We have a lot of experience with Agilent GC-MS instruments which use the 6890 GC together with a quadrupole mass spectrometer. They perform well and are rugged and reliable. We are analysing complex vapour samples and we cannot always resolve the peaks on the GC, making the MS identification difficult in some cases. This is even with mixed phase 60m long capillaries with slow temperature ramps.
Would it be advantageous to move to GC-MSMS to try to resolve these peaks? I believe you can do this on an ion trap instrument. However, we believe these may be less rugged, and the results less quantitative than on our quadruploe. Can anyone comment on this?

You re right for the 6890-5973ms.
I have three 5973,and one polarisq(ion trap),and i could say that the ion trap becomes dirty faster as the quadrupole,and that's inherent to the ion trap..you must more frequently clean your source in general,they are simply less rugged!

We use it only for HS-GC-Ms to minimyze cleaning of the lenses.
The main purpose of my ion trap is to qualify,it's more difficult to quantitize as with the 5973.

Both are equaly sensible,but for ms/ms you need to find a parent ion ideally different for your coeluted peaks,or when similar,wich gives a different daughter ion after fragmentation
When you coeluted peaks spectrum are too similar,there is a lot of chance,that the fragmentation will not enough differ to find a different daughter ion.

But in case of totally different substances,and mass spectra,that will be helpful.