Automated extraction of isotopologues

Automated extraction of isotopologues Yasin  2018-09-28

Hello Skyline Team,

I have a problem regarding the automated extraction of isotopologues for small molecules (High res instrument). I want to extract 4 isotopologues for all my compounds and adducts. However, for some compounds it is extracting all of them for some compounds just some of them and for others just a single one,..
I don't really see a pattern there.

Thanks for your help in advance!

Yasin responded:  2018-09-28

Oh and here is the skyline file

Nick Shulman responded:  2018-09-28
Skyline only allows you to choose precursor masses whose predicted abundance is at least 1%.
So, even though you have the correct setting on:
Settings > Transition Settings > Full Scan > MS1 filtering > Isotope Peaks Included
Skyline is not going to give you 4 precursor transitions if the molecule is not large enough that it has 4 different masses with an abundance above 1%.

May I ask why you want chromatograms for these low abundance isotopes? Is it to help with distinguishing the molecule from something else whose mass is maybe 1 Dalton different from what you are looking for?

Skyline does allow you to add the M-1 precursor. To do this, select a precursor in the Targets tree and choose the right-click menu item "Pick Children", and then click the button that looks like a funnel to turn off filtering, and then you can choose the M-1 transition. That transition can be useful for distinguishing molecules that differ by one Dalton. (I don't know how to add the M-1 transition to all of the precursors in your document-- I think you might have to do it one at a time like this).

I am not sure how having the M+2 transition or M+3 transition on such a small molecule would be helpful, but if it is, I could imagine us making that possible in a future version of Skyline.
- Nick
Yasin responded:  2018-09-29
Thank you for the quick response.
Extracting low abundant isotopologues is useful to check the instrument performance regarding dynamic range and precision and accuracy at low intensities. In fact I often observe isotopologues below this 1% limit. It would be very useful for me to be able to do these extractions in an automatized way!

Thanks a lot.
dgmccaskill responded:  2018-10-01
When I saw the term isotopologue, I thought about the possibility of using Skyline to extract data from stable isotope flux experiments (where with 13C labeling there could be abundant isotopologues up to the number of carbons in the target molecule). I don't recall seeing this application for Skyline. Is anyone using Skyline like this?


Brian Pratt responded:  2018-10-01
dgmccaskill responded:  2018-10-01
Very cool. I missed that presentation. I'll have to read through this in detail.