The high resolution, mass range and sensitivity of Fourier transform mass spectrometry (FTMS) suggest that it could be a valuable tool for the quantitative analysis of biomolecules. To determine the applicability of electrospray ionization combined with FTMS to the quantitation of biomolecules in multi-component samples, mixtures of varying compositions and concentrations of cytochrome c, angiotensin II, insulin and chicken egg white lysozyme were examined. The instrument used has an electrospray source with a hexapole trap to accumulate ions for injection into an ion cyclotron resonance mass analyzer. Linear responses for single component samples of angiotensin II and insulin were in the range 0.031-3 microM and those of both cytochrome c and lysozyme were between 0.031 and 1 microM. In examining various mixtures of the proteins with angiotensin II, it was found that the presence of the large molecules suppresses the signal of the smaller molecules. This is suggested to be a result of ion-ion interactions producing selective ion loss from either the hexapole trap or the ion cyclotron resonance mass analyzer trap. More massive, more highly charged ions can collisionally transfer large amounts of translational energy to smaller, less highly charged ions, ejecting the smaller ions from the trap. Mass discrimination effects resulting from the trapping voltage were also examined. It was found that relative signal intensities of ions of different masses depend on trapping voltage for externally produced ions. The effect is most significant for spectra including masses that differ by 30% or more. This suggests that for quantitation all samples and standards be run at a constant trapping potential.