Accurate mass measurements for peptide and protein mixtures by using matrix-assisted laser desorption/ionization Fourier transform mass spectrometry

A new analytical scheme based on a combination of scanning FTMS, multiple-ion filling, and potential ramping methods has been developed for accurate molecular mass measurement of peptide and protein mixtures using broadband MALDI-FTMS. The scanning FTMS method alleviates the problems of time-of-flight effect for FTMS with an external MALDI ion source and provides a systematic means of sampling ions of different mass-to-charge ratios. The multiple-ion filling method is an effective way of trapping and retaining ions from successive ion generation/accumulation events. The potential ramping method allows the use of high trapping potentials for effective trapping of ions of high kinetic energies and the use of low trapping potentials for high-resolution detection of the trapped ions. With this analytical scheme, high-resolution broadband MALDI mass spectra covering a wide mass range of 1000-5700 Da were obtained. For peptide mixtures of mass range 1000-3500 Da, calibration errors of low part-per-millions were demonstrated using a parabolic calibration equation f2 = ML1/m2 + ML2/m + ML3, where f is the measured cyclotron frequency and ML1, ML2, and ML3 are calibration constants.