I just wanted to chime in about 4 years late... :D

I'm an Agilent "Fan-boy."

I've worked with Agilent Systems (5971-5975C) for about 13 years now. They are the most dependable and easy to maintain system I have ever worked with. They are affordable, robust and come with a plethora of options.

I prefer the turbo pumps as I never know if I'll be running He at 3.0 mL/min and in NCI for research applications. The new little Pfeiffer Turbos they put in the 5975C are incredible. The Triple Axis Detector is also very impressive. EM is at about 1200V after 5 years of operation. I haven't replaced it yet. On the old 5973 it would be about every year.

I've worked with a Thermo Trace Ultra GC and TriPlus Auto-sampler coupled to a DFS magnetic sector HRAM-MS for the last 7 years. The Trace GC was awful as was the Auto-Sampler. Neither of them made it to 5 years without MAJOR issues. Major design flaws in my opinion.

That being said, I have been fortunate enough, recently, to acquire a new QExactive GC Orbitrap system with TriPlus RSH (CTC designed) auto-sampler. Everything Thermo says it will do... IT CAN. I have had it for about 8 months and it is, so far, extremely reliable. ExtractaBrite source is easy to remove and clean; Columns swaps are relatively easy (no-venting); and the 1310 Trace GC is WAY Better than the Old Trace system. So far I like it better than the Agilent 6890 as Everything is modular (ie., The Mass Flow controller, filters, Inlet body, heater and Electronic Control Module are all in one drop-in part). This may increase the cost a bit, however. The SSL uses all Agilent-style consumables (or Restek). The PTV is similar in design to the old TraceGC system but the bottom fitting is removable for easy cleaning. The transfer line is a very solid design and has no apparent "Cold-Spots." This was a problem I observed on the DFS transferline when analyzing chemicals in the 900-1000 Da range.

Also, the software (Tracefinder) is very powerful and moderately intuitive. Like any new software, it will take some time to learn. I came from exclusively MS Chemstation (Rev B - F) and I now prefer both Masshunter (Agilent) and Tracefinder to Chemstation. I never thought I would admit that.

I can't say enough good things about the Instrument or the Service we have received so far from Thermo. We currently have one lab full of Agilent instruments (5973N, 5975C, 6410 LCQQQ and 6490 LCQQQ) and One with Thermo Instruments (QE-GC and soon an ISQ - LC/MS).

Agilent service (in the Mid-West USA) is and has always been the GOLD STANDARD as far as I'm concerned. Thermo is quickly catching up, though.

If you have any questions about the Thermo QE-GC system feel free to PM me or reply to this post. I'd be glad to help.