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,

Fredrik
 
 
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.

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=431
https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=432

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

--Brendan