When exporting a transition list for a document that does not have Collision Energy configured under Settings > Transition Settings > Prediction, a message is displayed (screenshot attached):

"The settings for this document do not match the instrument type <instrument_type>
Collision energy: None
Would you like to use the defaults instead?"

This dialog should show the name(s) of the "default" settings, or even offer a list of choices for the user to select from. The selected choice should be saved to the document settings and included in the audit log.

This message dates back to 2008/9 when Skyline only did SRM and all vendors had only 1 possible settings choice. Even now, Thermo is the only vendor with a choice:

CE:
Agilent QQQ
SCIEX
Shimadzu QQQ
Thermo TSQ Quantiva
Thermo TSQ Ultra
Thermo TSQ Vantage
Waters Xevo

DP:
SCIEX

And ideally, we would add a Thermo TSQ Altis option. Though, the settings would be identical to the Quantiva.

The current algorithm uses the first in the list with the matching instrument name, which is currently Quantiva for Thermo, and because of the alphabetic sorting, I think adding Altis would make it the default.

So, the message could simply be altered to:

1.
The settings for this document do not match the instrument type <instrument_type>
Collision energy: None
Would you like to use the defaults instead?
Collision energy: Thermo TSQ Quantiva

2.
The settings for this document do not match the instrument type <instrument_type>
Collision energy: Thermo TSQ Quantiva
Declustering potential: None
Would you like to use the defaults instead?
Collision energy: SCIEX
Declustering potential: SCIEX

And then make sure the settings get changed to match and that this change shows up in the audit log. Or, for the Thermo case, we could show a drop-down list of all possible settings options instead of simply using the first option. Though, this would require a custom form. So, it may not be worth the effort.

We definitely want to be more explicit about what the change will be, and then we want to update the document with full audit logging to reflect the choice made by the user. Especially, if they are exporting optimization methods, those will not even work when imported, if the document does not get updated to what the user chose.