HCD nCE used fredrik edfors  2015-09-08
Dear Skyline Team,

I'm trying to optimize the collision energy for a larger set of peptides that we want to analyze using a PRM-method on a QEHF. It would be really nice if you could find the HCD energy used for each spectra in the "Full scan"-window when using Skyline. I'm currently working with both Skyline and Xcalibur in parallel, trying to figure out what spectra (from the raw file where I can find the nCE used for that specific spectra) that is corresponding to the extracted chromatogram visualized in Skyline.

It would also help a lot if you would be able to visualize spectra in the "Full-scan"-window with the "View>Transitions>Total" option.

Thanks a lot,

Brendan MacLean responded:  2015-09-09
Hi Fredrik,
We are currently focused on the next fall release, and may not have time to get to these before then, but thanks for you feedback. I have posted your suggestions as issues on our issues list. Hopefully we will be able to get to them in the next cycle.


Thanks again for taking the time to let us know how we could improve your efficiency using Skyline.