Your question is far too broad to answer. An estimate could only be obtained after answering dozens of questions regarding the exact type of MS system, options required, ancillary items needed, availability of supplies to you and especially training and servicing requirements.

Examples of things to consider: To find out more information, start by contacting the various instrument vendors in your area that offer the type of equipment you need. Hire an expert to help you with this if your team does not have the expertise needed. This would be money well spent for someone without the proper training and experience.  Next, specify and define the exact instrument with options you need and also specify the location it would be installed. This info is needed to determine the site prep and operating supplies needed. Confirm that the location has all of the appropriate services (electrical, HVAC and gas) needed plus can handle the additional heat load, exhaust and air quality issues produced by the system. Note: Std office environmental spaces are not designed to handle the loads of these complex systems. Climate control and power conditioning are critical (you will want a UPS system too). Consider in your calculations the types of routine PM services needed (the costs of), service/repairs, power and gas usage (esp Nitrogen gas), Solvents and other consumables, plus the costs of the staff to keep the system running 24/7 too.

Thank you very much Bill for your time in explaining to me all the details. I really valuable appreciate your time.

We are planning to buy Waters Micromass Quattro Micro LCMS/MS with waters 2795 front end HPLC (PDA detector). I have got all the information about the training expenses, site preparation information like electrical requirements, UPS/power conditioners etc. But what I am trying to find out is how much would be the estimate price for annual maintenance and consumables and also what are the initial supplies that I might need to set up  this instrument at our lab. 

Thank you

Hasitha  

The manufacturer (Waters Corp) could supply those answers to you. Depending on your experience level(s), if you are developing new methods or running existing ones, the recommended "supplies" will change. Remember that even if you purchase maintenance or service contracts (through a third party or the manufacturer), there will still be plenty of other types of required services needed to keep everything running well. One area which is often overlooked by clients though is training. You can never have enough training. Better training can equate to lower overall operating costs and higher overall accuracy.

*I have installed and set up many LC/MS systems in all kinds of laboratories. Costs vary so much that no general estimate can be provided (at least not an honest one). Everyone is different. Everyone has different needs, applications, sample types, facilities and esp experience levels. Even two labs set up to run similar samples will have entirely different operational costs,mostly due to equipment variances and especially operator training. As such, the answers will always vary too.