A method of analyzing macromolecular complex ions, such protein complex ions, by mass spectrometry and apparatus for performing the method, wherein the method comprises: introducing macromolecular complex ions into a first fragmentation device and trapping the complex ions therein for a trapping period; fragmenting the trapped complex ions in the first fragmentation device to produce monomer subunit ions; optionally selecting one or more species of subunit ions by m/z; introducing one or more of the species of subunit ions into a second fragmentation device, spatially separated from the first fragmentation device; fragmenting the subunit ions in the second fragmentation device to produce a plurality of first fragment ions of the subunit ions; and mass analyzing the first fragment ions in a mass analyzer, or subjecting the first fragment ions to one or more further steps of fragmentation to form further fragment ions and mass analyzing the further fragment ions.