If they are just looking for a few signature metabolites, you can easily do that on a single quadrupole for <$100k. Realistically, I would expect something more precise for medical purposes. Say a QExactive orbitrap -gives you phenomenal performance (<5ppm accuracy) and can be had for $500k.

The only mass specs I think of costing multiple millions of dollars are accelerator mass spectrometers (AMS) which are meant for isotopic analysis.