|Title||»||Limiting Transition Settings - Instrument - Max m/z has unintended consequences on spectral library transition picking|
I encountered a file recently which had a spectral library and Transition Settings - Library - Pick 6 product ions and 4 minimum product ions.
It also had Transition Settings - Instrument - Max m/z 1000.
The unexpected impact of this settings combination was that there were some precursors with 1 or even zero transitions. Things got better when I raised the Max m/z to 1500 and the problem went away entirely when I raised it to 2000 (which was likely the true limit of the instrument the produced the library).
What seemed to happen was that Skyline excluded peaks above the Max m/z limit, but it did not re-rank the peaks (despite the Spectrum Match view appearing correct in this regard). So that Skyline would pick peaks ranked like 1, 2, 4, 6 where the 3 and 5 peaks were above the cut-off. They appeared unranked in the Spectrum Match view until you relaxed the limit to 2000 and then you could see the ranking that Skyline seemed to be using for picking. Somehow the picking ranking is not consistent with the plotting ranking in Spectrum Match view.
And, it seems like we are making the minimum product ions calculation based on what we see in the picking ranking before the cutoff gets applied. So, even though we ended up with 1 or zero transitions, the precursor was not removed from the document, because the picker felt it should have ended up with more.