Hi Adler_LAB
Speaking for myself and most of the stories I've heard from close colleagues, yes, the pump is the problem because it often fails catastrophically. When you're pulling parts of the rotor out of your mass spec its not difficult to see where the problem is.
I have a bunch of new & old mass specs here and never had to deal with a turbo problem, it seems to be specifically this model of pump, the Leybold TW 290-20-20 UHV.
I got a refurbished pump from mascom, they will send out a refurb. pump as soon as they receive yours for fixing, so its a fairly quick turnaround, that was the only company I could find. 3100/4250 euro depending on bearings or rotor repair.
http://www.mascom-bremen.de/html/en/vac ... 20290.html
Talking to Oerlikon/Leybold I got an offer to buy a new pump for ~$9,000 - that's with a 'generous discount' (Thermo asks ~$6,500!!) and they gave me some advice to spin up my turbo every week or so if it sitting not being used... ?? not at all useful when you never turn them off. They said the lube on the bearings separates if it is not spun up regularly, well guess what, the lube fails even if it is spinning, to the point of spectacular failure... metal shavings or torn up rotor everywhere. ugh.