Strange idotp behaviour in small molecule mode Chris Ashwood  2019-12-11
 

Dear Skyline support,

I've noticed a couple of times that the values of idotp can change drastically if certain precursor transitions are turned off and on again. In the attached Skyline document, the idotp values are all around 0.3-0.45 (pretty low for how they visually look) yet if I disable and then re-enable the monoisotopic precursor transition, my idotp values increase at least two-fold (0.84 - 0.94).

The final idotp values look to be correct based on the workaround, but I could imagine this could cause some trouble for people that don't know about it and automatically filter their transitions based on idotp.

Cheers,
Chris

 
 
Nick Shulman responded:  2019-12-11
Chris,

I do not see the low idotp values that you are referring to.

Can you attach a screenshot of what you corrected the problem by disabling and reenabling a transition?

It might be that the act of creating the .sky.zip fixed the problem. If I could see a picture of what you saw I might be able to figure out what might have gone wrong.
-- Nick
 
Chris Ashwood responded:  2019-12-11
Hi Nick,

I think saving and re-opening it did the trick as I can't reproduce the low idotp values. I'll keep an eye out if it happens again to take a screenshot.

Cheers,
Chris
 
Chris Ashwood responded:  2019-12-11
Just had it happen again. Please find attached screenshots. Saving and opening it again fixed it. If I encounter it again, I will attempt a filter of precursors with < 0.95 idotp and see if it culls them.

- Chris
 
Nick Shulman responded:  2019-12-11
Can you send us your Skyline document again? The one you sent us the first time does not have the same molecules in it as the ones in your screenshot.

When you right-click on the Targets tree, which do you have selected: "Replicates > Single" or "Replicates > Best"?
-- Nick
 
Chris Ashwood responded:  2019-12-11
I'll get you a Skyline assay and screenshots the next time I create an assay.

I use replicates single.

Cheers,
Chris