Hi Lee,

Sorry, the answer is still no, and likely to remain so. That would be a pretty fundamental redesign of Skyline's UI and internals. With our limited resources it's just not likely to become a priority.

That said, if you could come up with some way to trick Skyline into doing that, in the spirit of the early adopters who first fooled Skyline into small molecule work with fanciful "peptide" modifications, you'd be a hero. No idea what that would look like though.

Wish I had a better answer for you!

Brian Pratt

Let me just add that for DDA, the only access to these spectra in Skyline would come from building a spectral library, where the spectrum and retention time would be recorded and then matched to your precursor during MS1 chromatogram extraction, where the spectrum retention time would get used in peak picking.

If you can come up with a way of creating a SSL (tab delimited) small molecule library specification that mapped you precursors of interest to your MS3 spectra of interest, this should work without a lot of change to the internals of Skyline itself. Skyline only cares about the matched molecule, matched spectrum and the retention time.

It would take a lot more work to do PRM from MS3 in Skyline, but I would expect you could fake BiblioSpec into building the spectral library you want and then just use it for MS1 extraction. I don't know whether BiblioSpec cares what MS level a spectrum is. I think it will take any spectrum listed in the SSL file regardless of level. But if level turned out to be a problem, I expect that would be an easy fix. Or you might be able to figure out some kind of conversion of an mzML file that faked the spectrum level as 2, if that were necessary.

Anyway, for what it sounds like you are asking, I think there should be a solution. What would be hard would be asking Skyline to extract chromatograms from MS3 spectra. But, it doesn't sound like you are asking for that.

--Brendan