A first mass analysis is executed in a condition that gas is not introduced into a loop-flight chamber (4), and a time-of-flight spectrum obtained in a data processor (12) is stored in a storage unit (13). Next, a second mass analysis is executed on the same sample as the one used in the first mass analysis in a condition that a valve (8) is opened and helium gas (He) is introduced into the loop-flight chamber (4), and the time-of-flight spectrum is obtained in the data processor (12). If different kinds of ions having the same m/z value exit, these ions form a single peak in the first time-of-flight spectrum, while these ions appear as separate peaks in the second time-of-flight spectrum even though they have the same m/z value. This is because, in the second mass analysis, the ions collide with the gas and have different times of flight depending on their difference in size. A spectrum comparator (14) judges a change in the position or shape of the peak by comparing the two spectra, and outputs information relating to the difference in the size of the ions (the molecular structure, charge state, or molecular class of the ions), and the like. Accordingly, a wider variety of information than ever before can be provided.

A system for expressing an ion path in a time-of-flight (TOF) mass spectrometer. The present invention uses two successive curved sectors, with the second one reversed, to form S-shaped configuration such that an output ion beam is parallel to an input ion beam, such that the ions makes two identical but opposed turns, and such that the geometry of the entire system folds into a very compact volume. Geometry of a TOF mass spectrometer system in accordance with embodiments of the present invention further includes straight drift regions positioned before and after the S-shaped configuration and, optionally, a short straight region positioned between the two curved sectors with total length equal to about the length of the central arc of both curved sectors.

A method of selecting ions comprises selecting ions corresponding to a target ion of interest by separating analyte ions according to their ion mobility, isolating first ions of the analyte ions, separating the first ions according to their ion mobility, and isolating second ions of the first ions. Preferably, the separation is accomplished by using a cyclic or closed-loop separator.