When you insert transitions with:
Edit > Insert > Transition List
Skyline interprets any transition which is the same as its precursor as being MS1. (That is, the precursor transition's chromatogram will be extracted from MS1 scans).

However, if you right-click on the precursor in the Targets tree and choose "Add Transition" then it seems that any transition you type in there will be a product ion transition extracted from MS2 scans.

Hope this works for you.
-- Nick

Hi Bing,

With the data you supplied privately, I have verified that Nick's suggestion of manually adding a transition with the same chemical formula as the precursor does work.

If monitoring the precursor in MS2 is a common scenario, we should work out a way to make that easier to do.

Best Regards,

Brian

Hi Nick and Brian,

Thanks a lot for the fast reply.
When I add transition with chemical formula of precursor, it didn't work. But it works when add monoisotopic m/z directly, it works. I don't know if you ever observe this. The version I used is Skyline-daily 4.1.1.18179.

Would be possible to separate precursor transition from MS1 and MS2? Like for proteomics analysis, one window for MS1 precursor and another for MS2 fragments. I think it will be absolutely helpful to monitor the precursor in MS2, and of course, in a easier way for high-throuput.

Thank you all again!

Best,
Bing

A while ago now, I was designing toward being able to monitor the same precursor m/z value in MS1 survey, SIM and MS/MS spectra in the same Skyline document. I never quite made it there, as it would require new UI to be able to specify that this is what you wanted, and very few people seemed to be requesting this.

Creating new options in the UI makes the software more complicated. So, we always need to balance that with how desirable the feature being created is. I eventually made the call that there was not enough call for this to warrant the extra work and complexity it would require.

Partly, because, you can always monitor chromatograms from MS1 and MS/MS in separate documents, simply by disabling the MS1 extraction parameters on the Transition Settings - Full-Scan tab in one document and enabling them in the other. The one with MS1 filtering disabled will extract precursor chromatograms from the MS/MS spectra and the one with MS1 filtering enabled will extract from the MS1 spectra and then you can compare side-by-side in two different instances of Skyline, or by exporting reports from the two documents.

Is this a usable solution for your, or can you give me more detail on why it is important to have the precursor chromatograms extracted from both sources (MS1 and MS/MS) in the same document? I can see that it would be nice, which is why I started the work. I am still just not sure how many people need this and whether it is worth the effort and complexity.

Thanks for posting your feedback to the Skyline support board.

--Brendan

Hi Brendan,

My aim is to monitor the precursor from MS/MS to evaluate the sufficiency of chosen collision energy. As Nick suggested, it is possible to extract precursor from MS/MS, but a bit complicate when I add 100 molecules at same time. When I disabled MS1 filtering, I don't get precursor from MS/MS spectra.

The reason for having precursor from MS1 is, sometimes it still needed to quantify small molecule from MS1 even though this molecule is identified in MS/MS level.

I totally understand that it will be additional work for you and you wonder if it is worth. I can't tell how important it is for other people. Maybe an adjustment on transition list (the import source) can easily solved the problem. What do you think?

Thank you all for your effort.

Kind regards,
Bing

>> Maybe an adjustment on transition list (the import source) can easily solved the problem. What do you think?

I think that is the way forward. I'm not sure what kind of cue we would look for though, any ideas? Perhaps a special fragment name like "unfragmented precursor".

Brian

Hi Brian,

What about an additional column with check box? Use this column as indicator to extract ion from MS1. By default, Skyline extract ion from MS2?
Or maybe you have better idea?

Best,
Bing

I was thinking in terms of CSV format to indicate that you want an unfragmented precursor MS2 transition. It would have to be something distinct, we can't just suddenly start including precursors as MS1 and MS2 transitions. (A checkbox doesn't really work, as we also want to be able to paste CSV directly into the Targets window).