High-accuracy molecular mass determination for peptides and proteins by Fourier transform mass spectrometry

A new calibration method has been developed for Fourier transform mass spectrometry (FTMS) that is accurate to better than 0.001% (10 ppm) for peptides and proteins up to 5700 Da. The custom-designed FTMS instrument used for this work has a matrix-assisted laser desorption/ionization (MALDI) source located outside of the magnetic field in a differentially pumped chamber, and ions are injected through the fringing fields of the magnet into the FTMS analyzer cell by a long quadrupole ion guide. The mass spectrometer is calibrated with four model compounds ([Arg8]-vasopressin, melittin, bovine insulin B-chain, and bovine insulin) of known molecular mass. The set of measured ion resonance frequencies (f) for these compounds are fit to a three-term calibration equation of the form f = A(z/m) + B(V) + C(V2) (m/z), where m/z is the mass-to-charge ratio of a calibrant peak, V is the trapping voltage, and A, B, and C are calibration coefficients that depend on the magnetic field strength and the dimensions of the analyzer cell. The same set of calibration coefficients can be used for many weeks because the magnet and the electronics of the FTMS instrument are very stable. This method is useful because unknowns can be run separately without the need to add an internal calibration compound in with the sample.