|Export Isolation List||benjamin.thomas||2013-07-30|
I'm trying to setup a scheduled PRM method on our QExactive and use Skyline to generate the scheduled inclusion/isolation list for the Qexactive PRM method file.
I've made a spectral library and imported a .raw file containing the target peptides and I've used the MS1 Full Scan method tutorial to identify the retention times and elution profiles of the peptides I'm interested in.
Then I'm using File -> Export -> Isolation List
to generate a scheduled list for the QExactive Inclusion list/Isolation List in the PRM method
I've got a couple of questions though (I've attached a screengrab of the isolation list and Skyline)
1) Where is the retention time window tolerance set for the Isolation List export? - currently it is using 2 min windows
2) Where is the NCE collision energy profile information coming from - I guess this is supplied by Thermo and I don't need to calibrate it? Any feeling how good the NCE estimates in Skyline are for QExactives?
Many thanks for your help