Hi Hilda,
Can you send screenshots of what you are seeing as well as your Transition Settings - Full-Scan tab?

That should help us understand. Thanks.

--Brendan

Hilda,

I think this is related to your request of yesterday, I'll let Brendan know we have the data.

- Brian

Brian,

Yes, however, I ran a different method using the mass generated by Skyline and I can see the precursor without having to open up the m/z tolerance but I still do not see the fragments. Here are the the screenshots of my settings and my Orbitrap method.

Thank you very much,

Hilda HB!

Other two screenshots

Hi Hilda,
Unfortunately, you have omitted the most informative screenshot, perhaps to avoid giving away your target peptides.

In the direct email you sent, however, it was clear that the problem is in your targets. You have not targeted anything other than the monoisotopic precursor peak, which makes your Full-Scan settings for MS1 with Peaks Count = 10 a bit strange. You could have more easily used a count of 1 to achieve what you show in your targets.

This means that your transitions must be manually edited already, and automatically calculated from your Transition Settings, or you would be targeting other isotopes of your precursors (e.g. M+1, M+2, M+3, etc.) You now need to manually edit them further to add fragment ion transitions.

I would suggest that you fully review the Targeted MS/MS (PRM) tutorial, as it covers all of this pretty thoroughly:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_prm

Hope this helps. Good luck with your experiment. Thanks for sending the screenshots.

--Brendan

Ok, I picked all children, re-imported data, selected product ions on the view option and I can finally see all my fragments. Not sure why it didn't work yesterday. Thank you very much for all the help. I greatly appreciate it.

Hilda HB!

Hi Hilda,
Great news! Thanks for the update. Good luck with your research.

--Brendan