In a time-of-flight mass spectrometer with orthogonal ion injection performed by a pulser to which the ions are fed by an RF ion guide, compensation is provided for mass discrimination that occurs when the ions are injected into the pulser. This is accomplished by designing at least a part of the ion guide as an ion storage device, by emptying the filled ion storage device mass-selectively in ion groups, group-by-group, and by serially feeding the ion groups to the pulser with correct timing, using the mass selectivity of the pulser filling process to compensate for the mass discrimination.