|Results from collision energy optimization||hober||2019-03-07|
I have recalibrated the CE predictor based on my previous results and this works really well. However, when I run samples with longer peptides Skyline predicts collision energies up to 80, while the instrument only allows for collision energies up to 65. IS there any way of setting a global maximum value for Skyline?
An additional problem that I have run into is that Skyline occasionally chooses 0 as the collision energy for some peptides Even though I get good results for them in the CE optimization. Is it possible to tell Skyline to use the default value for the collision energy rather than 0 in these cases?
Another, more rare, issue that I've had is that Skyline sometimes provides me with duplicated Precursor-Product ion pairs which make Xcalibur complain. Is there any way around this?
I know that these are quite a few questions, but if you have any solution to any of the problems it would be much appreciated.