Hi Benoit,

Skyline currently doesn't have any way to directly track or emit these instrument tuning parameters, sorry.

A bit of hand-waving here: you could possibly use Skyline's Attributes capability to track those values, and use a custom report to create something that might be easy to turn into a method.

Best,

Brian Pratt

Thanks for your reply Brian!
Do you mind guiding me towards the Skyline's Attributes so I can see if it is possible/feasible?
Thanks,
Best,
Benoit

Hi Benoit,

Sorry, I meant "Annotation", not "Attribute".

At any rate, have a look at https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Best,

Brian

Hi Benoit,
One thing to be clear on is that Skyline never touches what we consider "method-level parameters". It only handles target-level parameters. On a triple quadrupole for SRM, those are the transition-level parameters. On a Q-TOF, Q-Orbitrap, Ion Trap for PRM those are the precursor isolation parameters.

So, when you ask about dwell time and pause time, we need to ask whether you want to control those separately for each target or set them once on the entire method. If the former, I wasn't aware that was possible with the Shimadzu triple quadrupole. If the latter, then Skyline's answer for you is to use File > Export > Method and supply a template method with the settings you want to use. Skyline will only ever change the transitions and leave the rest of the template method as is.

Hope this helps. If you do feel that you are asking for transition-level control, please explain and maybe provide a screenshot of how this looks in the Shimadzu method editing software.

--Brendan

Thanks for your reply Brendan!

Basically, when I export a Shimadzu method from Skyline, the pause time is always set 3 ms and the dwell time is always set to 5 ms no matter if it is un-scheduled or scheduled MRM method (even if the template method has different pause/dwell times).
According to your reply, what I am asking is to set the same pause/dwell times for all transition pairs.

Let me know if you need more information.
Thanks,
Benoit

Hi Benoit,
Just a quick update:
Shimadzu has informed us that their libraries which Skyline uses to export methods do not yet support pause time or dwell time, but plan to add this in the future.

Thanks,
Kaipo