Question

Are there any disadvantages of a mass spectrometer

Answer 1

Of course there are but doesn't it all depend upon what you want it to do? For example, it is very good at measuring the masses of groups of atoms but not very good at measuring the boiling point or freezing point of a material.

Answer 2

Your question is very broad, because there are many types and techniques available.

advantages:
small sample size
fast
differentiates isotopes
can be combined with GC and LC to run mixtures, or can be run in tandem for proteins etc.

disadvantages:
doesn't directly give structural information (although we can often figure it out)
Needs pure compounds
Difficult with non-volatile compounds