Skyline Tuning optimisation vs instrument software Tuning optimisation Shimadzu 8060?

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Skyline Tuning optimisation vs instrument software Tuning optimisation Shimadzu 8060? jxg918  2022-06-27
 

Hey all!

Does anyone have any experience comparing an instrument-automatic optimisation process to select the best voltage settings vs Skyline's CE optimisation? Does Skyline also optimise other voltage settings (such as interface voltage, DL bias, Qarray RF, Q1 and Q3 pre-rod bias)?
I'm using a Shimadzu LC-MS/MS 8060NX (QQQ).

I've been using skyline for a proteomics project to quantify very-low abundant proteins in very rare samples.. So I'd need to have my instrument settings as optimal as can be. Just don't know if it's best to use Skyline or the vendor-specific optimisation tool.
I already have my MRM transitions selected and I know the retention times of my peptides, so it's just the final step of finetuning the triple quad before running all samples, but I'm running low on heavy standard..

If anyone with experience on a Shimadzu 8060 could help me with this, would be much appreciated!

Many thanks,
Jan

 
 
Brian Pratt responded:  2022-06-27

Hi Jan,

We're working on other optimizations but those are extremely system specific, so if the instrument software handles tuning all those parameters I'd go with that. Probably start with Skyline's CE optimization for convenience, and go from there.

Thanks for using the Skyline support board,

Brian Pratt