There are a number of factors that must be considered when switching from helium to hydrogen as a carrier gas in mass spectrometry.
The first issue is that hydrogen is a reducing agent and it will ‘scrub’ the system. This includes the carrier gas lines, traps, GC and MS. The initial effect is a higher than normal background or noise in the system. Generally speaking it may take weeks or even months for the scrubbing the system depending upon the initial conditions.
(see document for more details)
Please also see Agilent 5975 Mass Selective Detector - Hydrogen Safety