I am running serum samples using an MRM method on an Agilent triple quad. Only product ion data is collected (at specified RT windows). There is no full MS data. I would like to use autoQC to monitor the signals of the deuterated internal standards spiked into a quality control sample. I have tried including and excluding the explicit retention times but Skyline isn't correctly integrating the ISTD peaks due to inter-batch retention time shifts(~0.2-0.8 min). Even with a window that captures the shift, Skyline is going in an peak picking noise at the explicit retention time instead of the nicer peaks.
I have attached 3 examples of 3 different compounds in the autoQC transition list that are being properly/improperly integrated.
Since this is for SST, I would prefer for this to be automated and not have to go in and manually adjust the peaks so that they show up correctly in Panorama. Is there something in the settings that can be adjusted to address this issue? Is there a way to set a minimum peak intensity for autoQC integration? There are many examples where there is an obvious peak in the RT window, but Skyline integrates noise instead.
If a iRT calculator was added to molecule settings, would Skyline be able to apply that as raw files came in via autoQC?