Exporting Isolation Lists cjeline1  2016-01-29
Dear all, we are experiencing a similar problem as that documented by Josua Troesch on the 27th. Running skyline version, exporting a Thermo fusion isolation list from a skyline file fails to render the generation of a .csv file. Do you have any suggestions to resolve this issue?


Pandey Laboratory
Johns Hopkins School of Medicine
Kaipo responded:  2016-01-29
Are you receiving any error messages (or that the file was exported successfully and does not exist)? Also, would you mind sharing the full command that you are using to export the list?

Kaipo responded:  2016-02-05
Hi Christine,
I've had a look and it turns out that the export is not producing a file due to there not being any transitions in the document - Skyline is skipping over any protein with no transitions in it. Unfortunately at the moment no warning is being produced to let you know that this is the case.
For now, you can add a transition(s) to each peptide and the export should be okay. Let me know how it goes.

roman sakson responded:  2020-04-20
Dear Skyline Team,

I just experienced the same issue (in both Skyline and daily), as I wanted to add some new peptides to an existing document for an extended inclusion list and decided to add to this older thread. While this is certainly no big deal, maybe you could add a warning in the future (if there is no good way to completely fix this).

Thank you for consideration and for the great work you are doing!

Nick Shulman responded:  2020-04-20

Are you saying that you have a Skyline document with no transitions in it, and Skyline either had no error message or not a helpful error message?
Or, are you having a different sort of problem when you try to export a transition list?

Either way, it would be helpful if you could send us your Skyline document and we can see what's going on.
In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
-- Nick
roman sakson responded:  2020-04-20
Hi Nick,

exactly, if I don't have any transitions, an isolation list is not created and no error message is given out. As soon as I add any type of transition ions to the document, everything works fine. This is not depend on the Skyline version (same error as reported above in 2016). I have attached a minimal example with just one precursor ion in daily (Test.sky.zip). In this case, the isolation list will not be created as there are no transitions.

However, in my opinion the missing error message actually becomes more dangerous if you have a long transition list but for a few precursor ions transitions are missing for some reason. In such a case, you would get an isolation list but only for those precursor ions that had transitions in the document, which is more likely to be missed by the user compared to the situation where there is no isolation list created at all and something is obviously wrong. That's why I decided to ask whether an error message could be implemented in one of the later releases.

Thank you for your time!