Mass spectrometry and appearance potential mass spectrometry (APMS) have recently gained importance for detection and quantitative measurements of reactive radical species in plasmas using line-of-sight sampling of reactive species. In this work, we have characterized the contributions to the mass spectrometer signal from the line-of-sight "beam" component and the background component of the species in the ionizer of the mass spectrometer. The beam signal is proportional to the number density of the species in the plasma, while the background component of the signal depends on Various factors like the vacuum system design and pump speeds. Single differential pumping of the mass spectrometer is found to be inadequate as the background signal dominates the beam signal for radical and stable neutral species. The beam to background ratio for CFx (x = 1-3) radicals is smaller than 0.25 and the large background signals of the species of interest necessitates implementation of modulated beam mass spectrometry using a mechanical chopper in the beam path. The uncertainty in the beam component measurement is found to be as large as +/-180%. High beam-to-background signal ratio is achieved using three stages of differential pumping, and this vastly reduces the uncertainty in the beam component measurement to less than +/- 10%.