|Bug in TL and Method Export for CEOpt and DPOpt Sciex 6500||Will Thompson||2019-03-11|
Hi Brendan and Brian
I recently was made aware of a bug similar to Waters TQ-S for the Sciex 6500 method and transition list export, for CE Optimization (and in the Sciex case, DP Optimization). Please see attached Skyline document for verification. There are two apparent issues, one generic and one specific to Sciex. The first issue goes back to apparently the storage of small molecule collision energies as a 'molecule' specific parameter, when in fact it should be a transition-specific parameter. Simply, the transition-level optimization function in Skyline is broken for small molecules. HOpefully this is not too difficult to be fixed (the bigger the methods get and the more often we have qualifier transitions for our small molecules, the more of a pain this is to correct manually, after the methods are exported). The second issue is with Sciex machines specifically; apparently whenever a CE Optimization or DP Optimization transition list (or method) is exported, the DP values for ALL transitions which are not set to the initial CE value are set to zero (i.e. as the CE iterates up or down, it does not carry the specified DP value along with it). Unless the user is paying close attention and manually checks the DP values for the new transitions, all of the MRMs for CE optimization will have extremely low intensity (because the DP value should be something like 70, and it is set to zero).
I know these are both Skyline issues and not vendor-specific issues, because the errors show up in the transition list export as well as the methods.
Thanks for looking at this!