Mass spectrometry is a multi-faceted beast, and has many applications. One that comes to mind is ion mobility spectrometry. I am most familiar with FAIMS which is an extremely selective method and can detect trace amounts of specific molecules.

The challenge is piecing together what you have detected to draw conclusions about the sample - in this instance you might detect a specific molecule, but to definitively conclude that it's caused by a particular fungus requires lots of prior testing.