Problem with transition list of light and heavy labelled small molecules Lisa Panzenboeck  2022-02-14 07:54
 

Dear Skyline team,
I’ve recently tried to import a transition list containing C12 and fully C13 labelled precursors with [M+H]+ and [M-H]- adducts and noticed that for small compounds containing only 2 carbon atoms the heavy [M-H]- precursors are not represented. I assume the problem might originate from the similar mass to charge ratios for light positive and heavy negative molecules. Do you have any idea how to deal with this issue? I’m using Windows 10 and Skyline (64-bit) 21.2.0.369 (2efacf038) and my transition list for Taurin looks like this:
Molecule List Name Precursor Name Precursor Formula Precursor Adduct Precursor Charge Label Type
compound_of_interest Taurin C2H7NO3S [M+H]+ 1 light
compound_of_interest Taurin C'2H7NO3S [M+H]+ 1 heavy
compound_of_interest Taurin C2H7NO3S [M-H]- -1 light
compound_of_interest Taurin C'2H7NO3S [M-H]- -1 heavy

Looking forward to hearing from you!
Best,
Lisa
 
 
Brian Pratt responded:  2022-02-14 11:00

Hi Lisa,

This certainly seems like a perfectly valid transition list- I am investigating.

Thanks for such a succinct report !

Brian Pratt
 
Lisa Panzenboeck responded:  2022-02-15 01:07

Thank you for looking into it!
 
Brian Pratt responded:  2022-02-15 08:45

Hi Lisa,

Your intuition is correct - the issue centers on C2H7NO3S[M+H] and C'2H7NO3S[M-H] which produce nearly identical m/z values. But of course they aren't actually ambiguous since they're different polarities, so Skyline should be tracking them both. This is a bug, it will be fixed in the next Skyline release, which should be in the next week or two.

Thanks again,

Brian Pratt
 
Lisa Panzenboeck responded:  2022-02-15 09:04

Hi Brian,

great to hear that it will be fixed so soon. Thank you for your support!

Best,
Lisa