I'm using a GC-MS/MS with masshunter GC/MS Aquisition software B.07.05 to analyse some 50 or 60 semi-volatile compounds (OCP's, PCB's etc...). Some of these compounds are isomers (eg. some PCB's, HCH's, ...) so they have the same transitions, but different retention times. I analyse these in dMRM, and when I want to update my retention times in my aquisition method after installing a new retention gap for instance, I follow the "Update dMRM method with Quant RT Data" instructions from the manual.
After doing this, some of the isomers are no longer in the correct order as they should be. The software decided somehow to alter the order of the isomers. I can't find any reason why it does this and I can't find any way to overcome it.
Has anyone encoutered this same issue before and how can I prevent this?