Hi Karin,
Certainly, my first impression is that this is not the right error message to be showing for this case, and I will certainly look into improving that.

The larger issue, however, is that the method export interface we have been given from Waters only allows a single retention time window for all transitions. I am interested to know whether you are able to set the retention time window for each transition separately in the MassLynx software now, in which case, we may want to return to Waters to request a library update to make this possible for Skyline also. Otherwise, if there truly is only one RT window allowed per method, then our only option is to give an error message when you try to export a method that requires multiple RT windows. At least I think this is what is going on. Though, the error message could be a lot more helpful.

You might try also making the RT window the same for both "use measured retention times when present" and your RT predictor and see whether that also causes the error message to go away.

Definitely, Skyline internally has a property "IsSingleWindowInstrumentType", which now seems to contain only Waters instruments. Though, I am pretty sure it once contained Sciex QTraps as well. So, if you end up with a scheduled method that requires multiple different RT windows, that would cause an error, and I now believe this error you report. I had hoped it would be something explaining the single window limitation.

Hope this helps. Thanks for reporting the issue.

--Brendan

It does look like the code will allow you to schedule if you set your time windows for measured RTs and your RT predictor to be the same. Again, sorry about the error message.

Hi Brendan,

thanks for the tip to set RTs the same for both settings. That indeed works, and I guess if that is the limitation of the Waters instruments, we will have to live with it.
I did ask my co-workers if they created assays with different retention time windows before on the Xevo and they said that they used it before (creating the method directly in MassLynx). I attached a screenshot from a method created by a co-worker that was run on the Xevo. So measuring like that should be possible on the Xevo, but maybe it is an issue importing transitions lists or so?

Karin

Hi Karin,
The ability to create methods like the one you show in your screenshot is definitely not yet enabled in the method writing library I have from Waters, but your support thread has initiated a new discussion with my contacts at Waters on this topic. I will post whatever I learn or any progress to this thread. For now, using a single time window for Waters methods remains a limitation for Skyline, and unfortunately, failing to do so produces this less than ideal message.

Thanks for starting this thread on the support board. Hopefully it will lead to improvement in Skyline support for Waters Xevo instruments.

--Brendan

Hi Karin,
Most recent word is that Waters has agreed to improve the method export library they supply us to support this case. It may still be some time before this makes it to a public release, though. Until then you should stay with using a single time window for Waters method export and then manually editing anything afterward that you feel really needs to change.

Thanks again for reporting the issue.

--Brendan