An ion beam supplied from a source is modulated so that ions at a constant flux is passed during on periods or portions thereof and are deflected or stopped during off periods according to a binary sequence in order to encode the ion beam with phase information of the sequence. The binary sequence is such that ions released during two consecutive on periods overlap before reaching a detector, thereby increasing the duty-cycle. The detector output signal is demodulated using the phase information of the binary sequence to recover an ion mass spectrum.