Incorrect Precursor mz imported for polarity switch transition list (order-dependent)

Incorrect Precursor mz imported for polarity switch transition list (order-dependent) alwest  2022-02-16

Observed that Skyline added incorrect precursor mz when inserting a transition list with a polarity switch (both + and - charge):

When adding a transition list of a small molecule with two transitions - a positive precursor of Mz1 and a negative precursor of Mz2 - Skyline set the precursor mass to Mz1 for both transitions (ie. two transitions, both having the same Mz1 precursor). This only happened if the transition with the largest precursor Mz was listed first. Swapping either rows, swapping the precursor m/z or setting all charges to +1 appeared to "fix" the error.

Note, on Insert -> Transition list, the list is displayed correctly and no errors are detected. But the error then appears in the Targets-panel (so during subsequent processing of the transition-list table?)

(Tested and found error in: Skyline-daily (64-bit) & Skyline (64-bit) )

Brian Pratt responded:  2022-02-16

Thanks for the report, and the detailed example.

This is kind of a strange transition list. It concerns a single molecule "Mol1" with two different kinds of ionization, which is fine, but it's unclear what those are. Whatever the two adducts are, they result in an ion mass difference of more than 200 AMU, which is remarkable.

My guess is that these aren't really different adducts of the same molecule "Mol1". But, since the transition list says they are, Skyline tries to puzzle that out using the mz and charge values it's been given. Clearly Skyline is getting this wrong, but I'm not quite sure how to get it right. Can you describe the intent here?

Thanks for using the Skyline support board!

Brian Pratt

alwest responded:  2022-02-17

Hi Brian,

The actual transitions in the example are not real, sorry for not making that clear. I observed the error when I attempted to use Skyline to analyze a dataset I had previously acquired and analysed (using Sciex Analyst/MultiQuant). During the troubleshooting I ended up making the list I uploaded that replicated the problem and narrowed down the issue.


Brian Pratt responded:  2022-02-17

Hi Alex,

I appreciate you taking the time to narrow down the issue. I'll go ahead and make sure this example performs correctly, though I'd still be curious to see the original as the example doesn't seem very real-world, and I worry that there may be other issues at play. I suppose could be some kind of flux experiment, though - at any rate it ought to just work regardless of order.

In this example case, "work" means
a molecule "Mol1" of mass 228.1,
with a precursor [M-] (negative charge)
with a fragment 144.1[M-]
and a precursor [M202.0011+] (positive charge, with an unknown label of mass 202.0011)
with a fragment 236.1[M+]

Thanks again,


Brian Pratt responded:  2022-02-18

Hi Alex,

Thanks for emailing the original transition list. I have confirmed that it now loads correctly. The fix will be available in the next Skyline-Daily and Skyline patch releases, which I think will be sometime next week.

Thanks again,