I find that questions asking for recommendations or "what other people use" may not provide YOU with suggestions that are applicable to YOUR own applications.

I am a professional scientific consultant in HPLC and MS systems and applications. Here is some quick advice that I provide to my consulting clients designed to save them the most money and time, plus move them towards their goals. (1) System choice should be tailored to the specific application, needs and training level. Best to first identify (or suggest) example compounds and what matrix they may be found in. Schedule a few days at two or three of the large instrument vendors application labs to run a few of them (3-5, no more) while you and your most experienced scientist (the person whom will actually use the proposed system and who has 10+ years of hands-on experience in industry using LC-MS/MS to analyze samples). This allows for on-site, hands-on time to see their Instrument expert use the equipment and SOFTWARE on sample types which are applicable to your needs. The money and time spent doing this upfront will save you thousands/millions of dollars; (2) Most down time on LC-MS systems is due to poorly trained operators not being able to discern if the problem(s) experienced are caused by the instrument or software (it usually is the operator). Never hire someone "out-of school" to run the system. You need someone with an industry background, preferably different companies, who maintained, operated and developed methods on a similar LC-MS/MS system. They should be a very technical and experienced liquid chromatographer first as a decade plus of HPLC experience is critical to use the LC-MS/MS. Very few people will meet this requirement; (3) Never purchase a used LC-MS/MS system (unless it is purchased by you directly from the manufacturer, not a third-party seller). A new system, installed by the vendor allows you to start off with a system that is known/proven to operate correctly vs spending years trying to get your used system "to-work".

I see so many clients make mistakes by not taking the needed time to select an instrument. Many select an instrument first, then have their untrained staff try to operate it and fail to show results (you can not learn how to use systems like these by "taking a class" or "figuring it out. Those are irrational expectations). Many spend huge amounts of money on hardware, with no results. Years go by and they end up with poor quality methods and still have untrained staff and no valid results. 10+ years of professional training are needed (people do not figure this out on their own. That strategy leads to failure every time. Please do not repeat others mistakes). Start by selecting a skilled operator first, then begin the process of selecting the instrumentation with your new team following the suggestions above.