short request non-quantitative transitions

short request non-quantitative transitions Tobi  2019-02-08

Dear Skyline team,

with the change of the M-1 chromatograms to non-quantitative, I noticed that all non-quantitative transitions appear always as unsmoothed chromatograms no matter which transformation is applied. Is there a reason that non-quantitative transitions are always displayed by untransformed chromatograms? Just from my side I would prefer having the same, selected transformation applied to all chromatograms.

Second small question: Is it possible to add the M-1 chromatogram to all peptides or to build a peptide list where all targets include showing the M-1, at least in the document grid?

Thank you very much for your support

Best regards,

Nick Shulman responded:  2019-02-11
It is a bug that Skyline is not properly applying the smoothing transformation to the non-quantifiable chromatograms. I will fix this. Thanks for pointing this out!

I do not think that there is any way to get Skyline to add the M-1 precursor transition to everything in your document.
Maybe someone else can think of a way to do this.
-- Nick
Tobi responded:  2019-02-13
one more thing, when multiplexing it might be important to use isochronous injection times for PRM, if this is not enabled the more intense isopololog might result in a reduced intensity and a false light/heavy ratio, isochronous injection times and high AGC (up to 1e6) are important. However, this might result in a reduced sensitivity, so multiplexing is a bit more complicated and if the instrument cycle time allows to measure PRM at a resolution of 60.000 or higher than it might not be wrong going for non-multiplexed acquisition. In principle multiplexing can still be used but from our limited experience only together with isochronous injection times and it only makes sense when doubling the resolution is actually needed.

Please also note that it seems that injection time and AGC written in the method editor might apply for each precursor, at least this is how it seems to us based on tests but we are still working on that.