt responded:  2021-06-25
Thanks for reporting the problem, it is indeed a small change to Skyline that causes the problem.

As a workaround, if you remove the quotes around the numeric values in your data file, it should work fine. Obviously that should not be necessary, and wasn't before, and we will get that fixed in the next Skyline-Daily and corrected in the current official release as well.

Best regards,

Brian Pratt
wlstutts responded:  2021-06-25
No problem! Thanks for looking into this. Do you have an estimated timeline for the next Skyline-Daily release with this fix?
wlstutts responded:  2021-08-04
Thanks for fixing this Brian!