well waters usually has nice software. AB sciex has machines that run ;-)

we bomb our AB machines 24/7 - need to clean the ion source every few months otherwise the beast just endure.

In my part of the world the AB people react within hours if there is probalmes with the machines - worth a lot as well.

agilent is gathering pace, but they would have to offer me a system for 50% of AB or waters before I would be tempted.

Having people near you that have already learnt a bit about the systems is also worth a lot.

I I get that right you are looking at a quantification machine with triplle quad geometry. the AB sciex is offering you some possibilities with the trap..

for quan purposes you have to optimise the MRM for all compounds on the machine you are working with anyway, so the help form the other machines is not that great.

Difficult to say: I guess if you get familiar with the machine quickly (ie you can focus on that) and you have a lot of samples the AB machine would still my best guess.

.....actually I have worked with thermo machines a while, with waters a bit and the last 15 years been very happy with AB Sciex

@Kai Bester,

Thanks a lot for your kindly reply. The Waters staff told me that "The UNIFI software in Waters Q-TOF could be easy and rapid to search for the huge database that constructed by the company and specific to Waters". I think almost all staff from company will say in confidence like this, but I am afraid that they might be exaggerate. How do you think about this, if the Waters Q-tof is so useful for identification of metabolites like staff?? 

My choice would be Waters due to the excellent support we get from them. I run a Waters Q-TOF 24/7 with very little problems. I would suggest you evaluate the various systems and even make an evaluation period part of you purchasing specifications. If a manufacturer is willing to install an instrument for evaluation, they usually have a system that would perform to specification.

depends- I understood you were asking for a quntification machine ie a tripple quad?

In my experience running high through put laboratories I have found that there is not a great difference between routine bench top MS instruments among the main MS vendors.  My choice comes down to who has the best service team in your area.  The quality of vendor service can vary greatly from region to region.

I fully agree with Joseph regarding the support and  service offered by vendors, Another aspect to consider is the LC-MS systems already in use in your lab as well as the software used to control them. Re-training your staff can be a costly exercise in  a high throughput environment.

As others have mentioned above, easy access to competent service personnel is a very important factor. Also, be sure to include the cost of the metabolite library in the purchase of the equipment, they often come as separate items. I work on a Waters Xevo G2XS and it's been good so far. Such a spectrometer is rather versitile because it can be used for both identification (with a library) and quantification running in msms mode. Best of luck with your purchase. 

 Thank you for all your replies. I got a lot.