|CE optimization on Agilent QQQ||Sarah Michaud||2017-11-06|
I getting some strange results when optimizing collision energies for an Agilent 6495 QQQ using Skyline. I am generating the transition list for CE optimization using skyline, then using the method to acquire the data, and importing the data back into Skyline. After importing the data, sometimes the transition results look fine and as expected, but other times the pattern in the peak area graph is really unusual (almost random instead of a curve shape), and other times the results are missing completely. When I check the same data file in the Agilent MassHunter software, the data appears to have been acquired correctly and the peak area pattern is normal. I've attached some slides with examples to try and show what I'm seeing.
I think the problem might be that for some transitions the product m/z value is for some reason different in the acquired data file compared to the method generated by Skyline, and when that data is imported back into Skyline the peak areas associated with each CE step gets jumbled.
Thank you for the help!