Our lab is going to purchase an LC/MS system. This will be a benchtop system. I know of three manufacturers: Thermoquest-Finnigan, Waters-Micromass, and Agilent. Do any of you have any experience with these vendors' LC/MS systems? Do you know of other vendors?

I am using an agilent LC/MS (Single Quad 1946 sprite 1D), and our system have been running since september last year with NO down-time except from preventive maintenance.

I have tested this against Waters/Micromass and they both have their strenghts and weaknesses, so I would say that which of these systems you want to choose should depend on your preferences:

Do you use Chemstation or Millenium right now?
If you are using one of these, why change?

Do you consider having a triple-Q later-on? If you do why not choose Waters, so that you can get some experience with the spray-interface (Which is the same)?

I think that the most important issue is if you want a single quad OR a iontrap, and that depends on what kind of work you have to do. Is it quantitative or mainly identification? Iontrap is a lot more usefull if you have to identify unknown impurities, but is still not used much to quantify components (even though ThermoQuest have made some studies on Quantitative analysis of compounds in biological matrices using iontrap MS.

I would certainly recommend that you send a sample that is representative for the kind of work you have to do to each of the three companies, and see if they can solve your problem. Then evaluate performance and in particular the service that you get.

Good luck on your purchase.